diff --git a/.circleci/config.yml b/.circleci/config.yml index d2c7f2c1465..bceed08e1ca 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -223,6 +223,134 @@ jobs: DOCKER_IMAGE_SESSION_SERVICE: cbioportal/session-service:0.5.0 FRONTEND_TEST_DO_NOT_LOAD_EXTERNAL_FRONTEND: true + pull_cbioportal_test_codebase: + machine: + image: ubuntu-2204:2024.08.1 + resource_class: medium + working_directory: /tmp/repos + steps: + - run: + name: Checkout cbioportal/cbioportal-test + environment: + TEST_REPO_URL: https://github.com/cBioPortal/cbioportal-test + command: | + git clone ${TEST_REPO_URL} + - persist_to_workspace: + root: /tmp/repos + paths: + - cbioportal-test + + pull_cbioportal_frontend_codebase: + machine: + image: ubuntu-2204:2024.08.1 + resource_class: medium + working_directory: /tmp/repos + steps: + - run: + name: Checkout cbioportal/cbioportal-frontend + environment: + FRONTEND_REPO_URL: https://github.com/cBioPortal/cbioportal-frontend.git + FRONTEND_REPO_BRANCH: clickhouse + command: | + git clone -b ${FRONTEND_REPO_BRANCH} --single-branch ${FRONTEND_REPO_URL} + - persist_to_workspace: + root: /tmp/repos + paths: + - cbioportal-frontend + + build_push_image: + machine: + image: ubuntu-2204:2024.08.1 + resource_class: medium + working_directory: /tmp/repos + steps: + - attach_workspace: + at: /tmp/repos + - checkout: + path: /tmp/repos/cbioportal + - run: + name: Build cBioPortal docker image + environment: + DOCKER_REPO: cbioportal/cbioportal-dev + command: | + export DOCKER_TAG=$CIRCLE_SHA1 + URL="https://hub.docker.com/v2/repositories/cbioportal/cbioportal-dev/tags/$DOCKER_TAG-web-shenandoah" + TAG_FOUND=$(curl -s $URL | jq -r .name) + if [ $TAG_FOUND = "$DOCKER_TAG-web-shenandoah" ]; then + echo "Image already exists. Skipping build step!" + exit 0 + fi + cd cbioportal-test + ./scripts/build-push-image.sh --src=/tmp/repos/cbioportal --push=true --skip_web_and_data=true + EXISTS=$(docker manifest inspect $DOCKER_REPO:$DOCKER_TAG-web-shenandoah > /dev/null; echo $?) + if [ $EXISTS -eq 0 ]; then + echo "Build succeeded!" + else + echo "Build failed!" + exit 1 + fi + + run_api_tests: + machine: + image: ubuntu-2204:2024.08.1 + docker_layer_caching: true + resource_class: large + working_directory: /tmp/repos + steps: + - attach_workspace: + at: /tmp/repos + - checkout: + path: /tmp/repos/cbioportal + - run: + name: Instantiate a cbioportal instance + environment: + DOCKER_REPO: cbioportal/cbioportal-dev + APP_CLICKHOUSE_MODE: "true" + command: | + cd cbioportal-test + export DOCKER_IMAGE_CBIOPORTAL=$DOCKER_REPO:$CIRCLE_SHA1-web-shenandoah + nohup ./scripts/docker-compose.sh >> /tmp/repos/docker-compose-logs.txt 2>&1 & + - run: + name: Wait for cbioportal to be live at localhost + command: | + cd cbioportal-test + ./utils/check-connection.sh --url=localhost:8080 + - run: + name: Confirm cbioportal config matches PR + command: | + cd cbioportal + echo "Matching gitCommitId..." + INSTANCE_COMMIT_ID=$(curl -s http://localhost:8080/api/info | jq -r '.["gitCommitId"]') + PR_COMMIT_ID=$CIRCLE_SHA1 + if [ "$INSTANCE_COMMIT_ID" = "$PR_COMMIT_ID" ]; then + echo "gitCommitId successfully matched!" + echo "cBioPortal is ready:" + curl -s http://localhost:8080/api/info | jq + exit 0 + else + echo "gitCommitIds do not match!" + echo "Instance Commit ID: $INSTANCE_COMMIT_ID" + echo "PR Commit ID: $PR_COMMIT_ID" + exit 1 + fi + - run: + name: Run API Tests + environment: + API_TEST_HOST: http://localhost:8080 + BACKEND_ROOT: /tmp/repos/cbioportal + command: | + cd cbioportal-frontend + nvm install 15.2.1 + nvm use 15.2.1 + npm install -g yarn@1.22.5 + yarn --ignore-engines + yarn run apitests + + - store_artifacts: + path: /tmp/repos/cbioportal-test/web-metadata.json + - store_artifacts: + path: /tmp/repos/docker-compose-logs.txt + workflows: version: 2 @@ -238,3 +366,26 @@ workflows: - build_backend - pull_frontend_codebase - install_yarn + api_tests: + jobs: + - pull_cbioportal_test_codebase + - pull_cbioportal_frontend_codebase + - wait_for_approval: + type: approval + requires: + - pull_cbioportal_test_codebase + - pull_cbioportal_frontend_codebase + - build_push_image: + context: + - api-tests + requires: + - wait_for_approval + - pull_cbioportal_test_codebase + - run_api_tests: + context: + - api-tests + requires: + - wait_for_approval + - pull_cbioportal_test_codebase + - pull_cbioportal_frontend_codebase + - build_push_image diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml index a87c052d155..080f26af165 100644 --- a/.github/workflows/sonarcloud.yml +++ b/.github/workflows/sonarcloud.yml @@ -34,7 +34,7 @@ jobs: cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties - name: Build and analyze env: - SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} + SONAR_TOKEN: de1b5cc660cd210dde840f492c371da6cc801763 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: mvn clean install verify org.sonarsource.scanner.maven:sonar-maven-plugin:sonar - name: 'Add host.testcontainers.internal to /etc/hosts' @@ -45,6 +45,6 @@ jobs: mvn verify -Pintegration-test - name: Code Coverage env: - SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} + SONAR_TOKEN: de1b5cc660cd210dde840f492c371da6cc801763 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: mvn sonar:sonar -Pcoverage diff --git a/pom.xml b/pom.xml index 2dd05f792ae..ca7f21587da 100644 --- a/pom.xml +++ b/pom.xml @@ -99,6 +99,7 @@ 4.17.0 7.1.0 5.2.1 + 1.19.7 @@ -354,6 +355,31 @@ test + + com.clickhouse + clickhouse-jdbc + 0.6.2 + + all + + + org.testcontainers + clickhouse + ${clickhouse_testcontainer.version} + test + + + org.mybatis.spring.boot + mybatis-spring-boot-test-autoconfigure + 3.0.3 + test + + + org.springframework.boot + spring-boot-testcontainers + test + @@ -418,9 +444,25 @@ cgds.sql migration.sql + clickhouse/clickhouse.sql + clickhouse/materialized_views.sql + + + src/main/resources/db-scripts + false + + clickhouse/clickhouse.sql + clickhouse/materialized_views.sql + + + + src/test/resources + false + + diff --git a/src/main/java/org/cbioportal/PortalApplication.java b/src/main/java/org/cbioportal/PortalApplication.java index c64043a1dbc..bfe458a121b 100644 --- a/src/main/java/org/cbioportal/PortalApplication.java +++ b/src/main/java/org/cbioportal/PortalApplication.java @@ -6,6 +6,7 @@ import org.springframework.boot.autoconfigure.mongo.MongoAutoConfiguration; import org.springframework.context.annotation.PropertySource; import org.springframework.context.annotation.PropertySources; +import org.springframework.transaction.annotation.EnableTransactionManagement; @SpringBootApplication(exclude = { MongoAutoConfiguration.class, @@ -18,6 +19,7 @@ @PropertySource(ignoreResourceNotFound = true, value = "classpath:git.properties"), @PropertySource(ignoreResourceNotFound = true, value = "classpath:springdoc.properties") }) +@EnableTransactionManagement public class PortalApplication { public static void main(String[] args) { SpringApplication.run(PortalApplication.class, args); diff --git a/src/main/java/org/cbioportal/WebAppConfig.java b/src/main/java/org/cbioportal/WebAppConfig.java index 0105465e96b..2f951690c33 100644 --- a/src/main/java/org/cbioportal/WebAppConfig.java +++ b/src/main/java/org/cbioportal/WebAppConfig.java @@ -2,6 +2,7 @@ import java.util.List; +import org.cbioportal.web.ExecuterTimeInterceptor; import org.cbioportal.web.util.InvolvedCancerStudyExtractorInterceptor; import org.springframework.beans.factory.annotation.Value; import org.springframework.context.annotation.Bean; @@ -12,6 +13,7 @@ import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry; import org.springframework.web.servlet.config.annotation.ViewControllerRegistry; import org.springframework.web.servlet.config.annotation.WebMvcConfigurer; +import org.springframework.web.servlet.handler.WebRequestHandlerInterceptorAdapter; // TODO Consider creating separate DispatcherServlets as in the original web.xml // See: https://stackoverflow.com/a/30686733/11651683 @@ -75,6 +77,9 @@ public HandlerInterceptor involvedCancerStudyExtractorInterceptor() { @Override public void addInterceptors(InterceptorRegistry registry) { registry.addInterceptor(involvedCancerStudyExtractorInterceptor()); + registry.addInterceptor(new WebRequestHandlerInterceptorAdapter( + new ExecuterTimeInterceptor() + )).addPathPatterns("/**"); } @Override diff --git a/src/main/java/org/cbioportal/model/AlterationType.java b/src/main/java/org/cbioportal/model/AlterationType.java index c7b77bea59d..b20a642669d 100644 --- a/src/main/java/org/cbioportal/model/AlterationType.java +++ b/src/main/java/org/cbioportal/model/AlterationType.java @@ -1,6 +1,8 @@ package org.cbioportal.model; public enum AlterationType { - MUTATION, - COPY_NUMBER_ALTERATION + MUTATION_EXTENDED, + COPY_NUMBER_ALTERATION, + STRUCTURAL_VARIANT, + GENERIC_ASSAY; } diff --git a/src/main/java/org/cbioportal/model/CaseListDataCount.java b/src/main/java/org/cbioportal/model/CaseListDataCount.java index 645c12282db..218a83ffd3c 100644 --- a/src/main/java/org/cbioportal/model/CaseListDataCount.java +++ b/src/main/java/org/cbioportal/model/CaseListDataCount.java @@ -1,6 +1,8 @@ package org.cbioportal.model; -public class CaseListDataCount { +import java.io.Serializable; + +public class CaseListDataCount implements Serializable { private String label; private String value; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java index d8d56d8d3bd..c2e24d4d4e2 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java +++ b/src/main/java/org/cbioportal/model/ClinicalViolinPlotBoxData.java @@ -1,6 +1,8 @@ package org.cbioportal.model; -public class ClinicalViolinPlotBoxData { +import java.io.Serializable; + +public class ClinicalViolinPlotBoxData implements Serializable { private double whiskerLower; private double whiskerUpper; private double median; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java index 89f9fc469c1..452cabf0bcd 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java +++ b/src/main/java/org/cbioportal/model/ClinicalViolinPlotData.java @@ -1,8 +1,9 @@ package org.cbioportal.model; +import java.io.Serializable; import java.util.List; -public class ClinicalViolinPlotData { +public class ClinicalViolinPlotData implements Serializable { private List rows; private Double axisStart; private Double axisEnd; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java index ede3c6b5267..7cff49930b0 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java +++ b/src/main/java/org/cbioportal/model/ClinicalViolinPlotIndividualPoint.java @@ -1,6 +1,8 @@ package org.cbioportal.model; -public class ClinicalViolinPlotIndividualPoint { +import java.io.Serializable; + +public class ClinicalViolinPlotIndividualPoint implements Serializable { private String sampleId; private String studyId; private double value; diff --git a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java b/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java index d89c601b0c8..3a2ef647e35 100644 --- a/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java +++ b/src/main/java/org/cbioportal/model/ClinicalViolinPlotRowData.java @@ -1,8 +1,9 @@ package org.cbioportal.model; +import java.io.Serializable; import java.util.List; -public class ClinicalViolinPlotRowData { +public class ClinicalViolinPlotRowData implements Serializable { private String category; private Integer numSamples; private List curveData; diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataCount.java b/src/main/java/org/cbioportal/model/GenericAssayDataCount.java index 78cd96be221..62c14562fca 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataCount.java +++ b/src/main/java/org/cbioportal/model/GenericAssayDataCount.java @@ -7,6 +7,13 @@ public class GenericAssayDataCount implements Serializable { private String value; private Integer count; + public GenericAssayDataCount() {} + + public GenericAssayDataCount(String value, Integer count) { + this.value = value; + this.count = count; + } + public String getValue() { return value; } diff --git a/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java b/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java index 70824a10531..c272b617f87 100644 --- a/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java +++ b/src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java @@ -7,6 +7,13 @@ public class GenericAssayDataCountItem implements Serializable { private String stableId; private List counts; + public GenericAssayDataCountItem() {} + + public GenericAssayDataCountItem(String stableId, List counts) { + this.stableId = stableId; + this.counts = counts; + } + public String getStableId() { return stableId; } diff --git a/src/main/java/org/cbioportal/model/GenomicDataCount.java b/src/main/java/org/cbioportal/model/GenomicDataCount.java index fcc8587c69c..f86fda5bc8f 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataCount.java +++ b/src/main/java/org/cbioportal/model/GenomicDataCount.java @@ -10,6 +10,21 @@ public class GenomicDataCount implements Serializable { private Integer count; private Integer uniqueCount; + public GenomicDataCount() {} + + public GenomicDataCount(String label, String value, Integer count) { + this.label = label; + this.value = value; + this.count = count; + } + + public GenomicDataCount(String label, String value, Integer count, Integer uniqueCount) { + this.label = label; + this.value = value; + this.count = count; + this.uniqueCount = uniqueCount; + } + public String getLabel() { return label; } diff --git a/src/main/java/org/cbioportal/model/GenomicDataCountItem.java b/src/main/java/org/cbioportal/model/GenomicDataCountItem.java index bd9ae14cdaf..a2123a9386c 100644 --- a/src/main/java/org/cbioportal/model/GenomicDataCountItem.java +++ b/src/main/java/org/cbioportal/model/GenomicDataCountItem.java @@ -9,6 +9,14 @@ public class GenomicDataCountItem implements Serializable { private String profileType; private List counts; + public GenomicDataCountItem() {} + + public GenomicDataCountItem(String hugoGeneSymbol, String profileType, List counts) { + this.hugoGeneSymbol = hugoGeneSymbol; + this.profileType = profileType; + this.counts = counts; + } + public String getHugoGeneSymbol() { return hugoGeneSymbol; } diff --git a/src/main/java/org/cbioportal/model/PatientTreatment.java b/src/main/java/org/cbioportal/model/PatientTreatment.java new file mode 100644 index 00000000000..c838d23777e --- /dev/null +++ b/src/main/java/org/cbioportal/model/PatientTreatment.java @@ -0,0 +1,7 @@ +package org.cbioportal.model; + +import java.io.Serializable; + +public record PatientTreatment (String treatment, int count) implements Serializable { + +} diff --git a/src/main/java/org/cbioportal/model/PatientTreatmentReport.java b/src/main/java/org/cbioportal/model/PatientTreatmentReport.java new file mode 100644 index 00000000000..d09a2276f06 --- /dev/null +++ b/src/main/java/org/cbioportal/model/PatientTreatmentReport.java @@ -0,0 +1,11 @@ +package org.cbioportal.model; + +import java.io.Serializable; +import java.util.Collections; +import java.util.List; + +public record PatientTreatmentReport (int totalPatients, int totalSamples, List patientTreatments) implements Serializable { + public PatientTreatmentReport(int totalPatients, int totalSamples) { + this(totalPatients, totalSamples, Collections.emptyList()); + } +} diff --git a/src/main/java/org/cbioportal/model/SampleTreatment.java b/src/main/java/org/cbioportal/model/SampleTreatment.java new file mode 100644 index 00000000000..edf9ef7541a --- /dev/null +++ b/src/main/java/org/cbioportal/model/SampleTreatment.java @@ -0,0 +1,4 @@ +package org.cbioportal.model; + +public record SampleTreatment(String treatment, int preSampleCount, int postSampleCount) { +} diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java b/src/main/java/org/cbioportal/model/SampleTreatmentReport.java new file mode 100644 index 00000000000..12cf93f4fa6 --- /dev/null +++ b/src/main/java/org/cbioportal/model/SampleTreatmentReport.java @@ -0,0 +1,6 @@ +package org.cbioportal.model; + +import java.util.Collection; + +public record SampleTreatmentReport(int totalSamples, Collection treatments) { +} diff --git a/src/main/java/org/cbioportal/model/StudyViewFilterContext.java b/src/main/java/org/cbioportal/model/StudyViewFilterContext.java new file mode 100644 index 00000000000..e23e5f7d9d4 --- /dev/null +++ b/src/main/java/org/cbioportal/model/StudyViewFilterContext.java @@ -0,0 +1,14 @@ +package org.cbioportal.model; + +import org.cbioportal.web.parameter.CustomSampleIdentifier; +import org.cbioportal.web.parameter.StudyViewFilter; + +import java.util.List; + +public record StudyViewFilterContext( + StudyViewFilter studyViewFilter, + List customDataFilterSamples, + List involvedCancerStudies +) { + +} diff --git a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java b/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java index af04bac392c..45b22f5bbf4 100644 --- a/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java +++ b/src/main/java/org/cbioportal/persistence/CacheEnabledConfig.java @@ -16,8 +16,11 @@ public class CacheEnabledConfig { @Value("${persistence.cache_type:no-cache}") private String cacheType; + @Value("${persistence.cache_type_clickhouse:no-cache}") + private String cacheTypeClickhouse; private boolean enabled; + private boolean enabledClickhouse; public static final String EHCACHE_DISK = "ehcache-disk"; public static final String EHCACHE_HEAP = "ehcache-heap"; @@ -30,6 +33,8 @@ public class CacheEnabledConfig { public void init() { this.enabled = enableCache(cacheType); LOG.info("Cache is enabled: " + this.enabled); + this.enabledClickhouse = enableCache(cacheTypeClickhouse); + LOG.info("Cache is enabled for clickhouse: " + this.enabledClickhouse); } public static boolean enableCache(String cacheType) { @@ -53,4 +58,16 @@ public boolean isEnabled() { return enabled; } + public String getEnabledClickhouse() { + if (enabledClickhouse) { + return "true"; + } else { + return "false"; + } + } + + public boolean isEnabledClickhouse() { + return enabledClickhouse; + } + } diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java new file mode 100644 index 00000000000..c39158ad433 --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java @@ -0,0 +1,92 @@ +package org.cbioportal.persistence; + +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.PatientTreatment; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatment; +import org.cbioportal.model.StudyViewFilterContext; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; + +import java.util.List; +import java.util.Map; +import java.util.Set; + +public interface StudyViewRepository { + List getFilteredSamples(StudyViewFilterContext studyViewFilterContext); + + List getFilteredStudyIds(StudyViewFilterContext studyViewFilterContext); + + List getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List attributeIds); + + List getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List attributeIds); + + List getMutatedGenes(StudyViewFilterContext studyViewFilterContext); + + List getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext); + List getCnaGenes(StudyViewFilterContext studyViewFilterContext); + + List getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List filteredAttributes); + + List getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext); + + Map getClinicalAttributeDatatypeMap(); + + List getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext); + + Map getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List molecularProfiles); + + List getClinicalAttributes(); + + List getClinicalAttributesForStudies(List studyIds); + + int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext); + + int getFilteredPatientCount(StudyViewFilterContext studyViewFilterContext); + + Map> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType); + + int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType); + + int getSampleProfileCountWithoutPanelData(StudyViewFilterContext studyViewFilterContext, String alterationType); + + List getClinicalEventTypeCounts(StudyViewFilterContext studyViewFilterContext); + + List getPatientTreatments(StudyViewFilterContext studyViewFilterContext); + + int getTotalPatientTreatmentCount(StudyViewFilterContext studyViewFilterContext); + + List getSampleTreatments(StudyViewFilterContext studyViewFilterContext); + + int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext); + + List getCNACounts(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters); + + List getGenericAssayDataCounts(StudyViewFilterContext studyViewFilterContext, List genericAssayDataFilters); + + Map getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter); + + List getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters); + + List getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List genomicDataBinFilters); + + List getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List genericAssayDataBinFilters); + + List getGenericAssayProfiles(); + + List getFilteredMolecularProfilesByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType); +} diff --git a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java b/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java index e58f04b6cf5..c492b2400b0 100644 --- a/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java +++ b/src/main/java/org/cbioportal/persistence/cachemaputil/SpringManagedCacheMapUtil.java @@ -57,6 +57,8 @@ public class SpringManagedCacheMapUtil implements CacheMapUtil { @Value("${persistence.cache_type:no-cache}") private String cacheType; + @Value("${persistence.cache_type_clickhouse:no-cache}") + private String cacheTypeClickhouse; @Value("${cache.cache-map-utils.spring-managed}") private boolean springManagedCacheMapUtils; @@ -67,7 +69,7 @@ public class SpringManagedCacheMapUtil implements CacheMapUtil { @PostConstruct public void init() { // Make sure the user does not have a conflicting configuration. Explode if there is. - if (cacheType.equals("no-cache") && springManagedCacheMapUtils) { + if (cacheType.equals("no-cache") && cacheTypeClickhouse.equals("no-cache") && springManagedCacheMapUtils) { throw new RuntimeException("cache.cache-map-utils.spring-managed property is set to 'true' but the portal is not " + "configured with a cache-implementation (persistence.cache_type property is 'no-cache'). Please set to 'false'" + " or configure the cache."); diff --git a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java b/src/main/java/org/cbioportal/persistence/config/RedisConfig.java index 2da81e8787c..99c225a33bd 100644 --- a/src/main/java/org/cbioportal/persistence/config/RedisConfig.java +++ b/src/main/java/org/cbioportal/persistence/config/RedisConfig.java @@ -3,8 +3,8 @@ import org.cbioportal.persistence.util.CustomKeyGenerator; import org.cbioportal.persistence.util.CustomRedisCachingProvider; import org.cbioportal.persistence.util.LoggingCacheErrorHandler; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.cache.CacheManager; import org.springframework.cache.annotation.CachingConfigurerSupport; import org.springframework.cache.annotation.EnableCaching; @@ -18,7 +18,9 @@ @Configuration @EnableCaching -@ConditionalOnProperty(name = "persistence.cache_type", havingValue = {"redis"}) +@ConditionalOnExpression( + "#{environment['persistence.cache_type'] == 'redis' or environment['persistence.cache_type_clickhouse'] == 'redis'}" +) public class RedisConfig extends CachingConfigurerSupport { @Value("${redis.name:cbioportal}") diff --git a/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java b/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java new file mode 100644 index 00000000000..591f67e117d --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/enums/ClinicalAttributeDataType.java @@ -0,0 +1,16 @@ +package org.cbioportal.persistence.enums; + +public enum ClinicalAttributeDataType { + CATEGORICAL("CATEGORICAL"), + NUMERIC("NUMERIC"); + + private final String value; + + ClinicalAttributeDataType(String value) { + this.value = value; + } + + public String getValue() { + return this.value; + } +} diff --git a/src/main/java/org/cbioportal/persistence/enums/DataSource.java b/src/main/java/org/cbioportal/persistence/enums/DataSource.java new file mode 100644 index 00000000000..09b81b79edb --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/enums/DataSource.java @@ -0,0 +1,15 @@ +package org.cbioportal.persistence.enums; + +public enum DataSource { + PATIENT("PATIENT"),SAMPLE("SAMPLE"); + + private final String value; + + DataSource(String value) { + this.value = value; + } + + public String getValue() { + return this.value; + } +} diff --git a/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java new file mode 100644 index 00000000000..1d8f63a55f2 --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/helper/AlterationFilterHelper.java @@ -0,0 +1,151 @@ +package org.cbioportal.persistence.helper; + +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.CNA; +import org.cbioportal.model.MutationEventType; +import org.cbioportal.model.util.Select; +import org.springframework.lang.NonNull; +import org.springframework.lang.Nullable; + +import java.util.Objects; + +public final class AlterationFilterHelper { + + public static AlterationFilterHelper build(@Nullable AlterationFilter alterationFilter) { + if (Objects.isNull(alterationFilter)) { + alterationFilter = new AlterationFilter(); + } + return new AlterationFilterHelper(alterationFilter); + } + + private final AlterationFilter alterationFilter; + private final Select mappedMutationTypes; + + private final Select mappedCnaTypes; + + private AlterationFilterHelper(@NonNull AlterationFilter alterationFilter){ + this.alterationFilter = alterationFilter; + this.mappedMutationTypes = buildMutationTypeList(); + this.mappedCnaTypes = buildCnaTypeList(); + } + + private Select buildMutationTypeList() { + if (alterationFilter.getMutationTypeSelect().hasNone()) { + return Select.none(); + } + if (alterationFilter.getMutationTypeSelect().hasAll()) { + return Select.all(); + } + Select typeSelects = alterationFilter.getMutationTypeSelect().map(MutationEventType::getMutationType); + typeSelects.inverse(alterationFilter.getMutationTypeSelect().inverse()); + + return typeSelects; + } + + public Select getMutationTypeList() { + return mappedMutationTypes; + } + + public Select getCnaTypeList() { + return mappedCnaTypes; + } + + public Select buildCnaTypeList() { + if (alterationFilter.getCNAEventTypeSelect().hasNone()) { + return Select.none(); + } + if (alterationFilter.getCNAEventTypeSelect().hasAll()) { + return Select.all(); + } + return alterationFilter.getCNAEventTypeSelect().map(CNA::getCode); + } + + public boolean hasDriver() { + return alterationFilter.getIncludeDriver(); + } + + public boolean hasVUSDriver() { + return alterationFilter.getIncludeVUS(); + } + + public boolean hasUnknownOncogenicity() { + return alterationFilter.getIncludeUnknownOncogenicity(); + } + + public boolean hasGermline() { + return alterationFilter.getIncludeGermline(); + } + + public boolean hasSomatic() { + return alterationFilter.getIncludeSomatic(); + } + + public boolean hasUnknownMutationStatus() { + return alterationFilter.getIncludeUnknownStatus(); + } + + public Select getSelectedTiers() { + return alterationFilter.getSelectedTiers(); + } + + public boolean hasUnknownTier() { + return alterationFilter.getIncludeUnknownTier(); + } + + public boolean isAllDriverAnnotationSelected() { + return alterationFilter.getIncludeDriver() && alterationFilter.getIncludeVUS() && alterationFilter.getIncludeUnknownOncogenicity(); + } + + public boolean isNoDriverAnnotationSelected() { + return !alterationFilter.getIncludeDriver() && !alterationFilter.getIncludeVUS() && !alterationFilter.getIncludeUnknownOncogenicity(); + } + + public boolean isSomeDriverAnnotationsSelected() { + return !isAllDriverAnnotationSelected() && !isNoDriverAnnotationSelected(); + } + + public boolean isAllMutationStatusSelected() { + return alterationFilter.getIncludeGermline() + && alterationFilter.getIncludeSomatic() + && alterationFilter.getIncludeUnknownStatus(); + } + + public boolean isNoMutationStatusSelected() { + return !alterationFilter.getIncludeGermline() + && !alterationFilter.getIncludeSomatic() + && !alterationFilter.getIncludeUnknownStatus(); + } + + public boolean isSomeMutationStatusSelected() { + return !isAllMutationStatusSelected() && !isNoMutationStatusSelected(); + } + + public boolean isAllTierOptionsSelected() { + return !Objects.isNull(alterationFilter.getSelectedTiers()) + && alterationFilter.getSelectedTiers().hasAll() + && alterationFilter.getIncludeUnknownTier(); + } + + public boolean isNoTierOptionsSelected() { + return (Objects.isNull(alterationFilter.getSelectedTiers()) || alterationFilter.getSelectedTiers().hasNone()) + && !alterationFilter.getIncludeUnknownTier(); + } + + public boolean isSomeTierOptionsSelected() { + return !isAllTierOptionsSelected() && !isNoTierOptionsSelected(); + } + + public boolean shouldApplyMutationAlterationFilter() { + return isSomeDriverAnnotationsSelected() + || isSomeMutationStatusSelected() + || isSomeTierOptionsSelected() + || mappedMutationTypes.hasNone() + || (!mappedMutationTypes.hasNone() && !mappedMutationTypes.hasAll()); + } + + public boolean shouldApplyCnaAlterationFilter() { + return isSomeDriverAnnotationsSelected() + || mappedCnaTypes.hasNone() + || (!mappedCnaTypes.hasNone() && !mappedCnaTypes.hasAll()); + } +} diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java new file mode 100644 index 00000000000..23615be0ef4 --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java @@ -0,0 +1,172 @@ +package org.cbioportal.persistence.helper; + +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.persistence.enums.DataSource; +import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.web.parameter.CategorizedGenericAssayDataCountFilter; +import org.cbioportal.web.parameter.CustomSampleIdentifier; +import org.cbioportal.web.parameter.DataFilter; +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.springframework.lang.NonNull; +import org.springframework.lang.Nullable; + +import java.math.BigDecimal; +import java.util.ArrayList; +import java.util.EnumMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; + +public final class StudyViewFilterHelper { + public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter, + @Nullable Map> genericAssayProfilesMap, + @Nullable List customDataSamples, + @Nullable List involvedCancerStudies) { + if (Objects.isNull(studyViewFilter)) { + studyViewFilter = new StudyViewFilter(); + } + if (Objects.isNull(genericAssayProfilesMap)) { + genericAssayProfilesMap = new EnumMap<>(DataSource.class); + } + if (Objects.isNull(customDataSamples)) { + customDataSamples = new ArrayList<>(); + } + if (Objects.isNull(involvedCancerStudies)) { + involvedCancerStudies = new ArrayList<>(); + } + if (studyViewFilter.getGenomicDataFilters() != null && !studyViewFilter.getGenomicDataFilters().isEmpty()) { + List mergedGenomicDataFilters = mergeDataFilters(studyViewFilter.getGenomicDataFilters()); + studyViewFilter.setGenomicDataFilters(mergedGenomicDataFilters); + } + if (studyViewFilter.getClinicalDataFilters() != null && !studyViewFilter.getClinicalDataFilters().isEmpty()) { + List mergedClinicalDataFilters = mergeDataFilters(studyViewFilter.getClinicalDataFilters()); + studyViewFilter.setClinicalDataFilters(mergedClinicalDataFilters); + } + if (studyViewFilter.getGenericAssayDataFilters() != null && !studyViewFilter.getGenericAssayDataFilters().isEmpty()) { + List mergedGenericAssayDataFilters = mergeDataFilters(studyViewFilter.getGenericAssayDataFilters()); + studyViewFilter.setGenericAssayDataFilters(mergedGenericAssayDataFilters); + } + return new StudyViewFilterHelper(studyViewFilter, genericAssayProfilesMap, customDataSamples, involvedCancerStudies); + } + + private final StudyViewFilter studyViewFilter; + private final CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFilter; + private final List customDataSamples; + private final List involvedCancerStudies; + + private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, + @NonNull Map> genericAssayProfilesMap, + @NonNull List customDataSamples, + @NonNull List involvedCancerStudies) { + this.studyViewFilter = studyViewFilter; + this.categorizedGenericAssayDataCountFilter = extractGenericAssayDataCountFilters(studyViewFilter, genericAssayProfilesMap); + this.customDataSamples = customDataSamples; + this.involvedCancerStudies = involvedCancerStudies; + } + + public StudyViewFilter studyViewFilter() { + return studyViewFilter; + } + + public CategorizedGenericAssayDataCountFilter categorizedGenericAssayDataCountFilter() { + return categorizedGenericAssayDataCountFilter; + } + + public List customDataSamples() { + return this.customDataSamples; + } + + public List involvedCancerStudies() { + return involvedCancerStudies; + } + + private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilters(final StudyViewFilter studyViewFilter, Map> genericAssayProfilesMap) { + if ((studyViewFilter.getGenericAssayDataFilters() == null || genericAssayProfilesMap.isEmpty())) + { + return CategorizedGenericAssayDataCountFilter.getBuilder().build(); + } + + CategorizedGenericAssayDataCountFilter.Builder builder = CategorizedGenericAssayDataCountFilter.getBuilder(); + + // No BINARY in the database yet + List sampleNumericalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE) + .stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE")) + .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", "")) + .toList(); + builder.setSampleNumericalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream() + .filter(genericAssayDataFilter -> sampleNumericalProfileTypes.contains(genericAssayDataFilter.getProfileType())) + .toList()); + List sampleCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE) + .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY")) + .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", "")) + .toList(); + builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream() + .filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType())) + .toList()); + List patientCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.PATIENT) + .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY")) + .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", "")) + .toList(); + builder.setPatientCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream() + .filter(genericAssayDataFilter -> patientCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType())) + .toList()); + return builder.build(); + } + + public boolean isCategoricalClinicalDataFilter(ClinicalDataFilter clinicalDataFilter) { + var filterValue = clinicalDataFilter.getValues().getFirst(); + return filterValue.getValue() != null; + } + + /** + * Merge the range of numerical bins in DataFilters to reduce the number of scans that runs on the database when filtering. + */ + public static List mergeDataFilters(List filters) { + boolean isNonNumericalOnly = true; + List mergedDataFilters = new ArrayList<>(); + + for (T filter : filters) { + List mergedValues = new ArrayList<>(); + List nonNumericalValues = new ArrayList<>(); + + BigDecimal mergedStart = null; + BigDecimal mergedEnd = null; + for (DataFilterValue dataFilterValue : filter.getValues()) { + // leave non-numerical values as they are + if (dataFilterValue.getValue() != null) { + nonNumericalValues.add(dataFilterValue); + } + // merge adjacent numerical bins + else { + isNonNumericalOnly = false; + BigDecimal start = dataFilterValue.getStart(); + BigDecimal end = dataFilterValue.getEnd(); + + if (mergedStart == null && mergedEnd == null) { + mergedStart = start; + mergedEnd = end; + } + else if (mergedEnd.equals(start)) { + mergedEnd = end; + } else { + mergedValues.add(new DataFilterValue(mergedStart, mergedEnd, null)); + mergedStart = start; + mergedEnd = end; + } + } + } + + if (!isNonNumericalOnly) { + mergedValues.add(new DataFilterValue(mergedStart, mergedEnd, null)); + } + mergedValues.addAll(nonNumericalValues); + filter.setValues(mergedValues); + mergedDataFilters.add(filter); + } + + return mergedDataFilters; + } +} diff --git a/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java b/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java new file mode 100644 index 00000000000..b02c24c7100 --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java @@ -0,0 +1,4 @@ +package org.cbioportal.persistence.model; + +public record SampleAcquisitionEventRecord(String sampleId, String patientUniqueId, String cancerStudyId, int timeTaken) { +} diff --git a/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java b/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java new file mode 100644 index 00000000000..aeeac35723b --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java @@ -0,0 +1,4 @@ +package org.cbioportal.persistence.model; + +public record TreatmentRecord(String patientUniqueId, String treatment, int startTime, int stopTime) { +} diff --git a/src/main/java/org/cbioportal/persistence/mybatis/UnImplementedStudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatis/UnImplementedStudyViewMyBatisRepository.java new file mode 100644 index 00000000000..bb34c5e040b --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/mybatis/UnImplementedStudyViewMyBatisRepository.java @@ -0,0 +1,198 @@ +package org.cbioportal.persistence.mybatis; + +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.PatientTreatment; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatment; +import org.cbioportal.model.StudyViewFilterContext; +import org.cbioportal.persistence.StudyViewRepository; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.springframework.stereotype.Repository; + +import java.util.List; +import java.util.Map; +import java.util.Set; + +@Repository +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "false", matchIfMissing = true) +public class UnImplementedStudyViewMyBatisRepository implements StudyViewRepository { + + private static final String UNSUPPORTED_OPERATION = "StudyViewRepository Feature Not supported... Contact cbio admin."; + + @Override + public List getFilteredSamples(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getFilteredStudyIds(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List attributeIds) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List attributeIds) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + + } + + @Override + public List getMutatedGenes(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getCnaGenes(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List filteredAttributes) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public Map getClinicalAttributeDatatypeMap() { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public Map getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List molecularProfiles) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getClinicalAttributes() { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getClinicalAttributesForStudies(List studyIds) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public int getFilteredPatientCount(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public Map> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public int getSampleProfileCountWithoutPanelData(StudyViewFilterContext studyViewFilterContext, String alterationType) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getClinicalEventTypeCounts(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getPatientTreatments(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public int getTotalPatientTreatmentCount(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getSampleTreatments(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getCNACounts(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getGenericAssayDataCounts(StudyViewFilterContext studyViewFilterContext, List genericAssayDataFilters) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public Map getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) { + throw new UnsupportedOperationException(UNSUPPORTED_OPERATION); + } + + @Override + public List getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters) { + return List.of(); + } + + @Override + public List getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List genomicDataBinFilters) { + return List.of(); + } + + @Override + public List getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List genericAssayDataBinFilters) { + return List.of(); + } + + @Override + public List getGenericAssayProfiles() { + return List.of(); + } + + @Override + public List getFilteredMolecularProfilesByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) { + return List.of(); + } +} diff --git a/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java b/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java index 933be27cc4a..b8dba141ae4 100644 --- a/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java +++ b/src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java @@ -2,19 +2,22 @@ import org.cbioportal.model.Sample; import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; import org.mybatis.spring.SqlSessionFactoryBean; import org.mybatis.spring.annotation.MapperScan; import org.mybatis.spring.boot.autoconfigure.ConfigurationCustomizer; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.context.ApplicationContext; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; +import org.springframework.jdbc.datasource.DataSourceTransactionManager; import javax.sql.DataSource; import java.io.IOException; @Configuration -@MapperScan("org.cbioportal.persistence.mybatis") +@MapperScan(value="org.cbioportal.persistence.mybatis", sqlSessionFactoryRef="sqlSessionFactory") public class PersistenceConfig { // This is the only way I was able to register the SampleType TypeHandler to MyBatis. @@ -30,8 +33,20 @@ public void customize(org.apache.ibatis.session.Configuration configuration) { }; } - @Bean - public SqlSessionFactoryBean sqlSessionFactory(DataSource dataSource, ApplicationContext applicationContext) throws IOException { + @Bean("sqlSessionFactory") + @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") + public SqlSessionFactoryBean sqlSessionFactorySpecifyDataSource(@Qualifier("mysqlDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException { + return sqlSessionFactory(dataSource, applicationContext); + } + + @Bean("sqlSessionFactory") + @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "false", matchIfMissing = true) + public SqlSessionFactoryBean sqlSessionFactoryDefault(DataSource dataSource, ApplicationContext applicationContext) throws IOException { + return sqlSessionFactory(dataSource, applicationContext); + } + + + private SqlSessionFactoryBean sqlSessionFactory(DataSource dataSource, ApplicationContext applicationContext) throws IOException { SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean(); sessionFactory.setDataSource(dataSource); sessionFactory.setMapperLocations( @@ -40,5 +55,10 @@ public SqlSessionFactoryBean sqlSessionFactory(DataSource dataSource, Applicatio sessionFactory.setTypeHandlers(new SampleTypeTypeHandler()); return sessionFactory; } - + + @Bean + @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") + public DataSourceTransactionManager transactionManager(@Qualifier("mysqlDataSource") DataSource dataSource) { + return new DataSourceTransactionManager(dataSource); + } } diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java new file mode 100644 index 00000000000..dca5ad64125 --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java @@ -0,0 +1,90 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.apache.ibatis.annotations.Param; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.GenePanelToGene; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.model.PatientTreatment; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatment; +import org.cbioportal.persistence.helper.AlterationFilterHelper; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; + +import java.util.List; +import java.util.Map; + + +public interface StudyViewMapper { + List getFilteredSamples(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getFilteredStudyIds(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getMolecularProfileSampleCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getMutatedGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper); + + List getCnaGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper); + + List getStructuralVariantGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper); + + List getClinicalDataCounts(StudyViewFilterHelper studyViewFilterHelper, List attributeIds, List filteredAttributeValues); + + List getCaseListDataCountsPerStudy(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getClinicalAttributes(); + + List getClinicalAttributesForStudies(List studyIds); + + List getSampleClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List attributeIds); + + List getPatientClinicalDataFromStudyViewFilter(StudyViewFilterHelper studyViewFilterHelper, List attributeIds); + + List getTotalProfiledCounts(StudyViewFilterHelper studyViewFilterHelper, String alterationType, List molecularProfiles); + + int getFilteredSamplesCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + int getFilteredPatientsCount(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getMatchingGenePanelIds(StudyViewFilterHelper studyViewFilterHelper, String alterationType); + + int getTotalProfiledCountByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType); + + int getSampleProfileCountWithoutPanelData(StudyViewFilterHelper studyViewFilterHelper, String alterationType); + + List getClinicalEventTypeCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getPatientTreatments(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + int getPatientTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + List getSampleTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + int getTotalSampleTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper); + + List getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List genomicDataFilters); + + List getGenericAssayDataCounts(StudyViewFilterHelper studyViewFilterHelper, List genericAssayDataFilters); + + Map getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter); + + List getMutationCountsByType(StudyViewFilterHelper studyViewFilterHelper, List genomicDataFilters); + + List getGenomicDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List genomicDataBinFilters); + + List getGenericAssayDataBinCounts(StudyViewFilterHelper studyViewFilterHelper, List genericAssayDataBinFilters); + + List getGenericAssayProfiles(); + + List getFilteredMolecularProfilesByAlterationType(StudyViewFilterHelper studyViewFilterHelper, String alterationType); +} diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java new file mode 100644 index 00000000000..d3f594d61be --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java @@ -0,0 +1,271 @@ +package org.cbioportal.persistence.mybatisclickhouse; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.GenePanelToGene; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.PatientTreatment; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatment; +import org.cbioportal.model.StudyViewFilterContext; +import org.cbioportal.persistence.StudyViewRepository; +import org.cbioportal.persistence.enums.DataSource; +import org.cbioportal.persistence.helper.AlterationFilterHelper; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Repository; + +import java.util.Collections; +import java.util.EnumMap; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +@Repository +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class StudyViewMyBatisRepository implements StudyViewRepository { + + private final StudyViewMapper studyViewMapper; + private Map> clinicalAttributesMap = new EnumMap<>(DataSource.class); + private Map> genericAssayProfilesMap = new EnumMap<>(DataSource.class); + + private static final List FILTERED_CLINICAL_ATTR_VALUES = Collections.emptyList(); + private final StudyViewMapper mapper; + + @Autowired + public StudyViewMyBatisRepository(StudyViewMapper mapper, StudyViewMapper studyViewMapper) { + this.mapper = mapper; + this.studyViewMapper = studyViewMapper; + } + + @Override + public List getFilteredSamples(StudyViewFilterContext studyViewFilterContext) { + return mapper.getFilteredSamples(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public List getFilteredStudyIds(StudyViewFilterContext studyViewFilterContext) { + return mapper.getFilteredStudyIds(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public List getMutatedGenes(StudyViewFilterContext studyViewFilterContext) { + return mapper.getMutatedGenes(createStudyViewFilterHelper(studyViewFilterContext), + AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter())); + } + + @Override + public List getCnaGenes(StudyViewFilterContext studyViewFilterContext) { + return mapper.getCnaGenes(createStudyViewFilterHelper(studyViewFilterContext), + AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter())); + } + + @Override + public List getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) { + return mapper.getStructuralVariantGenes(createStudyViewFilterHelper(studyViewFilterContext), + AlterationFilterHelper.build(studyViewFilterContext.studyViewFilter().getAlterationFilter())); + } + + @Override + public List getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List filteredAttributes) { + return mapper.getClinicalDataCounts(createStudyViewFilterHelper(studyViewFilterContext), + filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES); + } + + @Override + public List getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext) { + var sampleCounts = mapper.getMolecularProfileSampleCounts(createStudyViewFilterHelper(studyViewFilterContext)); + return StudyViewColumnarServiceUtil.mergeGenomicDataCounts(sampleCounts); + + } + + public StudyViewFilterHelper createStudyViewFilterHelper(StudyViewFilterContext studyViewFilterContext) { + return StudyViewFilterHelper.build( + studyViewFilterContext.studyViewFilter(), + getGenericAssayProfilesMap(), + studyViewFilterContext.customDataFilterSamples(), + studyViewFilterContext.involvedCancerStudies() + ); + } + + @Override + public List getClinicalAttributes() { + return mapper.getClinicalAttributes(); + } + + @Override + public List getGenericAssayProfiles() { + return mapper.getGenericAssayProfiles(); + } + + @Override + public List getFilteredMolecularProfilesByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) { + return studyViewMapper.getFilteredMolecularProfilesByAlterationType(createStudyViewFilterHelper(studyViewFilterContext), alterationType); + } + + @Override + public Map getClinicalAttributeDatatypeMap() { + if (clinicalAttributesMap.isEmpty()) { + buildClinicalAttributeNameMap(); + } + + Map attributeDatatypeMap = new HashMap<>(); + + clinicalAttributesMap + .get(DataSource.SAMPLE) + .forEach(attribute -> attributeDatatypeMap.put(attribute.getAttrId(), ClinicalDataType.SAMPLE)); + + clinicalAttributesMap + .get(DataSource.PATIENT) + .forEach(attribute -> attributeDatatypeMap.put(attribute.getAttrId(), ClinicalDataType.PATIENT)); + + return attributeDatatypeMap; + } + + @Override + public List getClinicalAttributesForStudies(List studyIds) { + return mapper.getClinicalAttributesForStudies(studyIds); + } + + @Override + public List getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext) { + return mapper.getCaseListDataCountsPerStudy(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public List getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List attributeIds) { + return mapper.getSampleClinicalDataFromStudyViewFilter(createStudyViewFilterHelper(studyViewFilterContext), attributeIds); + } + + @Override + public List getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List attributeIds) { + return mapper.getPatientClinicalDataFromStudyViewFilter(createStudyViewFilterHelper(studyViewFilterContext), attributeIds); + } + + @Override + public Map getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List molecularProfiles) { + return mapper.getTotalProfiledCounts(createStudyViewFilterHelper(studyViewFilterContext), alterationType, molecularProfiles) + .stream() + .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol, + Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue)))); + } + + @Override + public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext) { + return mapper.getFilteredSamplesCount(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public int getFilteredPatientCount(StudyViewFilterContext studyViewFilterContext) { + return mapper.getFilteredPatientsCount(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public Map> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) { + return mapper.getMatchingGenePanelIds(createStudyViewFilterHelper(studyViewFilterContext), alterationType) + .stream() + .collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol, + Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet()))); + } + + @Override + public int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) { + return mapper.getTotalProfiledCountByAlterationType(createStudyViewFilterHelper(studyViewFilterContext), alterationType); + } + + @Override + public int getSampleProfileCountWithoutPanelData(StudyViewFilterContext studyViewFilterContext, String alterationType) { + return mapper.getSampleProfileCountWithoutPanelData(createStudyViewFilterHelper(studyViewFilterContext), alterationType); + } + + + @Override + public List getClinicalEventTypeCounts(StudyViewFilterContext studyViewFilterContext) { + return mapper.getClinicalEventTypeCounts(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public List getPatientTreatments(StudyViewFilterContext studyViewFilterContext) { + return mapper.getPatientTreatments(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public int getTotalPatientTreatmentCount(StudyViewFilterContext studyViewFilterContext) { + return mapper.getPatientTreatmentCounts(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public List getSampleTreatments(StudyViewFilterContext studyViewFilterContext) { + return mapper.getSampleTreatmentCounts(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext) { + return mapper.getTotalSampleTreatmentCounts(createStudyViewFilterHelper(studyViewFilterContext)); + } + + @Override + public List getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List genomicDataBinFilters) { + return mapper.getGenomicDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataBinFilters); + } + + @Override + public List getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List genericAssayDataBinFilters) { + return mapper.getGenericAssayDataBinCounts(createStudyViewFilterHelper(studyViewFilterContext), genericAssayDataBinFilters); + } + + private void buildClinicalAttributeNameMap() { + clinicalAttributesMap = this.getClinicalAttributes() + .stream() + .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE)); + } + + private void buildGenericAssayProfilesMap() { + genericAssayProfilesMap = this.getGenericAssayProfiles() + .stream() + .collect(Collectors.groupingBy(ca -> ca.getPatientLevel().booleanValue() ? DataSource.PATIENT : DataSource.SAMPLE)); + } + + private Map> getGenericAssayProfilesMap() { + if (genericAssayProfilesMap.isEmpty()) { + buildGenericAssayProfilesMap(); + } + return genericAssayProfilesMap; + } + + @Override + public List getCNACounts(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters) { + return mapper.getCNACounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters); + } + + @Override + public List getGenericAssayDataCounts(StudyViewFilterContext studyViewFilterContext, List genericAssayDataFilters) { + return mapper.getGenericAssayDataCounts(createStudyViewFilterHelper(studyViewFilterContext), genericAssayDataFilters); + } + + public Map getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) { + return mapper.getMutationCounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilter); + } + + public List getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List genomicDataFilters) { + return mapper.getMutationCountsByType(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters); + } + +} \ No newline at end of file diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java new file mode 100644 index 00000000000..7acea62ecec --- /dev/null +++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java @@ -0,0 +1,32 @@ +package org.cbioportal.persistence.mybatisclickhouse.config; + +import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.mybatis.spring.SqlSessionFactoryBean; +import org.mybatis.spring.annotation.MapperScan; +import org.springframework.beans.factory.annotation.Qualifier; +import org.springframework.context.ApplicationContext; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import javax.sql.DataSource; +import java.io.IOException; + + +@Configuration +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +@MapperScan(value= "org.cbioportal.persistence.mybatisclickhouse", sqlSessionFactoryRef ="sqlColumnarSessionFactory") +public class PersistenceColumnarConfig { + + @Bean("sqlColumnarSessionFactory") + public SqlSessionFactoryBean sqlColumnarSessionFactory(@Qualifier("clickhouseDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException { + SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean(); + sessionFactory.setDataSource(dataSource); + sessionFactory.setMapperLocations( + applicationContext.getResources("classpath:org/cbioportal/persistence/mybatisclickhouse/*.xml") + ); + sessionFactory.setTypeHandlers(new SampleTypeTypeHandler()); + return sessionFactory; + } + +} diff --git a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java b/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java index 1ae254cef05..948d5d344c5 100644 --- a/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java +++ b/src/main/java/org/cbioportal/persistence/util/CustomKeyGenerator.java @@ -64,7 +64,7 @@ public class CustomKeyGenerator implements KeyGenerator { private static final Logger LOG = LoggerFactory.getLogger(CustomKeyGenerator.class); public Object generate(Object target, Method method, Object... params) { - if (!cacheEnabledConfig.isEnabled()) { + if (!cacheEnabledConfig.isEnabled() && !cacheEnabledConfig.isEnabledClickhouse()) { return ""; } String key = target.getClass().getSimpleName() + CACHE_KEY_PARAM_DELIMITER diff --git a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java b/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java index 67639dc75b5..ec5579c544d 100644 --- a/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java +++ b/src/main/java/org/cbioportal/persistence/util/RedisCacheUtils.java @@ -3,9 +3,9 @@ import static org.cbioportal.persistence.util.CustomRedisCache.DELIMITER; -import org.cbioportal.utils.config.annotation.ConditionalOnProperty; import org.redisson.api.RedissonClient; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.cache.Cache; import org.springframework.cache.CacheManager; import org.springframework.stereotype.Component; @@ -14,7 +14,9 @@ import java.util.stream.Collectors; @Component -@ConditionalOnProperty(name = "persistence.cache_type", havingValue = "redis") +@ConditionalOnExpression( + "#{environment['persistence.cache_type'] == 'redis' or environment['persistence.cache_type_clickhouse'] == 'redis'}" +) public class RedisCacheUtils implements CacheUtils { @Autowired diff --git a/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java b/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java new file mode 100644 index 00000000000..f71d07b1393 --- /dev/null +++ b/src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java @@ -0,0 +1,39 @@ +package org.cbioportal.properties; + +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties; +import org.springframework.boot.context.properties.ConfigurationProperties; +import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Configuration; + +import javax.sql.DataSource; + +@Configuration +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class CustomDataSourceConfiguration { + @Bean + @ConfigurationProperties("spring.datasource.mysql") + public DataSourceProperties mysqlDataSourceProperties() { + return new DataSourceProperties(); + } + + @Bean + @ConfigurationProperties("spring.datasource.clickhouse") + public DataSourceProperties clickhouseDatSourceProperties() { + return new DataSourceProperties(); + } + + @Bean("mysqlDataSource") + public DataSource mysqlDataSource() { + return mysqlDataSourceProperties() + .initializeDataSourceBuilder() + .build(); + } + + @Bean("clickhouseDataSource") + public DataSource clickhouseDataSource() { + return clickhouseDatSourceProperties() + .initializeDataSourceBuilder() + .build(); + } +} diff --git a/src/main/java/org/cbioportal/security/config/CorsConfig.java b/src/main/java/org/cbioportal/security/config/CorsConfig.java index cd92394da49..d96050013cc 100644 --- a/src/main/java/org/cbioportal/security/config/CorsConfig.java +++ b/src/main/java/org/cbioportal/security/config/CorsConfig.java @@ -30,7 +30,7 @@ CorsConfigurationSource corsConfigurationSource() { configuration.setAllowedHeaders(List.of("user-agent", "Origin", "Accept", "X-Requested-With","Content-Type", "Access-Control-Request-Method","Access-Control-Request-Headers","Content-Encoding", "X-Proxy-User-Agreement", "x-current-url")); - configuration.setExposedHeaders(List.of("total-count", "sample-count")); + configuration.setExposedHeaders(List.of("total-count", "sample-count", "elapsed-time")); source.registerCorsConfiguration("/**", configuration); return source; } diff --git a/src/main/java/org/cbioportal/service/AlterationCountService.java b/src/main/java/org/cbioportal/service/AlterationCountService.java index 5966f725a8d..eaec004682e 100644 --- a/src/main/java/org/cbioportal/service/AlterationCountService.java +++ b/src/main/java/org/cbioportal/service/AlterationCountService.java @@ -3,6 +3,11 @@ import org.apache.commons.math3.util.Pair; import org.cbioportal.model.*; import org.cbioportal.model.util.Select; +import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; +import org.cbioportal.web.parameter.CustomSampleIdentifier; +import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.web.parameter.StudyViewFilter; import java.util.List; @@ -75,4 +80,9 @@ Pair, Long> getPatientCnaGeneCounts(List getMutatedGenes(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException; + List getCnaGenes(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException; + + List getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException; + } diff --git a/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java b/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java new file mode 100644 index 00000000000..211963e11b8 --- /dev/null +++ b/src/main/java/org/cbioportal/service/ClinicalDataDensityPlotService.java @@ -0,0 +1,13 @@ +package org.cbioportal.service; + +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.DensityPlotData; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.util.DensityPlotParameters; + +import java.math.BigDecimal; +import java.util.List; + +public interface ClinicalDataDensityPlotService { + DensityPlotData getDensityPlotData(List filteredClinicalData, DensityPlotParameters densityPlotParameters, StudyViewFilter studyViewFilter); +} diff --git a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java b/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java index 429f3346a77..abe7f299226 100644 --- a/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java +++ b/src/main/java/org/cbioportal/service/FrontendPropertiesServiceImpl.java @@ -192,8 +192,12 @@ public enum FrontendProperty { download_custom_buttons_json("download_custom_buttons_json", null), enable_study_tags("enable_study_tags", null), - enable_darwin("enable_darwin", null); + enable_darwin("enable_darwin", null), + clickhouse_mode("clickhouse_mode", "false"); + + + private final String propertyName; private final String defaultValue; diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java new file mode 100644 index 00000000000..4f13dc68f78 --- /dev/null +++ b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java @@ -0,0 +1,61 @@ +package org.cbioportal.service; + +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.PatientTreatmentReport; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatmentReport; +import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; + +import java.util.List; +import java.util.Map; + +public interface StudyViewColumnarService { + + List getFilteredSamples(StudyViewFilter studyViewFilter); + + List getMutatedGenes(StudyViewFilter interceptedStudyViewFilter) throws StudyNotFoundException; + List getCnaGenes(StudyViewFilter interceptedStudyViewFilter) throws StudyNotFoundException; + List getStructuralVariantGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException; + + Map getClinicalAttributeDatatypeMap(StudyViewFilter studyViewFilter); + + List getClinicalDataCounts(StudyViewFilter studyViewFilter, List filteredAttributes); + + List getCaseListDataCounts(StudyViewFilter studyViewFilter); + + List getPatientClinicalData(StudyViewFilter studyViewFilter, List attributeIds); + + List getSampleClinicalData(StudyViewFilter studyViewFilter, List attributeIds); + + List getMolecularProfileSampleCounts(StudyViewFilter studyViewFilter); + + List getClinicalEventTypeCounts(StudyViewFilter studyViewFilter); + PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter); + SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter); + + List getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters); + + List getGenericAssayDataCounts(StudyViewFilter studyViewFilter, List genericAssayDataFilters); + + List getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters); + + List getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List genomicDataBinFilters); + + List getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List genericAssayDataBinFilters); + + List getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters); +} diff --git a/src/main/java/org/cbioportal/service/ViolinPlotService.java b/src/main/java/org/cbioportal/service/ViolinPlotService.java index 2737ffc24a1..37eade2f739 100644 --- a/src/main/java/org/cbioportal/service/ViolinPlotService.java +++ b/src/main/java/org/cbioportal/service/ViolinPlotService.java @@ -3,6 +3,7 @@ import org.cbioportal.model.ClinicalData; import org.cbioportal.model.ClinicalViolinPlotData; import org.cbioportal.model.Sample; +import org.cbioportal.web.parameter.StudyViewFilter; import java.math.BigDecimal; import java.util.List; @@ -15,6 +16,7 @@ ClinicalViolinPlotData getClinicalViolinPlotData( BigDecimal axisEnd, BigDecimal numCurvePoints, Boolean useLogScale, - BigDecimal sigmaMultiplier + BigDecimal sigmaMultiplier, + StudyViewFilter studyViewFilter ); } diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java index 4175ce3cf10..28f3d34611f 100644 --- a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java +++ b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java @@ -1,17 +1,40 @@ package org.cbioportal.service.impl; -import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; +import org.cbioportal.model.AlterationCountBase; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.AlterationCountByStructuralVariant; +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.AlterationType; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.Gistic; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.MolecularProfileCaseIdentifier; +import org.cbioportal.model.MutSig; +import org.cbioportal.model.StudyViewFilterContext; import org.cbioportal.model.util.Select; import org.cbioportal.persistence.AlterationRepository; import org.cbioportal.persistence.MolecularProfileRepository; +import org.cbioportal.persistence.StudyViewRepository; import org.cbioportal.service.AlterationCountService; +import org.cbioportal.service.SignificantCopyNumberRegionService; +import org.cbioportal.service.SignificantlyMutatedGeneService; +import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.service.util.AlterationCountServiceUtil; import org.cbioportal.service.util.AlterationEnrichmentUtil; +import org.cbioportal.web.parameter.Projection; import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.lang.NonNull; import org.springframework.stereotype.Service; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeSet; import java.util.concurrent.atomic.AtomicReference; import java.util.function.BiFunction; import java.util.function.Function; @@ -20,17 +43,32 @@ @Service public class AlterationCountServiceImpl implements AlterationCountService { - @Autowired - private AlterationRepository alterationRepository; - @Autowired - private AlterationEnrichmentUtil alterationEnrichmentUtil; - @Autowired - private AlterationEnrichmentUtil alterationEnrichmentUtilCna; - @Autowired - private AlterationEnrichmentUtil alterationEnrichmentUtilStructVar; - @Autowired - private MolecularProfileRepository molecularProfileRepository; + private final AlterationRepository alterationRepository; + private final AlterationEnrichmentUtil alterationEnrichmentUtil; + private final AlterationEnrichmentUtil alterationEnrichmentUtilCna; + private final AlterationEnrichmentUtil alterationEnrichmentUtilStructVar; + private final MolecularProfileRepository molecularProfileRepository; + private final SignificantlyMutatedGeneService significantlyMutatedGeneService; + private final StudyViewRepository studyViewRepository; + private final SignificantCopyNumberRegionService significantCopyNumberRegionService; + + @Autowired + public AlterationCountServiceImpl(AlterationRepository alterationRepository, AlterationEnrichmentUtil alterationEnrichmentUtil, + AlterationEnrichmentUtil alterationEnrichmentUtilCna, + AlterationEnrichmentUtil alterationEnrichmentUtilStructVar, + MolecularProfileRepository molecularProfileRepository, + StudyViewRepository studyViewRepository, SignificantlyMutatedGeneService significantlyMutatedGeneService, + SignificantCopyNumberRegionService significantCopyNumberRegionService) { + this.alterationRepository = alterationRepository; + this.alterationEnrichmentUtil = alterationEnrichmentUtil; + this.alterationEnrichmentUtilCna = alterationEnrichmentUtilCna; + this.alterationEnrichmentUtilStructVar = alterationEnrichmentUtilStructVar; + this.molecularProfileRepository = molecularProfileRepository; + this.studyViewRepository = studyViewRepository; + this.significantlyMutatedGeneService = significantlyMutatedGeneService; + this.significantCopyNumberRegionService = significantCopyNumberRegionService; + } @Override public Pair, Long> getSampleAlterationGeneCounts(List molecularProfileCaseIdentifiers, Select entrezGeneIds, @@ -223,6 +261,105 @@ public Pair, Long> getPatientCnaGeneCounts(List getMutatedGenes(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + var alterationCountByGenes = populateAlterationCounts(AlterationCountServiceUtil.combineAlterationCountsWithConflictingHugoSymbols( studyViewRepository.getMutatedGenes(studyViewFilterContext)), + studyViewFilterContext, AlterationType.MUTATION_EXTENDED); + return populateAlterationCountsWithMutSigQValue(alterationCountByGenes, studyViewFilterContext); + } + + public List getCnaGenes(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + var copyNumberAlterationCounts = populateAlterationCounts(AlterationCountServiceUtil.combineCopyNumberCountsWithConflictingHugoSymbols(studyViewRepository.getCnaGenes(studyViewFilterContext)), studyViewFilterContext, AlterationType.COPY_NUMBER_ALTERATION); + return populateAlterationCountsWithCNASigQValue(copyNumberAlterationCounts, studyViewFilterContext); + } + + @Override + public List getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + var alterationCountByGenes = populateAlterationCounts(AlterationCountServiceUtil.combineAlterationCountsWithConflictingHugoSymbols(studyViewRepository.getStructuralVariantGenes(studyViewFilterContext)), + studyViewFilterContext, AlterationType.STRUCTURAL_VARIANT); + return populateAlterationCountsWithMutSigQValue(alterationCountByGenes, studyViewFilterContext); + } + + private < T extends AlterationCountByGene> List populateAlterationCounts(@NonNull List alterationCounts, + @NonNull StudyViewFilterContext studyViewFilterContext, + @NonNull AlterationType alterationType) { + final var firstMolecularProfileForEachStudy = getFirstMolecularProfileGroupedByStudy(studyViewFilterContext, alterationType); + final int totalProfiledCount = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilterContext, alterationType.toString()); + var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilterContext, alterationType.toString(), firstMolecularProfileForEachStudy); + final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilterContext, alterationType.toString()); + final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilterContext, alterationType.toString()); + + alterationCounts.parallelStream() + .forEach(alterationCountByGene -> { + String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol(); + Set matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ? + matchingGenePanelIdsMap.get(hugoGeneSymbol) : Collections.emptySet(); + + int alterationTotalProfiledCount = AlterationCountServiceUtil.computeTotalProfiledCount(AlterationCountServiceUtil.hasGenePanelData(matchingGenePanelIds), + profiledCountsMap.getOrDefault(hugoGeneSymbol, 0), + sampleProfileCountWithoutGenePanelData, totalProfiledCount); + + alterationCountByGene.setNumberOfProfiledCases(alterationTotalProfiledCount); + + alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds); + + }); + return alterationCounts; + } + + private List populateAlterationCountsWithMutSigQValue(List alterationCountByGenes, StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + final var mutSigs = getMutSigs(studyViewFilterContext); + // If MutSig is not empty update Mutated Genes + return AlterationCountServiceUtil.updateAlterationCountsWithMutSigQValue(alterationCountByGenes, mutSigs); + } + + private List populateAlterationCountsWithCNASigQValue(List alterationCountByGenes, StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + final var gisticMap = getGisticMap(studyViewFilterContext); + + return AlterationCountServiceUtil.updateAlterationCountsWithCNASigQValue(alterationCountByGenes, gisticMap); + } + + private List getFirstMolecularProfileGroupedByStudy(StudyViewFilterContext studyViewFilterContext, AlterationType alterationType) { + final var molecularProfiles = studyViewRepository.getFilteredMolecularProfilesByAlterationType(studyViewFilterContext, alterationType.toString()); + + return AlterationCountServiceUtil.getFirstMolecularProfileGroupedByStudy(molecularProfiles); + } + + private Map getMutSigs(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + var distinctStudyIds = studyViewRepository.getFilteredStudyIds(studyViewFilterContext); + Map mutSigs = new HashMap<>(); + if (distinctStudyIds.size() == 1) { + var studyId = distinctStudyIds.getFirst(); + mutSigs = significantlyMutatedGeneService.getSignificantlyMutatedGenes( + studyId, + Projection.SUMMARY.name(), + null, + null, + null, + null) + .stream() + .collect(Collectors.toMap(MutSig::getHugoGeneSymbol, Function.identity())); + } + return mutSigs; + } + + private Map, Gistic> getGisticMap(StudyViewFilterContext studyViewFilterContext) throws StudyNotFoundException { + var distinctStudyIds = studyViewRepository.getFilteredStudyIds(studyViewFilterContext); + Map, Gistic> gisticMap = new HashMap<>(); + if (distinctStudyIds.size() == 1) { + var studyId = distinctStudyIds.getFirst(); + List gisticList = significantCopyNumberRegionService.getSignificantCopyNumberRegions( + studyId, + Projection.SUMMARY.name(), + null, + null, + null, + null); + AlterationCountServiceUtil.setupGisticMap(gisticList, gisticMap); + } + return gisticMap; + } + private Pair, Long> getAlterationGeneCounts( List molecularProfileCaseIdentifiers, boolean includeFrequency, @@ -256,26 +393,7 @@ private Pair, Long> getAlterationGeneCou Long studyProfiledCasesCount = includeFrequencyFunction.apply(studyMolecularProfileCaseIdentifiers, studyAlterationCountByGenes); profiledCasesCount.updateAndGet(v -> v + studyProfiledCasesCount); } - studyAlterationCountByGenes.forEach(datum -> { - String key = datum.getUniqueEventKey(); - if (totalResult.containsKey(key)) { - S alterationCountByGene = totalResult.get(key); - alterationCountByGene.setTotalCount(alterationCountByGene.getTotalCount() + datum.getTotalCount()); - alterationCountByGene.setNumberOfAlteredCases(alterationCountByGene.getNumberOfAlteredCases() + datum.getNumberOfAlteredCases()); - alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + datum.getNumberOfProfiledCases()); - Set matchingGenePanelIds = new HashSet<>(); - if (!alterationCountByGene.getMatchingGenePanelIds().isEmpty()) { - matchingGenePanelIds.addAll(alterationCountByGene.getMatchingGenePanelIds()); - } - if (!datum.getMatchingGenePanelIds().isEmpty()) { - matchingGenePanelIds.addAll(datum.getMatchingGenePanelIds()); - } - alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds); - totalResult.put(key, alterationCountByGene); - } else { - totalResult.put(key, datum); - } - }); + AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult); }); alterationCountByGenes = new ArrayList<>(totalResult.values()); } diff --git a/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java new file mode 100644 index 00000000000..cb4d8d780e9 --- /dev/null +++ b/src/main/java/org/cbioportal/service/impl/ClinicalDataDensityPlotServiceImpl.java @@ -0,0 +1,146 @@ +package org.cbioportal.service.impl; + +import org.apache.commons.lang3.math.NumberUtils; +import org.apache.commons.math3.stat.correlation.PearsonsCorrelation; +import org.apache.commons.math3.stat.correlation.SpearmansCorrelation; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.DensityPlotBin; +import org.cbioportal.model.DensityPlotData; +import org.cbioportal.service.ClinicalDataDensityPlotService; +import org.cbioportal.web.columnar.StudyViewColumnStoreController; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.util.DensityPlotParameters; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Service; + +import java.math.BigDecimal; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + + +@Service +public class ClinicalDataDensityPlotServiceImpl implements ClinicalDataDensityPlotService { + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public DensityPlotData getDensityPlotData(List sampleClinicalData, DensityPlotParameters densityPlotParameters, StudyViewFilter studyViewFilter) { + DensityPlotData result = new DensityPlotData(); + result.setBins(new ArrayList<>()); + + Map> clinicalDataGroupedBySampleId = sampleClinicalData.stream(). + collect(Collectors.groupingBy(c -> c.getStudyId() + "_" + c.getSampleId())); + + List extractedXYClinicalData = clinicalDataGroupedBySampleId.entrySet().stream() + .filter(entry -> entry.getValue().size() == 2 && + NumberUtils.isCreatable(entry.getValue().get(0).getAttrValue()) && + NumberUtils.isCreatable(entry.getValue().get(1).getAttrValue()) + ).flatMap(entry -> entry.getValue().stream()) + .toList(); + + if (extractedXYClinicalData.isEmpty()) { + return result; + } + + Map> partition = extractedXYClinicalData.stream().collect( + Collectors.partitioningBy(c -> c.getAttrId().equals(densityPlotParameters.getXAxisAttributeId()))); + + boolean useXLogScale = densityPlotParameters.getXAxisLogScale() && ClinicalDataDensityPlotServiceImpl.isLogScalePossibleForAttribute(densityPlotParameters.getXAxisAttributeId()); + boolean useYLogScale = densityPlotParameters.getYAxisLogScale() && ClinicalDataDensityPlotServiceImpl.isLogScalePossibleForAttribute(densityPlotParameters.getYAxisAttributeId()); + + double[] xValues = partition.get(true).stream().mapToDouble( + useXLogScale ? ClinicalDataDensityPlotServiceImpl::parseValueLog : ClinicalDataDensityPlotServiceImpl::parseValueLinear + ).toArray(); + double[] yValues = partition.get(false).stream().mapToDouble( + useYLogScale ? ClinicalDataDensityPlotServiceImpl::parseValueLog : ClinicalDataDensityPlotServiceImpl::parseValueLinear + ).toArray(); + double[] xValuesCopy = Arrays.copyOf(xValues, xValues.length); + double[] yValuesCopy = Arrays.copyOf(yValues, yValues.length); // Why copy these? + Arrays.sort(xValuesCopy); + Arrays.sort(yValuesCopy); + + double xAxisStartValue = densityPlotParameters.getXAxisStart() == null ? xValuesCopy[0] : + (useXLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getXAxisStart().doubleValue()) : densityPlotParameters.getXAxisStart().doubleValue()); + double xAxisEndValue = densityPlotParameters.getXAxisEnd() == null ? xValuesCopy[xValuesCopy.length - 1] : + (useXLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getXAxisEnd().doubleValue()) : densityPlotParameters.getXAxisEnd().doubleValue()); + double yAxisStartValue = densityPlotParameters.getYAxisStart() == null ? yValuesCopy[0] : + (useYLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getYAxisStart().doubleValue()) : densityPlotParameters.getYAxisStart().doubleValue()); + double yAxisEndValue = densityPlotParameters.getYAxisEnd() == null ? yValuesCopy[yValuesCopy.length - 1] : + (useYLogScale ? ClinicalDataDensityPlotServiceImpl.logScale(densityPlotParameters.getYAxisEnd().doubleValue()) : densityPlotParameters.getYAxisEnd().doubleValue()); + double xAxisBinInterval = (xAxisEndValue - xAxisStartValue) / densityPlotParameters.getXAxisBinCount(); + double yAxisBinInterval = (yAxisEndValue - yAxisStartValue) / densityPlotParameters.getYAxisBinCount(); + List bins = result.getBins(); + for (int i = 0; i < densityPlotParameters.getXAxisBinCount(); i++) { + for (int j = 0; j < densityPlotParameters.getYAxisBinCount(); j++) { + DensityPlotBin densityPlotBin = new DensityPlotBin(); + densityPlotBin.setBinX(BigDecimal.valueOf(xAxisStartValue + (i * xAxisBinInterval))); + densityPlotBin.setBinY(BigDecimal.valueOf(yAxisStartValue + (j * yAxisBinInterval))); + densityPlotBin.setCount(0); + bins.add(densityPlotBin); + } + } + + for (int i = 0; i < xValues.length; i++) { + double xValue = xValues[i]; + double yValue = yValues[i]; + int xBinIndex = (int) ((xValue - xAxisStartValue) / xAxisBinInterval); + int yBinIndex = (int) ((yValue - yAxisStartValue) / yAxisBinInterval); + int index = (int) (((xBinIndex - (xBinIndex == densityPlotParameters.getXAxisBinCount() ? 1 : 0)) * densityPlotParameters.getYAxisBinCount()) + + (yBinIndex - (yBinIndex == densityPlotParameters.getYAxisBinCount() ? 1 : 0))); + DensityPlotBin densityPlotBin = bins.get(index); + densityPlotBin.setCount(densityPlotBin.getCount() + 1); + BigDecimal xValueBigDecimal = BigDecimal.valueOf(xValue); + BigDecimal yValueBigDecimal = BigDecimal.valueOf(yValue); + + // Set new min and max as needed + if (densityPlotBin.getMinX() == null || densityPlotBin.getMinX().compareTo(xValueBigDecimal) > 0){ + densityPlotBin.setMinX(xValueBigDecimal); + } + if (densityPlotBin.getMaxX() == null || densityPlotBin.getMaxX().compareTo(xValueBigDecimal) < 0){ + densityPlotBin.setMaxX(xValueBigDecimal); + } + if (densityPlotBin.getMinY() == null || densityPlotBin.getMinY().compareTo(yValueBigDecimal) > 0){ + densityPlotBin.setMinY(yValueBigDecimal); + } + if (densityPlotBin.getMaxY() == null || densityPlotBin.getMaxY().compareTo(yValueBigDecimal) < 0){ + densityPlotBin.setMaxY(yValueBigDecimal); + } + } + + if (xValues.length > 1) { + // need at least 2 entries in each to compute correlation + result.setPearsonCorr(new PearsonsCorrelation().correlation(xValues, yValues)); + result.setSpearmanCorr(new SpearmansCorrelation().correlation(xValues, yValues)); + } else { + // if less than 1 entry, just set 0 correlation + result.setSpearmanCorr(0.0); + result.setPearsonCorr(0.0); + } + + // filter out empty bins + result.setBins(result.getBins().stream().filter((bin)->(bin.getCount() > 0)).collect(Collectors.toList())); + return result; + } + + + private static boolean isLogScalePossibleForAttribute(String clinicalAttributeId) { + return clinicalAttributeId.equals("MUTATION_COUNT"); + } + + private static double logScale(double val) { + return Math.log(1+val); + } + + private static double parseValueLog(ClinicalData c) { + return ClinicalDataDensityPlotServiceImpl.logScale(Double.parseDouble(c.getAttrValue())); + } + + private static double parseValueLinear(ClinicalData c) { + return Double.parseDouble(c.getAttrValue()); + } +} diff --git a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java b/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java index e6abafc1cc5..ef8e447355a 100644 --- a/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java +++ b/src/main/java/org/cbioportal/service/impl/RedisCacheStatisticsServiceImpl.java @@ -7,6 +7,7 @@ import org.cbioportal.utils.config.annotation.ConditionalOnProperty; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.autoconfigure.condition.ConditionalOnExpression; import org.springframework.cache.Cache; import org.springframework.cache.CacheManager; import org.springframework.security.access.AccessDeniedException; @@ -19,7 +20,9 @@ import java.util.stream.Collectors; @Service -@ConditionalOnProperty(name = "persistence.cache_type", havingValue = {"redis"}) +@ConditionalOnExpression( + "#{environment['persistence.cache_type'] == 'redis' or environment['persistence.cache_type_clickhouse'] == 'redis'}" +) public class RedisCacheStatisticsServiceImpl implements CacheStatisticsService { @Autowired diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java new file mode 100644 index 00000000000..47c7fb87a2f --- /dev/null +++ b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java @@ -0,0 +1,291 @@ +package org.cbioportal.service.impl; + +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.PatientTreatmentReport; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatmentReport; +import org.cbioportal.model.StudyViewFilterContext; +import org.cbioportal.persistence.StudyViewRepository; +import org.cbioportal.service.AlterationCountService; +import org.cbioportal.service.StudyViewColumnarService; +import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.service.treatment.TreatmentCountReportService; +import org.cbioportal.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.CustomSampleIdentifier; +import org.cbioportal.web.parameter.GenericAssayDataBinFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.columnar.util.CustomDataFilterUtil; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Service; + +import java.util.*; +import java.util.stream.Collectors; + +@Service +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class StudyViewColumnarServiceImpl implements StudyViewColumnarService { + + + private final StudyViewRepository studyViewRepository; + private final CustomDataFilterUtil customDataFilterUtil; + + private final AlterationCountService alterationCountService; + private final TreatmentCountReportService treatmentCountReportService; + + @Autowired + public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository, AlterationCountService alterationCountService, TreatmentCountReportService treatmentCountReportService, CustomDataFilterUtil customDataFilterUtil) { + this.studyViewRepository = studyViewRepository; + this.alterationCountService = alterationCountService; + this.treatmentCountReportService = treatmentCountReportService; + this.customDataFilterUtil = customDataFilterUtil; + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getFilteredSamples(StudyViewFilter studyViewFilter) { + + return studyViewRepository.getFilteredSamples(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getMutatedGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException { + return alterationCountService.getMutatedGenes(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getMolecularProfileSampleCounts(StudyViewFilter studyViewFilter) { + return studyViewRepository.getMolecularProfileSampleCounts(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) { + return studyViewRepository.getClinicalEventTypeCounts(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) { + return treatmentCountReportService.getPatientTreatmentReport(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) { + return treatmentCountReportService.getSampleTreatmentReport(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getGenomicDataBinCounts(StudyViewFilter studyViewFilter, List genomicDataBinFilters) { + return generateDataCountItemsFromDataCounts(studyViewRepository.getGenomicDataBinCounts(createContext(studyViewFilter), genomicDataBinFilters)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getGenericAssayDataBinCounts(StudyViewFilter studyViewFilter, List genericAssayDataBinFilters) { + return generateDataCountItemsFromDataCounts(studyViewRepository.getGenericAssayDataBinCounts(createContext(studyViewFilter), genericAssayDataBinFilters)); + } + + public List getCnaGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException { + return alterationCountService.getCnaGenes(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getStructuralVariantGenes(StudyViewFilter studyViewFilter) throws StudyNotFoundException { + return alterationCountService.getStructuralVariantGenes(createContext(studyViewFilter)); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public Map getClinicalAttributeDatatypeMap(StudyViewFilter studyViewFilter) { + return studyViewRepository.getClinicalAttributeDatatypeMap(); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getClinicalDataCounts(StudyViewFilter studyViewFilter, List filteredAttributes) { + + var context = createContext(studyViewFilter); + + List involvedCancerStudies = context.involvedCancerStudies(); + + var result = studyViewRepository.getClinicalDataCounts(context, filteredAttributes); + + // attributes may be missing in result set because they have been filtered out + // e.g. if the filtered samples happen to have no SEX data, they will not appear in the list + // even though the inferred value of those attributes is NA + // the following code restores these counts for missing attributes + if (result.size() != filteredAttributes.size()) { + var attributes = getClinicalAttributesForStudies(involvedCancerStudies) + .stream() + .filter(attribute -> filteredAttributes.contains(attribute.getAttrId())) + .toList(); + + Integer filteredSampleCount = studyViewRepository.getFilteredSamplesCount(createContext(studyViewFilter)); + Integer filteredPatientCount = studyViewRepository.getFilteredPatientCount(createContext(studyViewFilter)); + + result = StudyViewColumnarServiceUtil.addClinicalDataCountsForMissingAttributes( + result, + attributes, + filteredSampleCount, + filteredPatientCount + ); + } + + return StudyViewColumnarServiceUtil.mergeClinicalDataCounts(result); + + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse()" + ) + public List getClinicalAttributesForStudies(List studyIds) { + return studyViewRepository.getClinicalAttributesForStudies(studyIds).stream().toList(); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getCaseListDataCounts(StudyViewFilter studyViewFilter) { + // the study view merges case lists by type across studies + // type is determined by the suffix of case list name (after study name) + var caseListDataCountsPerStudy = studyViewRepository.getCaseListDataCountsPerStudy(createContext(studyViewFilter)); + return StudyViewColumnarServiceUtil.mergeCaseListCounts(caseListDataCountsPerStudy); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getPatientClinicalData(StudyViewFilter studyViewFilter, List attributeIds) { + return studyViewRepository.getPatientClinicalData(createContext(studyViewFilter), attributeIds); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getSampleClinicalData(StudyViewFilter studyViewFilter, List attributeIds) { + return studyViewRepository.getSampleClinicalData(createContext(studyViewFilter), attributeIds); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters) { + return studyViewRepository.getCNACounts(createContext(studyViewFilter), genomicDataFilters); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getGenericAssayDataCounts(StudyViewFilter studyViewFilter, List genericAssayDataFilters) { + return studyViewRepository.getGenericAssayDataCounts(createContext(studyViewFilter), genericAssayDataFilters); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters) { + List genomicDataCountItemList = new ArrayList<>(); + for (GenomicDataFilter genomicDataFilter : genomicDataFilters) { + Map counts = studyViewRepository.getMutationCounts(createContext(studyViewFilter), genomicDataFilter); + genomicDataCountItemList.add(StudyViewColumnarServiceUtil.createGenomicDataCountItemFromMutationCounts(genomicDataFilter, counts)); + } + return genomicDataCountItemList; + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) + @Override + public List getMutationTypeCountsByGeneSpecific(StudyViewFilter studyViewFilter, List genomicDataFilters) { + return studyViewRepository.getMutationCountsByType(createContext(studyViewFilter), genomicDataFilters); + } + + + private StudyViewFilterContext createContext(StudyViewFilter studyViewFilter) { + List customSampleIdentifiers = customDataFilterUtil.extractCustomDataSamples(studyViewFilter); + List involvedCancerStudies = customDataFilterUtil.extractInvolvedCancerStudies(studyViewFilter); + return new StudyViewFilterContext(studyViewFilter, customSampleIdentifiers, involvedCancerStudies); + } + + private List generateDataCountItemsFromDataCounts(List dataCounts) { + return dataCounts.stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId)) + .entrySet().parallelStream().map(e -> { + ClinicalDataCountItem item = new ClinicalDataCountItem(); + item.setAttributeId(e.getKey()); + item.setCounts(StudyViewColumnarServiceUtil.normalizeDataCounts(e.getValue())); + return item; + }).toList(); + } + + + +} diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java index e84f146e459..05ea4056aee 100644 --- a/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java +++ b/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java @@ -86,12 +86,15 @@ public List getGenomicDataCounts(List studyIds, List molecularProfileSampleIdentifiers = molecularProfileService.getMolecularProfileCaseIdentifiers(studyIds, sampleIds); + + // first get all molecular profiles List molecularProfiles = molecularProfileService .getMolecularProfilesInStudies(new ArrayList<>(new HashSet<>(studyIds)), Projection.SUMMARY.name()); Map molecularProfileMap = molecularProfiles .stream() .collect(Collectors.toMap(MolecularProfile::getStableId, Function.identity())); + // get gene panels Map molecularProfileCaseCountSet = genePanelService .fetchGenePanelDataInMultipleMolecularProfiles(molecularProfileSampleIdentifiers) .stream() @@ -167,10 +170,10 @@ public List getMutationCountsByGeneSpecific(List s return genomicDataFilters .stream() - .flatMap(gdFilter -> { + .flatMap(genomicDataFilter -> { GenomicDataCountItem genomicDataCountItem = new GenomicDataCountItem(); - String hugoGeneSymbol = gdFilter.getKey(); - String profileType = gdFilter.getValue(); + String hugoGeneSymbol = genomicDataFilter.getKey(); + String profileType = genomicDataFilter.getValue(); genomicDataCountItem.setHugoGeneSymbol(hugoGeneSymbol); genomicDataCountItem.setProfileType(profileType); @@ -231,9 +234,9 @@ public List getMutationTypeCountsByGeneSpecific(List { - String hugoGeneSymbol = gdFilter.getKey(); - String profileType = gdFilter.getValue(); + .flatMap(genomicDataFilter -> { + String hugoGeneSymbol = genomicDataFilter.getKey(); + String profileType = genomicDataFilter.getValue(); List stableIds = Collections.singletonList(geneSymbolIdMap.get(hugoGeneSymbol)); @@ -356,10 +359,10 @@ public List getCNAAlterationCountsByGeneSpecific(List { + .flatMap(genomicDataFilter -> { GenomicDataCountItem genomicDataCountItem = new GenomicDataCountItem(); - String hugoGeneSymbol = gdFilter.getKey(); - String profileType = gdFilter.getValue(); + String hugoGeneSymbol = genomicDataFilter.getKey(); + String profileType = genomicDataFilter.getValue(); genomicDataCountItem.setHugoGeneSymbol(hugoGeneSymbol); genomicDataCountItem.setProfileType(profileType); diff --git a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java index fc90318d280..92c0ef233a9 100644 --- a/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java +++ b/src/main/java/org/cbioportal/service/impl/ViolinPlotServiceImpl.java @@ -5,6 +5,8 @@ import org.apache.commons.math3.stat.descriptive.rank.Percentile; import org.cbioportal.model.*; import org.cbioportal.service.ViolinPlotService; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.springframework.cache.annotation.Cacheable; import org.springframework.stereotype.Service; import java.math.BigDecimal; @@ -16,7 +18,11 @@ public class ViolinPlotServiceImpl implements ViolinPlotService { // If a row has less than this many points, do not compute a // violin, because it doesn't make sense. static final int SHOW_ONLY_POINTS_THRESHOLD = 7; - + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabledClickhouse() && @studyViewFilterUtil.isUnfilteredQuery(#studyViewFilter)" + ) public ClinicalViolinPlotData getClinicalViolinPlotData( List sampleClinicalDataForViolinPlot, List samplesForSampleCounts, @@ -24,7 +30,8 @@ public ClinicalViolinPlotData getClinicalViolinPlotData( BigDecimal axisEnd, BigDecimal numCurvePoints, Boolean useLogScale, - BigDecimal sigmaMultiplier + BigDecimal sigmaMultiplier, + StudyViewFilter studyViewFilter ) { ClinicalViolinPlotData result = new ClinicalViolinPlotData(); result.setAxisStart(Double.POSITIVE_INFINITY); @@ -32,7 +39,7 @@ public ClinicalViolinPlotData getClinicalViolinPlotData( result.setRows(new ArrayList<>()); // collect filtered samples into a set for quick lookup - Set samplesForSampleCountsIds = + Set samplesForSampleCountsIds = samplesForSampleCounts.stream() .map(Sample::getInternalId) .collect(Collectors.toSet()); @@ -78,11 +85,13 @@ public ClinicalViolinPlotData getClinicalViolinPlotData( double max = Double.NEGATIVE_INFINITY; int valuesIndex = 0; for (ClinicalData d: data) { - Double value = useLogScale ? ViolinPlotServiceImpl.logScale(Double.parseDouble(d.getAttrValue())) : Double.parseDouble(d.getAttrValue()); - values[valuesIndex] = value; - min = Math.min(value, min); - max = Math.max(value, max); - valuesIndex += 1; + if (NumberUtils.isCreatable(d.getAttrValue())) { + Double value = useLogScale ? ViolinPlotServiceImpl.logScale(Double.parseDouble(d.getAttrValue())) : Double.parseDouble(d.getAttrValue()); + values[valuesIndex] = value; + min = Math.min(value, min); + max = Math.max(value, max); + valuesIndex += 1; + } } percentile.setData(values); @@ -102,24 +111,26 @@ public ClinicalViolinPlotData getClinicalViolinPlotData( List detailedData = groupedDetailedData.get(category); int numSuspectedOutliers = 0; for (ClinicalData d: detailedData) { - Double value = useLogScale ? ViolinPlotServiceImpl.logScale(Double.parseDouble(d.getAttrValue())) : Double.parseDouble(d.getAttrValue()); - boolean isOutlier = false; - if (value <= suspectedOutlierThresholdLower) { - numSuspectedOutliers += 1; - if (value <= outlierThresholdLower) { - isOutlier = true; + if (NumberUtils.isCreatable(d.getAttrValue())) { + Double value = useLogScale ? ViolinPlotServiceImpl.logScale(Double.parseDouble(d.getAttrValue())) : Double.parseDouble(d.getAttrValue()); + boolean isOutlier = false; + if (value <= suspectedOutlierThresholdLower) { + numSuspectedOutliers += 1; + if (value <= outlierThresholdLower) { + isOutlier = true; + } + } else if (value >= suspectedOutlierThresholdUpper) { + numSuspectedOutliers += 1; + if (value >= outlierThresholdUpper) { + isOutlier = true; + } } - } else if (value >= suspectedOutlierThresholdUpper) { - numSuspectedOutliers += 1; - if (value >= outlierThresholdUpper) { - isOutlier = true; + if (isOutlier) { + _outliers.add(d); + } else { + _nonOutliers.add(d); } } - if (isOutlier) { - _outliers.add(d); - } else { - _nonOutliers.add(d); - } } ClinicalViolinPlotBoxData _boxData = new ClinicalViolinPlotBoxData(); @@ -174,9 +185,9 @@ public ClinicalViolinPlotData getClinicalViolinPlotData( Double value = useLogScale ? ViolinPlotServiceImpl.logScale(Double.parseDouble(d.getAttrValue())) : Double.parseDouble(d.getAttrValue()); gaussians.add(new Gaussian(value, sigma)); } - + row.setCurveData( - curvePoints.stream().map(p -> { + curvePoints.parallelStream().map(p -> { BigDecimal sum = new BigDecimal(0); for (Gaussian g : gaussians) { sum = sum.add(BigDecimal.valueOf(g.value(p))); diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java new file mode 100644 index 00000000000..66305eb5fe8 --- /dev/null +++ b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java @@ -0,0 +1,14 @@ +package org.cbioportal.service.treatment; + +import org.cbioportal.model.PatientTreatmentReport; +import org.cbioportal.model.SampleTreatmentReport; +import org.cbioportal.model.StudyViewFilterContext; +import org.cbioportal.web.parameter.CustomSampleIdentifier; +import org.cbioportal.web.parameter.StudyViewFilter; + +import java.util.List; + +public interface TreatmentCountReportService { + PatientTreatmentReport getPatientTreatmentReport(StudyViewFilterContext studyViewFilterContext); + SampleTreatmentReport getSampleTreatmentReport(StudyViewFilterContext studyViewFilterContext); +} diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java new file mode 100644 index 00000000000..4a96bcdaf85 --- /dev/null +++ b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java @@ -0,0 +1,48 @@ +package org.cbioportal.service.treatment; + +import org.cbioportal.model.PatientTreatmentReport; +import org.cbioportal.model.SampleTreatmentReport; +import org.cbioportal.model.SampleTreatmentRow; +import org.cbioportal.model.StudyViewFilterContext; +import org.cbioportal.model.TemporalRelation; +import org.cbioportal.persistence.StudyViewRepository; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Service; + +import java.util.Set; +import java.util.stream.Stream; + +@Service +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class TreatmentCountReportServiceImpl implements TreatmentCountReportService { + + private final StudyViewRepository studyViewRepository; + + @Autowired + public TreatmentCountReportServiceImpl(StudyViewRepository studyViewRepository) { + this.studyViewRepository = studyViewRepository; + } + + @Override + public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilterContext studyViewFilterContext) { + var patientTreatments = studyViewRepository.getPatientTreatments(studyViewFilterContext); + var totalPatientTreatmentCount = studyViewRepository.getTotalPatientTreatmentCount(studyViewFilterContext); + return new PatientTreatmentReport(totalPatientTreatmentCount, 0, patientTreatments); + } + + @Override + public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilterContext studyViewFilterContext) { + var sampleTreatments = studyViewRepository.getSampleTreatments(studyViewFilterContext) + .stream() + .flatMap(sampleTreatment -> + Stream.of(new SampleTreatmentRow(TemporalRelation.Pre, sampleTreatment.treatment(), sampleTreatment.preSampleCount(), Set.of()), + new SampleTreatmentRow(TemporalRelation.Post, sampleTreatment.treatment(), sampleTreatment.postSampleCount(), Set.of() )) + ) + .filter(sampleTreatment -> sampleTreatment.getCount() > 0 ) + .toList(); + var totalSampleTreatmentCount = studyViewRepository.getTotalSampleTreatmentCount(studyViewFilterContext); + return new SampleTreatmentReport(totalSampleTreatmentCount, sampleTreatments); + } + +} diff --git a/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java b/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java new file mode 100644 index 00000000000..9f565e216fc --- /dev/null +++ b/src/main/java/org/cbioportal/service/util/AlterationCountServiceUtil.java @@ -0,0 +1,168 @@ +package org.cbioportal.service.util; + +import org.apache.commons.math3.util.Pair; +import org.cbioportal.model.AlterationCountBase; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.Gistic; +import org.cbioportal.model.GisticToGene; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.MutSig; +import org.springframework.lang.NonNull; + +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.function.Function; +import java.util.stream.Collectors; + +public class AlterationCountServiceUtil { + + private AlterationCountServiceUtil() {} + + private static final String WHOLE_EXOME_SEQUENCING = "WES"; + + public static int computeTotalProfiledCount(boolean hasGenePanelData, int alterationsProfiledCount, int sampleProfileCountWithoutGenePanelData, int totalProfiledCount) { + int profiledCount = hasGenePanelData ? alterationsProfiledCount + sampleProfileCountWithoutGenePanelData + : sampleProfileCountWithoutGenePanelData; + return profiledCount == 0 ? totalProfiledCount : profiledCount; + } + + public static List updateAlterationCountsWithMutSigQValue( + List alterationCountByGenes, + Map mutSigs) { + + if (!mutSigs.isEmpty()) { + alterationCountByGenes.parallelStream() + .filter(alterationCount -> mutSigs.containsKey(alterationCount.getHugoGeneSymbol())) + .forEach(alterationCount -> + alterationCount.setqValue(mutSigs.get(alterationCount.getHugoGeneSymbol()).getqValue()) + ); + } + return alterationCountByGenes; + } + + public static List updateAlterationCountsWithCNASigQValue( + List alterationCountByGenes, + Map, Gistic> gisticMap) { + + if (!gisticMap.isEmpty()) { + alterationCountByGenes.parallelStream() + .filter(alterationCount -> gisticMap.containsKey(Pair.create(alterationCount.getHugoGeneSymbol(), alterationCount.getAlteration()))) + .forEach(alterationCount -> + alterationCount.setqValue(gisticMap.get(Pair.create(alterationCount.getHugoGeneSymbol(), alterationCount.getAlteration())).getqValue()) + ); + } + return alterationCountByGenes; + } + + public static List getFirstMolecularProfileGroupedByStudy(List molecularProfiles) { + return molecularProfiles.stream() + .collect(Collectors.toMap( + MolecularProfile::getCancerStudyIdentifier, + Function.identity(), + (existing, replacement) -> existing // Keep the first occurrence + )) + .values() + .stream() + .toList(); + } + + /** + * Combines alteration counts by Hugo gene symbols. If multiple entries exist for the same + * gene symbol, their number of altered cases and total counts are summed up. Returns a + * list of unique AlterationCountByGene objects where each gene symbol is represented only once. + * + * This appears in the Data where Genes have similar Hugo Gene Symbols but different Entrez Ids + * + * @param alterationCounts List of AlterationCountByGene objects, potentially with duplicate gene symbols + * @return List of AlterationCountByGene objects with unique gene symbols and combined counts + */ + public static List combineAlterationCountsWithConflictingHugoSymbols(List alterationCounts) { + Map alterationCountByGeneMap = new HashMap<>(); + for (var alterationCount : alterationCounts) { + if (alterationCountByGeneMap.containsKey(alterationCount.getHugoGeneSymbol())){ + AlterationCountByGene toUpdate = alterationCountByGeneMap.get(alterationCount.getHugoGeneSymbol()); + toUpdate.setNumberOfAlteredCases(toUpdate.getNumberOfAlteredCases() + alterationCount.getNumberOfAlteredCases()); + toUpdate.setTotalCount(toUpdate.getTotalCount() + alterationCount.getTotalCount()); + } else { + alterationCountByGeneMap.put(alterationCount.getHugoGeneSymbol(), alterationCount); + } + } + return alterationCountByGeneMap.values().stream().toList(); + } + + /** + * Combines alteration counts by Hugo gene symbols. If multiple entries exist for the same + * gene symbol, their number of altered cases and total counts are summed up. Returns a + * list of unique AlterationCountByGene objects where each gene symbol is represented only once. + * + * This appears in the Data where Genes have similar Hugo Gene Symbols but different Entrez Ids. + * This is a special case to handle Copy Number Mutations where the Alteration type should be a part of the key + * + * @param alterationCounts List of CopyNumberCountByGene objects, potentially with duplicate gene symbols + * @return List of AlterationCountByGene objects with unique gene symbols and combined counts + */ + public static List combineCopyNumberCountsWithConflictingHugoSymbols(List alterationCounts) { + Map, CopyNumberCountByGene> alterationCountByGeneMap = new HashMap<>(); + for (var alterationCount : alterationCounts) { + var copyNumberKey = Pair.create(alterationCount.getHugoGeneSymbol(), alterationCount.getAlteration()); + if (alterationCountByGeneMap.containsKey(copyNumberKey)) { + CopyNumberCountByGene toUpdate = alterationCountByGeneMap.get(copyNumberKey); + toUpdate.setNumberOfAlteredCases(toUpdate.getNumberOfAlteredCases() + alterationCount.getNumberOfAlteredCases()); + toUpdate.setTotalCount(toUpdate.getTotalCount() + alterationCount.getTotalCount()); + } else { + alterationCountByGeneMap.put(copyNumberKey, alterationCount); + } + } + return alterationCountByGeneMap.values().stream().toList(); + } + + public static boolean hasGenePanelData(@NonNull Set matchingGenePanelIds) { + return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) + && matchingGenePanelIds.size() > 1 || !matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) && !matchingGenePanelIds.isEmpty(); + } + + public static void setupGisticMap(List gisticList, Map, Gistic> gisticMap) { + for (Gistic gistic : gisticList) { + var amp = gistic.getAmp().booleanValue() ? 2 : -2; + for (GisticToGene gene : gistic.getGenes()) { + var key = Pair.create(gene.getHugoGeneSymbol(), amp); + Gistic currentGistic = gisticMap.get(key); + if (currentGistic == null || gistic.getqValue().compareTo(currentGistic.getqValue()) < 0) { + gisticMap.put(key, gistic); + } + } + } + } + + public static void setupAlterationGeneCountsMap( + List studyAlterationCountByGenes, + Map totalResult) { + + studyAlterationCountByGenes.forEach(datum -> { + String key = datum.getUniqueEventKey(); + if (totalResult.containsKey(key)) { + S alterationCountByGene = totalResult.get(key); + alterationCountByGene.setTotalCount(alterationCountByGene.getTotalCount() + datum.getTotalCount()); + alterationCountByGene.setNumberOfAlteredCases(alterationCountByGene.getNumberOfAlteredCases() + datum.getNumberOfAlteredCases()); + alterationCountByGene.setNumberOfProfiledCases(alterationCountByGene.getNumberOfProfiledCases() + datum.getNumberOfProfiledCases()); + Set matchingGenePanelIds = new HashSet<>(); + if (!alterationCountByGene.getMatchingGenePanelIds().isEmpty()) { + matchingGenePanelIds.addAll(alterationCountByGene.getMatchingGenePanelIds()); + } + if (!datum.getMatchingGenePanelIds().isEmpty()) { + matchingGenePanelIds.addAll(datum.getMatchingGenePanelIds()); + } + alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds); + totalResult.put(key, alterationCountByGene); + } else { + totalResult.put(key, datum); + } + }); + } + + +} \ No newline at end of file diff --git a/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java new file mode 100644 index 00000000000..981dbb80cf2 --- /dev/null +++ b/src/main/java/org/cbioportal/service/util/StudyViewColumnarServiceUtil.java @@ -0,0 +1,176 @@ +package org.cbioportal.service.util; + +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.web.parameter.GenomicDataFilter; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +public class StudyViewColumnarServiceUtil { + + private StudyViewColumnarServiceUtil() {} + + public static final String MUTATED_COUNT = "mutatedCount"; + public static final String NOT_MUTATED_COUNT = "notMutatedCount"; + public static final String NOT_PROFILED_COUNT = "notProfiledCount"; + + public static List mergeClinicalDataCounts( + List items + ) { + items.forEach(attr -> { + Map> countsPerType = attr.getCounts().stream() + .collect(Collectors.groupingBy(ClinicalDataCount::getValue)); + List res = countsPerType.entrySet().stream().map(entry -> { + ClinicalDataCount mergedCount = new ClinicalDataCount(); + mergedCount.setAttributeId(attr.getAttributeId()); + mergedCount.setValue(entry.getKey()); + mergedCount.setCount(entry.getValue().stream().mapToInt(ClinicalDataCount::getCount).sum()); + return mergedCount; + }).toList(); + attr.setCounts(res); + }); + return items; + } + + public static List addClinicalDataCountsForMissingAttributes( + List counts, + List attributes, + Integer filteredSampleCount, + Integer filteredPatientCount + ) { + Map map = counts.stream() + .collect(Collectors.toMap(ClinicalDataCountItem::getAttributeId, item -> item)); + + List result = new ArrayList<>(counts); + + attributes.forEach(attr -> { + Integer count = attr.getPatientAttribute().booleanValue() ? filteredPatientCount : filteredSampleCount; + + if (!map.containsKey(attr.getAttrId())) { + ClinicalDataCountItem newItem = new ClinicalDataCountItem(); + newItem.setAttributeId(attr.getAttrId()); + ClinicalDataCount countObj = new ClinicalDataCount(); + countObj.setCount(count); + countObj.setValue("NA"); + countObj.setAttributeId(attr.getAttrId()); + newItem.setCounts(List.of(countObj)); + result.add(newItem); + } + }); + + return result; + } + + public static List mergeGenomicDataCounts(List sampleCounts) { + Map> countsPerType = sampleCounts.stream() + .collect(Collectors.groupingBy(GenomicDataCount::getValue)); + + List mergedCounts = new ArrayList<>(); + for (Map.Entry> entry : countsPerType.entrySet()) { + var dc = new GenomicDataCount(); + dc.setValue(entry.getKey()); + dc.setLabel(entry.getValue().get(0).getLabel()); + Integer sum = entry.getValue().stream() + .map(GenomicDataCount::getCount) + .collect(Collectors.summingInt(Integer::intValue)); + dc.setCount(sum); + mergedCounts.add(dc); + } + return mergedCounts; + } + + public static List mergeCaseListCounts(List counts) { + Map> countsPerListType = counts.stream() + .collect((Collectors.groupingBy(CaseListDataCount::getValue))); + + // different cancer studies combined into one cohort will have separate case lists + // of a given type (e.g. rppa). We need to merge the counts for these + // different lists based on the type and choose a label + // this code just picks the first label, which assumes that the labels will match for a give type + List mergedCounts = new ArrayList<>(); + for (Map.Entry> entry : countsPerListType.entrySet()) { + var dc = new CaseListDataCount(); + dc.setValue(entry.getKey()); + // here just snatch the label of the first profile + dc.setLabel(entry.getValue().get(0).getLabel()); + Integer sum = entry.getValue().stream() + .map(x -> x.getCount()) + .collect(Collectors.summingInt(Integer::intValue)); + dc.setCount(sum); + mergedCounts.add(dc); + } + return mergedCounts; + } + + /** + * Normalizes data counts by merging attribute values in a case-insensitive way. + * For example attribute values "TRUE", "True", and 'true' will be merged into a single aggregated count. + * This method assumes that all the counts in the given dataCounts list has the same attributeId. + * + * @param dataCounts list of data counts for a single attribute + * + * @return normalized list of data counts + */ + public static List normalizeDataCounts(List dataCounts) { + Collection normalizedDataCounts = dataCounts + .stream() + .collect( + Collectors.groupingBy( + c -> c.getValue().toLowerCase(), + Collectors.reducing(new ClinicalDataCount(), (count1, count2) -> { + // assuming attribute ids are the same for all data counts, just pick the first one + String attributeId = + count1.getAttributeId() != null + ? count1.getAttributeId() + : count2.getAttributeId(); + + // pick the value in a deterministic way by prioritizing lower case over upper case. + // for example, 'True' will be picked in case of 2 different values like 'TRUE', and 'True', + // and 'true' will be picked in case of 3 different values like 'TRUE', 'True', and 'true' + String value = count1.getValue() != null + ? count1.getValue() + : count2.getValue(); + if (count1.getValue() != null && count2.getValue() != null) { + value = count1.getValue().compareTo(count2.getValue()) > 0 + ? count1.getValue() + : count2.getValue(); + } + + // aggregate counts for the merged values + Integer count = (count1.getCount() != null ? count1.getCount(): 0) + + (count2.getCount() != null ? count2.getCount(): 0); + + ClinicalDataCount aggregated = new ClinicalDataCount(); + aggregated.setAttributeId(attributeId); + aggregated.setValue(value); + aggregated.setCount(count); + return aggregated; + }) + ) + ) + .values(); + + return new ArrayList<>(normalizedDataCounts); + } + + public static GenomicDataCountItem createGenomicDataCountItemFromMutationCounts(GenomicDataFilter genomicDataFilter, Map counts) { + List genomicDataCountList = new ArrayList<>(); + if (counts.getOrDefault(MUTATED_COUNT, 0) > 0) + genomicDataCountList.add(new GenomicDataCount("Mutated", "MUTATED", counts.get(MUTATED_COUNT), counts.get(MUTATED_COUNT))); + if (counts.getOrDefault(NOT_MUTATED_COUNT, 0) > 0) + genomicDataCountList.add(new GenomicDataCount("Not Mutated", "NOT_MUTATED", counts.get(NOT_MUTATED_COUNT), counts.get(NOT_MUTATED_COUNT))); + if (counts.getOrDefault(NOT_PROFILED_COUNT, 0) > 0) + genomicDataCountList.add(new GenomicDataCount("Not Profiled", "NOT_PROFILED", counts.get(NOT_PROFILED_COUNT), counts.get(NOT_PROFILED_COUNT))); + return new GenomicDataCountItem(genomicDataFilter.getHugoGeneSymbol(), "mutations", genomicDataCountList); + } + + +} \ No newline at end of file diff --git a/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java b/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java new file mode 100644 index 00000000000..cd53de8c347 --- /dev/null +++ b/src/main/java/org/cbioportal/web/ExecuterTimeInterceptor.java @@ -0,0 +1,27 @@ +package org.cbioportal.web; + +import org.springframework.ui.ModelMap; +import org.springframework.web.context.request.WebRequest; +import org.springframework.web.context.request.WebRequestInterceptor; + +public class ExecuterTimeInterceptor implements WebRequestInterceptor { + + @Override + public void postHandle(WebRequest webRequest, ModelMap modelMap) { + //unimplemented + } + + @Override + public void afterCompletion(WebRequest webRequest, Exception e) { + //unimplemented + } + + @Override + public void preHandle(WebRequest webRequest) { + + long startTime = System.currentTimeMillis(); + webRequest.setAttribute("startTime", startTime, 0); + + } + +} \ No newline at end of file diff --git a/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java b/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java new file mode 100644 index 00000000000..dbf2fc9d867 --- /dev/null +++ b/src/main/java/org/cbioportal/web/GeneralControllerAdvice.java @@ -0,0 +1,31 @@ +package org.cbioportal.web; + +import org.springframework.core.MethodParameter; +import org.springframework.http.MediaType; +import org.springframework.http.converter.HttpMessageConverter; +import org.springframework.http.server.ServerHttpRequest; +import org.springframework.http.server.ServerHttpResponse; +import org.springframework.http.server.ServletServerHttpRequest; +import org.springframework.web.bind.annotation.ControllerAdvice; +import org.springframework.web.servlet.mvc.method.annotation.ResponseBodyAdvice; + +@ControllerAdvice +public class GeneralControllerAdvice implements ResponseBodyAdvice { + + @Override + public boolean supports(MethodParameter returnType, Class> converterType) { + return true; + } + + @Override + public Object beforeBodyWrite(Object body, MethodParameter returnType, MediaType selectedContentType, Class> selectedConverterType, ServerHttpRequest request, ServerHttpResponse response) { + ServletServerHttpRequest servletServerRequest = (ServletServerHttpRequest) request; + + // report the procesing time of all api endpoints to aid in benchmarking as we transition + // to clickhouse + long startTime = (long) servletServerRequest.getServletRequest().getAttribute("startTime"); + long timeElapsed = System.currentTimeMillis() - startTime; + response.getHeaders().add("Elapsed-Time", String.valueOf(timeElapsed)); + return body; + } +} \ No newline at end of file diff --git a/src/main/java/org/cbioportal/web/StudyViewController.java b/src/main/java/org/cbioportal/web/StudyViewController.java index 55d93d4f430..90e53af20b7 100644 --- a/src/main/java/org/cbioportal/web/StudyViewController.java +++ b/src/main/java/org/cbioportal/web/StudyViewController.java @@ -864,7 +864,8 @@ public ResponseEntity fetchClinicalDataViolinPlots( axisEnd, numCurvePoints, useLogScale, - sigmaMultiplier + sigmaMultiplier, + interceptedStudyViewFilter ); return new ResponseEntity<>(result, HttpStatus.OK); @@ -958,15 +959,15 @@ public ResponseEntity> fetchGenomicDataCounts( @Parameter(required = true, description = "Intercepted Genomic Data Count Filter") @Valid @RequestAttribute(required = false, value = "interceptedGenomicDataCountFilter") GenomicDataCountFilter interceptedGenomicDataCountFilter ) throws StudyNotFoundException { - List gdFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters(); + List genomicDataFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters(); StudyViewFilter studyViewFilter = interceptedGenomicDataCountFilter.getStudyViewFilter(); // when there is only one filter, it means study view is doing a single chart filter operation // remove filter from studyViewFilter to return all data counts // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart - if (gdFilters.size() == 1) { + if (genomicDataFilters.size() == 1) { studyViewFilterUtil.removeSelfFromGenomicDataFilter( - gdFilters.get(0).getHugoGeneSymbol(), - gdFilters.get(0).getProfileType(), + genomicDataFilters.get(0).getHugoGeneSymbol(), + genomicDataFilters.get(0).getProfileType(), studyViewFilter); } List filteredSampleIdentifiers = studyViewFilterApplier.apply(studyViewFilter); @@ -982,7 +983,7 @@ public ResponseEntity> fetchGenomicDataCounts( List result = studyViewService.getCNAAlterationCountsByGeneSpecific( studyIds, sampleIds, - gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).collect(Collectors.toList())); + genomicDataFilters.stream().map(genomicDataFilter -> new Pair<>(genomicDataFilter.getHugoGeneSymbol(), genomicDataFilter.getProfileType())).collect(Collectors.toList())); return new ResponseEntity<>(result, HttpStatus.OK); } @@ -1182,15 +1183,15 @@ public ResponseEntity> fetchMutationDataCounts( @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface @Valid @RequestAttribute(required = false, value = "interceptedGenomicDataCountFilter") GenomicDataCountFilter interceptedGenomicDataCountFilter ) { - List gdFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters(); + List genomicDataFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters(); StudyViewFilter studyViewFilter = interceptedGenomicDataCountFilter.getStudyViewFilter(); // when there is only one filter, it means study view is doing a single chart filter operation // remove filter from studyViewFilter to return all data counts // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart - if (gdFilters.size() == 1 && projection == Projection.SUMMARY) { + if (genomicDataFilters.size() == 1 && projection == Projection.SUMMARY) { studyViewFilterUtil.removeSelfFromMutationDataFilter( - gdFilters.get(0).getHugoGeneSymbol(), - gdFilters.get(0).getProfileType(), + genomicDataFilters.get(0).getHugoGeneSymbol(), + genomicDataFilters.get(0).getProfileType(), MutationOption.MUTATED, studyViewFilter); } @@ -1211,13 +1212,13 @@ public ResponseEntity> fetchMutationDataCounts( studyViewService.getMutationCountsByGeneSpecific( studyIds, sampleIds, - gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).toList(), + genomicDataFilters.stream().map(genomicDataFilter -> new Pair<>(genomicDataFilter.getHugoGeneSymbol(), genomicDataFilter.getProfileType())).toList(), studyViewFilter.getAlterationFilter() - ) : + ) : studyViewService.getMutationTypeCountsByGeneSpecific( studyIds, sampleIds, - gdFilters.stream().map(gdFilter -> new Pair<>(gdFilter.getHugoGeneSymbol(), gdFilter.getProfileType())).toList() + genomicDataFilters.stream().map(genomicDataFilter -> new Pair<>(genomicDataFilter.getHugoGeneSymbol(), genomicDataFilter.getProfileType())).toList() ); return new ResponseEntity<>(result, HttpStatus.OK); diff --git a/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java new file mode 100644 index 00000000000..1efaa2b01b9 --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java @@ -0,0 +1,349 @@ +package org.cbioportal.web.columnar; + +import org.cbioportal.model.*; +import org.cbioportal.service.CustomDataService; +import org.cbioportal.service.StudyViewColumnarService; +import org.cbioportal.service.util.CustomDataSession; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.web.columnar.util.CustomDataFilterUtil; +import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.web.parameter.*; +import org.cbioportal.web.util.DataBinner; +import org.cbioportal.web.util.StudyViewFilterUtil; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.stream.Collectors; + +import static java.util.Collections.emptyList; +import static java.util.stream.Collectors.toMap; + +// BasicDataBinner is a generalized class derived from ClinicalDataBinner +// BasicDataBinner should eventually deprecate ClinicalDataBinner +// we are using BasicDataBinner for genomic data, generic assay, and custom data bin counts now +// but BasicDataBinner can support clinical data counts too +// after we switched clinical data counts to use this, then We can remove ClinicalDataBinner +@Component +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class BasicDataBinner { + private final StudyViewColumnarService studyViewColumnarService; + private final DataBinner dataBinner; + private final CustomDataFilterUtil customDataFilterUtil; + private final CustomDataService customDataService; + private final StudyViewFilterUtil studyViewFilterUtil; + + @Autowired + public BasicDataBinner( + StudyViewColumnarService studyViewColumnarService, + DataBinner dataBinner, + CustomDataFilterUtil customDataFilterUtil, + CustomDataService customDataService, + StudyViewFilterUtil studyViewFilterUtil + ) { + this.studyViewColumnarService = studyViewColumnarService; + this.dataBinner = dataBinner; + this.customDataFilterUtil = customDataFilterUtil; + this.customDataService = customDataService; + this.studyViewFilterUtil = studyViewFilterUtil; + } + + // convert from counts to clinical data + private List convertCountsToData(List clinicalDataCounts) + { + return clinicalDataCounts + .stream() + .map(NewClinicalDataBinUtil::generateClinicalDataFromClinicalDataCount) + .flatMap(Collection::stream) + .toList(); + } + + @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()") + public List getDataBins( + DataBinMethod dataBinMethod, + T dataBinCountFilter, + boolean shouldRemoveSelfFromFilter) { + // get data bin filters based on the type of the filter + // either Genomic data or Generic Assay data or custom data or clinical data + List dataBinFilters = fetchDataBinFilters(dataBinCountFilter); + StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); + // define result variables + List resultDataBins = Collections.emptyList(); + // if no data bin filters or no study view filer object is passed in + // return empty result + if (dataBinFilters.isEmpty() || studyViewFilter == null) { + return resultDataBins; + } + + if (shouldRemoveSelfFromFilter && dataBinFilters.size() == 1) { + removeSelfFromFilter(dataBinFilters.get(0), studyViewFilter); + } + + List uniqueKeys = dataBinFilters.stream().map(this::getDataBinFilterUniqueKey).toList(); + + // a new StudyView filter to partially filter by study and sample ids only + // we need this additional partial filter because we always need to know the bins generated for the initial state + // which allows us to keep the number of bins and bin ranges consistent even if there are additional data filters. + // we only want to update the counts for each bin, we don't want to regenerate the bins for the filtered data. + // NOTE: partial filter is only needed when dataBinMethod == DataBinMethod.STATIC but that's always the case + // for the frontend implementation. we can't really use dataBinMethod == DataBinMethod.DYNAMIC because of the + // complication it brings to the frontend visualization and filtering + StudyViewFilter partialFilter = new StudyViewFilter(); + partialFilter.setStudyIds(studyViewFilter.getStudyIds()); + partialFilter.setSampleIdentifiers(studyViewFilter.getSampleIdentifiers()); + + // we need to fetch data for the partial filter in order to generate the bins for initial state + // we use the filtered data to calculate the counts for each bin, we do not regenerate bins for the filtered data + List unfilteredClinicalDataCounts; + List filteredClinicalDataCounts; + Map attributeDatatypeMap; + switch (dataBinCountFilter) { + // TODO: first case is to support clinical data, but clinical data is not using this now. We should update controller to use this method later + case ClinicalDataBinCountFilter clinicalDataBinCountFilter when !customDataService.getCustomDataSessions(uniqueKeys).isEmpty() -> { + Map customDataSessions = customDataService.getCustomDataSessions(uniqueKeys); + List unfilteredSampleIdentifiers = studyViewColumnarService.getFilteredSamples(partialFilter).stream().map(sample -> studyViewFilterUtil.buildSampleIdentifier(sample.getCancerStudyIdentifier(), sample.getStableId())).toList(); + unfilteredClinicalDataCounts = customDataFilterUtil.getCustomDataCounts(unfilteredSampleIdentifiers, customDataSessions); + List filteredSampleIdentifiers = studyViewColumnarService.getFilteredSamples(studyViewFilter).stream().map(sample -> studyViewFilterUtil.buildSampleIdentifier(sample.getCancerStudyIdentifier(), sample.getStableId())).toList(); + filteredClinicalDataCounts = customDataFilterUtil.getCustomDataCounts(filteredSampleIdentifiers, customDataSessions); + attributeDatatypeMap = customDataSessions.entrySet().stream().collect(toMap( + Map.Entry::getKey, + NewClinicalDataBinUtil::getDataType + )); + } + case ClinicalDataBinCountFilter clinicalDataBinCountFilter -> { + unfilteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(partialFilter, uniqueKeys); + filteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, uniqueKeys); + attributeDatatypeMap = studyViewColumnarService.getClinicalAttributeDatatypeMap(studyViewFilter); + } + case GenomicDataBinCountFilter genomicDataBinCountFilter -> { + unfilteredClinicalDataCounts = studyViewColumnarService.getGenomicDataBinCounts(partialFilter, genomicDataBinCountFilter.getGenomicDataBinFilters()); + filteredClinicalDataCounts = studyViewColumnarService.getGenomicDataBinCounts(studyViewFilter, genomicDataBinCountFilter.getGenomicDataBinFilters()); + attributeDatatypeMap = Collections.emptyMap(); + } + case GenericAssayDataBinCountFilter genericAssayDataBinCountFilter -> { + unfilteredClinicalDataCounts = studyViewColumnarService.getGenericAssayDataBinCounts(partialFilter, genericAssayDataBinCountFilter.getGenericAssayDataBinFilters()); + filteredClinicalDataCounts = studyViewColumnarService.getGenericAssayDataBinCounts(studyViewFilter, genericAssayDataBinCountFilter.getGenericAssayDataBinFilters()); + attributeDatatypeMap = Collections.emptyMap(); + } + default -> { + unfilteredClinicalDataCounts = Collections.emptyList(); + filteredClinicalDataCounts = Collections.emptyList(); + attributeDatatypeMap = Collections.emptyMap(); + } + } + + // TODO ignoring conflictingPatientAttributeIds for now + List unfilteredClinicalData = convertCountsToData( + unfilteredClinicalDataCounts.stream().flatMap(c -> c.getCounts().stream()).toList() + ); + List filteredClinicalData = convertCountsToData( + filteredClinicalDataCounts.stream().flatMap(c -> c.getCounts().stream()).toList() + ); + + Map> unfilteredClinicalDataByAttributeId = + unfilteredClinicalData.stream().collect(Collectors.groupingBy(Binnable::getAttrId)); + + Map> filteredClinicalDataByAttributeId = + filteredClinicalData.stream().collect(Collectors.groupingBy(Binnable::getAttrId)); + + // TODO: need to update attributeDatatypeMap to include patient level data for Generic Assay Profiles + if (dataBinMethod == DataBinMethod.STATIC) { + if (!unfilteredClinicalData.isEmpty()) { + resultDataBins = calculateStaticDataBins( + dataBinner, + dataBinFilters, + attributeDatatypeMap, + unfilteredClinicalDataByAttributeId, + filteredClinicalDataByAttributeId + ); + } + } + // TODO: need to update attributeDatatypeMap to include patient level data for Generic Assay Profiles + else { // dataBinMethod == DataBinMethod.DYNAMIC + // TODO we should consider removing dynamic binning support + // we never use dynamic binning in the frontend because number of bins and the bin ranges can change + // each time there is a new filter which makes the frontend implementation complicated + if (!filteredClinicalData.isEmpty()) { + resultDataBins = calculateDynamicDataBins( + dataBinner, + dataBinFilters, + attributeDatatypeMap, + filteredClinicalDataByAttributeId + ); + } + } + + return resultDataBins; + } + + private void removeSelfFromFilter(S dataBinFilter, StudyViewFilter studyViewFilter) { + switch (dataBinFilter) { + case ClinicalDataBinFilter clinicalDataBinFilter -> { + if (studyViewFilter.getClinicalDataFilters() != null) { + studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId())); + } + if (studyViewFilter.getCustomDataFilters() != null) { + studyViewFilter.getCustomDataFilters().removeIf(f -> f.getAttributeId().equals(clinicalDataBinFilter.getAttributeId())); + } + } + case GenomicDataBinFilter genomicDataBinFilter when studyViewFilter.getGenomicDataFilters() != null -> + studyViewFilter.getGenomicDataFilters().removeIf(f -> + f.getHugoGeneSymbol().equals(genomicDataBinFilter.getHugoGeneSymbol()) + && f.getProfileType().equals(genomicDataBinFilter.getProfileType()) + ); + case GenericAssayDataBinFilter genericAssayDataBinFilter when studyViewFilter.getGenericAssayDataFilters() != null -> + studyViewFilter.getGenericAssayDataFilters().removeIf(f -> + f.getStableId().equals(genericAssayDataBinFilter.getStableId()) + && f.getProfileType().equals(genericAssayDataBinFilter.getProfileType()) + ); + default -> { + // Do not remove any filters + } + } + } + + private List fetchDataBinFilters(T dataBinCountFilter) { + switch (dataBinCountFilter) { + case ClinicalDataBinCountFilter clinicalDataBinCountFilter -> { + return (List) clinicalDataBinCountFilter.getAttributes(); + } + case GenomicDataBinCountFilter genomicDataBinCountFilter -> { + return (List) genomicDataBinCountFilter.getGenomicDataBinFilters(); + } + case GenericAssayDataBinCountFilter genericAssayDataBinCountFilter -> { + return (List) genericAssayDataBinCountFilter.getGenericAssayDataBinFilters(); + } + default -> { + return new ArrayList<>(); + } + } + } + + private String getDataBinFilterUniqueKey(S dataBinFilter) { + switch (dataBinFilter) { + case ClinicalDataBinFilter clinicalDataBinFilter -> { + return clinicalDataBinFilter.getAttributeId(); + } + case GenomicDataBinFilter genomicDataBinFilter -> { + return genomicDataBinFilter.getHugoGeneSymbol() + genomicDataBinFilter.getProfileType(); + } + case GenericAssayDataBinFilter genericAssayDataBinFilter -> { + return genericAssayDataBinFilter.getStableId() + genericAssayDataBinFilter.getProfileType(); + } + default -> { + return null; + } + } + } + + private List calculateStaticDataBins( + DataBinner dataBinner, + List dataBinFilters, + Map attributeDatatypeMap, + Map> unfilteredClinicalDataByAttributeId, + Map> filteredClinicalDataByAttributeId + ) { + List result = new ArrayList<>(); + + for (T dataBinFilter : dataBinFilters) { + // if there is data for requested attribute + if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) { + List dataBins = dataBinner + .calculateClinicalDataBins( + dataBinFilter, + filteredClinicalDataByAttributeId.getOrDefault(getDataBinFilterUniqueKey(dataBinFilter), emptyList()), + unfilteredClinicalDataByAttributeId.getOrDefault(getDataBinFilterUniqueKey(dataBinFilter), emptyList()) + ) + .stream() + .map(dataBin -> (U) transform(dataBinFilter, dataBin)) + .toList(); + + result.addAll(dataBins); + } + } + + return result; + } + + private List calculateDynamicDataBins( + DataBinner dataBinner, + List dataBinFilters, + Map attributeDatatypeMap, + Map> filteredClinicalDataByAttributeId + ) { + List result = new ArrayList<>(); + + for (T dataBinFilter : dataBinFilters) { + // if there is data for requested attribute + if (attributeDatatypeMap.isEmpty() || attributeDatatypeMap.containsKey(getDataBinFilterUniqueKey(dataBinFilter))) { + List dataBins = dataBinner + .calculateDataBins( + dataBinFilter, + filteredClinicalDataByAttributeId.getOrDefault(getDataBinFilterUniqueKey(dataBinFilter), emptyList()) + ) + .stream() + .map(dataBin -> (U) transform(dataBinFilter, dataBin)) + .toList(); + result.addAll(dataBins); + } + } + + return result; + } + + private T transform(S dataBinFilter, DataBin dataBin) { + switch (dataBinFilter) { + case ClinicalDataBinFilter clinicalDataBinFilter -> { + return (T) dataBinToClinicalDataBin(clinicalDataBinFilter, dataBin); + } + case GenomicDataBinFilter genomicDataBinFilter -> { + return (T) dataBintoGenomicDataBin(genomicDataBinFilter, dataBin); + } + case GenericAssayDataBinFilter genericAssayDataBinFilter -> { + return (T) dataBintoGenericAssayDataBin(genericAssayDataBinFilter, dataBin); + } + default -> { + return null; + } + } + } + + private ClinicalDataBin dataBinToClinicalDataBin(ClinicalDataBinFilter attribute, DataBin dataBin) { + ClinicalDataBin clinicalDataBin = new ClinicalDataBin(); + clinicalDataBin.setAttributeId(attribute.getAttributeId()); + setCommonDataBinProperties(dataBin, clinicalDataBin); + return clinicalDataBin; + } + + private GenomicDataBin dataBintoGenomicDataBin(GenomicDataBinFilter genomicDataBinFilter, DataBin dataBin) { + GenomicDataBin genomicDataBin = new GenomicDataBin(); + genomicDataBin.setHugoGeneSymbol(genomicDataBinFilter.getHugoGeneSymbol()); + genomicDataBin.setProfileType(genomicDataBinFilter.getProfileType()); + setCommonDataBinProperties(dataBin, genomicDataBin); + return genomicDataBin; + } + + private GenericAssayDataBin dataBintoGenericAssayDataBin(GenericAssayDataBinFilter genericAssayDataBinFilter, + DataBin dataBin) { + GenericAssayDataBin genericAssayDataBin = new GenericAssayDataBin(); + genericAssayDataBin.setStableId(genericAssayDataBinFilter.getStableId()); + genericAssayDataBin.setProfileType(genericAssayDataBinFilter.getProfileType()); + setCommonDataBinProperties(dataBin, genericAssayDataBin); + return genericAssayDataBin; + } + + private void setCommonDataBinProperties(DataBin originalDataBin, U targetDatabin) { + targetDatabin.setCount(originalDataBin.getCount()); + if (originalDataBin.getSpecialValue() != null) { + targetDatabin.setSpecialValue(originalDataBin.getSpecialValue()); + } + if (originalDataBin.getStart() != null) { + targetDatabin.setStart(originalDataBin.getStart()); + } + if (originalDataBin.getEnd() != null) { + targetDatabin.setEnd(originalDataBin.getEnd()); + } + } + +} diff --git a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java b/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java new file mode 100644 index 00000000000..b14d6726dbc --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java @@ -0,0 +1,127 @@ +package org.cbioportal.web.columnar; + +import org.cbioportal.model.Binnable; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataBin; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.service.StudyViewColumnarService; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; +import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.DataBinMethod; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.util.DataBinner; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.cache.annotation.Cacheable; +import org.springframework.stereotype.Component; + +import java.util.*; +import java.util.stream.Collectors; + +@Component +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class ClinicalDataBinner { + private final StudyViewColumnarService studyViewColumnarService; + private final DataBinner dataBinner; + + @Autowired + public ClinicalDataBinner( + StudyViewColumnarService studyViewColumnarService, + DataBinner dataBinner + ) { + this.studyViewColumnarService = studyViewColumnarService; + this.dataBinner = dataBinner; + } + + private List convertCountsToData(List clinicalDataCounts) + { + return clinicalDataCounts + .stream() + .map(NewClinicalDataBinUtil::generateClinicalDataFromClinicalDataCount) + .flatMap(Collection::stream) + .toList(); + } + + @Cacheable( + cacheResolver = "staticRepositoryCacheOneResolver", + condition = "@cacheEnabledConfig.getEnabled()" + ) + public List fetchClinicalDataBinCounts( + DataBinMethod dataBinMethod, + ClinicalDataBinCountFilter dataBinCountFilter, + boolean shouldRemoveSelfFromFilter + ) { + List attributes = dataBinCountFilter.getAttributes(); + StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); + + if (shouldRemoveSelfFromFilter) { + studyViewFilter = NewClinicalDataBinUtil.removeSelfFromFilter(dataBinCountFilter); + } + + List attributeIds = attributes.stream().map(ClinicalDataBinFilter::getAttributeId).collect(Collectors.toList()); + + // a new StudyView filter to partially filter by study and sample ids only + // we need this additional partial filter because we always need to know the bins generated for the initial state + // which allows us to keep the number of bins and bin ranges consistent even if there are additional data filters. + // we only want to update the counts for each bin, we don't want to regenerate the bins for the filtered data. + // NOTE: partial filter is only needed when dataBinMethod == DataBinMethod.STATIC but that's always the case + // for the frontend implementation. we can't really use dataBinMethod == DataBinMethod.DYNAMIC because of the + // complication it brings to the frontend visualization and filtering + StudyViewFilter partialFilter = new StudyViewFilter(); + partialFilter.setStudyIds(studyViewFilter.getStudyIds()); + partialFilter.setSampleIdentifiers(studyViewFilter.getSampleIdentifiers()); + + // we need the clinical data for the partial filter in order to generate the bins for initial state + // we use the filtered data to calculate the counts for each bin, we do not regenerate bins for the filtered data + List unfilteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(partialFilter, attributeIds); + List filteredClinicalDataCounts = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, attributeIds); + + // TODO ignoring conflictingPatientAttributeIds for now + List unfilteredClinicalData = convertCountsToData( + unfilteredClinicalDataCounts.stream().flatMap(c -> c.getCounts().stream()).toList() + ); + List filteredClinicalData = convertCountsToData( + filteredClinicalDataCounts.stream().flatMap(c -> c.getCounts().stream()).toList() + ); + + Map attributeDatatypeMap = studyViewColumnarService.getClinicalAttributeDatatypeMap(studyViewFilter); + + Map> unfilteredClinicalDataByAttributeId = + unfilteredClinicalData.stream().collect(Collectors.groupingBy(Binnable::getAttrId)); + + Map> filteredClinicalDataByAttributeId = + filteredClinicalData.stream().collect(Collectors.groupingBy(Binnable::getAttrId)); + + List clinicalDataBins = Collections.emptyList(); + + if (dataBinMethod == DataBinMethod.STATIC) { + if (!unfilteredClinicalData.isEmpty()) { + clinicalDataBins = NewClinicalDataBinUtil.calculateStaticDataBins( + dataBinner, + attributes, + attributeDatatypeMap, + unfilteredClinicalDataByAttributeId, + filteredClinicalDataByAttributeId + ); + } + } + else { // dataBinMethod == DataBinMethod.DYNAMIC + // TODO we should consider removing dynamic binning support + // we never use dynamic binning in the frontend because number of bins and the bin ranges can change + // each time there is a new filter which makes the frontend implementation complicated + if (!filteredClinicalData.isEmpty()) { + clinicalDataBins = NewClinicalDataBinUtil.calculateDynamicDataBins( + dataBinner, + attributes, + attributeDatatypeMap, + filteredClinicalDataByAttributeId + ); + } + } + + return clinicalDataBins; + } +} diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java new file mode 100644 index 00000000000..bff2f6c1e58 --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java @@ -0,0 +1,683 @@ +package org.cbioportal.web.columnar; + +import io.swagger.v3.oas.annotations.Hidden; +import io.swagger.v3.oas.annotations.Operation; +import io.swagger.v3.oas.annotations.Parameter; +import io.swagger.v3.oas.annotations.media.ArraySchema; +import io.swagger.v3.oas.annotations.media.Content; +import io.swagger.v3.oas.annotations.media.Schema; +import io.swagger.v3.oas.annotations.responses.ApiResponse; +import jakarta.validation.Valid; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataBin; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.ClinicalEventKeyCode; +import org.cbioportal.model.ClinicalEventTypeCount; +import org.cbioportal.model.ClinicalViolinPlotData; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.DensityPlotData; +import org.cbioportal.model.GenericAssayDataBin; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.model.GenomicDataBin; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.PatientTreatmentReport; +import org.cbioportal.model.Sample; +import org.cbioportal.model.SampleTreatmentReport; +import org.cbioportal.service.ClinicalDataDensityPlotService; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.service.CustomDataService; +import org.cbioportal.service.StudyViewColumnarService; +import org.cbioportal.service.ViolinPlotService; +import org.cbioportal.service.exception.StudyNotFoundException; +import org.cbioportal.service.util.CustomDataSession; +import org.cbioportal.utils.config.annotation.ConditionalOnProperty; +import org.cbioportal.web.columnar.util.CustomDataFilterUtil; +import org.cbioportal.web.columnar.util.NewStudyViewFilterUtil; +import org.cbioportal.web.config.annotation.InternalApi; +import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.web.parameter.ClinicalDataCountFilter; +import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.web.parameter.DataBinMethod; +import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter; +import org.cbioportal.web.parameter.GenericAssayDataCountFilter; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.GenomicDataBinCountFilter; +import org.cbioportal.web.parameter.GenomicDataCountFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.MutationOption; +import org.cbioportal.web.parameter.Projection; +import org.cbioportal.web.parameter.SampleIdentifier; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.util.DensityPlotParameters; +import org.cbioportal.web.util.StudyViewFilterUtil; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.http.HttpStatus; +import org.springframework.http.MediaType; +import org.springframework.http.ResponseEntity; +import org.springframework.security.access.prepost.PreAuthorize; +import org.springframework.validation.annotation.Validated; +import org.springframework.web.bind.annotation.RequestAttribute; +import org.springframework.web.bind.annotation.RequestBody; +import org.springframework.web.bind.annotation.RequestMapping; +import org.springframework.web.bind.annotation.RequestMethod; +import org.springframework.web.bind.annotation.RequestParam; +import org.springframework.web.bind.annotation.RestController; + +import java.math.BigDecimal; +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +import static org.cbioportal.web.columnar.util.ClinicalDataXyPlotUtil.fetchClinicalDataForXyPlot; + +@InternalApi +@RestController() +@RequestMapping("/api") +@Validated +@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true") +public class StudyViewColumnStoreController { + + private final StudyViewColumnarService studyViewColumnarService; + private final ClinicalDataBinner clinicalDataBinner; + + private final BasicDataBinner basicDataBinner; + private final ClinicalDataDensityPlotService clinicalDataDensityPlotService; + private final ViolinPlotService violinPlotService; + private final CustomDataService customDataService; + private final StudyViewFilterUtil studyViewFilterUtil; + private final CustomDataFilterUtil customDataFilterUtil; + + @Autowired + public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnarService, + ClinicalDataBinner clinicalDataBinner, + BasicDataBinner basicDataBinner, + ClinicalDataDensityPlotService clinicalDataDensityPlotService, + ViolinPlotService violinPlotService, + CustomDataService customDataService, + StudyViewFilterUtil studyViewFilterUtil, + CustomDataFilterUtil customDataFilterUtil + ) { + this.studyViewColumnarService = studyViewColumnarService; + this.clinicalDataBinner = clinicalDataBinner; + this.basicDataBinner = basicDataBinner; + this.clinicalDataDensityPlotService = clinicalDataDensityPlotService; + this.violinPlotService = violinPlotService; + this.customDataService = customDataService; + this.studyViewFilterUtil = studyViewFilterUtil; + this.customDataFilterUtil = customDataFilterUtil; + } + + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/filtered-samples/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> fetchFilteredSamples( + @RequestParam(defaultValue = "false") Boolean negateFilters, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter, + @RequestBody(required = false) StudyViewFilter studyViewFilter) { + return new ResponseEntity<>( + studyViewColumnarService.getFilteredSamples(interceptedStudyViewFilter), + HttpStatus.OK + ); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/mutated-genes/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> fetchMutatedGenes( + @RequestBody(required = false) StudyViewFilter studyViewFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter + ) throws StudyNotFoundException { + AlterationFilter annotationFilters = interceptedStudyViewFilter.getAlterationFilter(); + return new ResponseEntity<>( + studyViewColumnarService.getMutatedGenes(interceptedStudyViewFilter), + HttpStatus.OK + ); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/molecular-profile-sample-counts/fetch", method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch sample counts by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenomicDataCount.class)))) + public ResponseEntity> fetchMolecularProfileSampleCounts( + @Parameter(required = true, description = "Study view filter") + @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter + ) + { + return new ResponseEntity>( + studyViewColumnarService.getMolecularProfileSampleCounts(interceptedStudyViewFilter) + , HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @RequestMapping(value = "/column-store/cna-genes/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> fetchCnaGenes( + @RequestBody(required = false) StudyViewFilter studyViewFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter + ) throws StudyNotFoundException { + return new ResponseEntity<>( + studyViewColumnarService.getCnaGenes(interceptedStudyViewFilter), + HttpStatus.OK + ); + } + + @Hidden // should unhide when we remove legacy controller + @RequestMapping(value = "/column-store/structuralvariant-genes/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method=RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch structural variant genes by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = AlterationCountByGene.class)))) + public ResponseEntity> fetchStructuralVariantGenes( + @Parameter(required = true, description = "Study view filter") + @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. This attribute is needed for the @PreAuthorize tag above. + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. + @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter + ) throws StudyNotFoundException { + return new ResponseEntity<>(studyViewColumnarService.getStructuralVariantGenes(interceptedStudyViewFilter), HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/clinical-data-counts/fetch", + method=RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> fetchClinicalDataCounts( + @RequestBody(required = false) ClinicalDataCountFilter clinicalDataCountFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedClinicalDataCountFilter") ClinicalDataCountFilter interceptedClinicalDataCountFilter) { + + List attributes = interceptedClinicalDataCountFilter.getAttributes(); + StudyViewFilter studyViewFilter = interceptedClinicalDataCountFilter.getStudyViewFilter(); + + if (attributes.size() == 1) { + NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getClinicalDataFilters()); + } + List result = studyViewColumnarService.getClinicalDataCounts( + studyViewFilter, + attributes.stream().map(ClinicalDataFilter::getAttributeId).collect(Collectors.toList())); + return new ResponseEntity<>(result, HttpStatus.OK); + + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/sample-lists-counts/fetch", method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch case list sample counts by study view filter") + public List fetchCaseListCounts( + @Parameter(required = true, description = "Study view filter") + @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter) { + + return studyViewColumnarService.getCaseListDataCounts(interceptedStudyViewFilter); + + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/clinical-data-bin-counts/fetch", method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + public ResponseEntity> fetchClinicalDataBinCounts( + @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod, + @RequestBody(required = false) ClinicalDataBinCountFilter clinicalDataBinCountFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedClinicalDataBinCountFilter") ClinicalDataBinCountFilter interceptedClinicalDataBinCountFilter + ) { + List clinicalDataBins = clinicalDataBinner.fetchClinicalDataBinCounts( + dataBinMethod, + interceptedClinicalDataBinCountFilter, + true + ); + return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/clinical-data-density-plot/fetch", + method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, + produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch clinical data density plot bins by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(schema = @Schema(implementation = DensityPlotData.class))) + @Validated + public ResponseEntity fetchClinicalDataDensityPlot( + @Parameter(required = true, description = "Clinical Attribute ID of the X axis") + @RequestParam String xAxisAttributeId, + @Parameter(description = "Number of the bins in X axis") + @RequestParam(defaultValue = "50") Integer xAxisBinCount, + @Parameter(description = "Starting point of the X axis, if different than smallest value") + @RequestParam(required = false) BigDecimal xAxisStart, + @Parameter(description = "Starting point of the X axis, if different than largest value") + @RequestParam(required = false) BigDecimal xAxisEnd, + @Parameter(required = true, description = "Clinical Attribute ID of the Y axis") + @RequestParam String yAxisAttributeId, + @Parameter(description = "Number of the bins in Y axis") + @RequestParam(defaultValue = "50") Integer yAxisBinCount, + @Parameter(description = "Starting point of the Y axis, if different than smallest value") + @RequestParam(required = false) BigDecimal yAxisStart, + @Parameter(description = "Starting point of the Y axis, if different than largest value") + @RequestParam(required = false) BigDecimal yAxisEnd, + @Parameter(description="Use log scale for X axis") + @RequestParam(required = false, defaultValue = "false") Boolean xAxisLogScale, + @Schema(defaultValue = "false") + @Parameter(description="Use log scale for Y axis") + @RequestParam(required = false, defaultValue = "false") Boolean yAxisLogScale, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter, + @Parameter(required = true, description = "Study view filter") + @RequestBody(required = false) StudyViewFilter studyViewFilter + ) { + DensityPlotParameters densityPlotParameters = + new DensityPlotParameters.Builder() + .xAxisAttributeId(xAxisAttributeId) + .yAxisAttributeId(yAxisAttributeId) + .xAxisBinCount(xAxisBinCount) + .yAxisBinCount(yAxisBinCount) + .xAxisStart(xAxisStart) + .yAxisStart(yAxisStart) + .xAxisEnd(xAxisEnd) + .yAxisEnd(yAxisEnd) + .xAxisLogScale(xAxisLogScale) + .yAxisLogScale(yAxisLogScale) + .build(); + + List combinedClinicalDataList = fetchClinicalDataForXyPlot( + studyViewColumnarService, + interceptedStudyViewFilter, + List.of(xAxisAttributeId, yAxisAttributeId), + false + ); + + DensityPlotData result = clinicalDataDensityPlotService.getDensityPlotData( + combinedClinicalDataList, + densityPlotParameters, + interceptedStudyViewFilter + ); + + return new ResponseEntity<>(result, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/clinical-data-violin-plots/fetch", + method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch violin plot curves per categorical clinical data value, filtered by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(schema = @Schema(implementation = ClinicalViolinPlotData.class))) + public ResponseEntity fetchClinicalDataViolinPlots( + @Parameter(required = true, description = "Clinical Attribute ID of the categorical attribute") + @RequestParam String categoricalAttributeId, + @Parameter(required = true, description = "Clinical Attribute ID of the numerical attribute") + @RequestParam String numericalAttributeId, + @Parameter(description = "Starting point of the violin plot axis, if different than smallest value") + @RequestParam(required = false) BigDecimal axisStart, + @Parameter(description = "Ending point of the violin plot axis, if different than largest value") + @RequestParam(required = false) BigDecimal axisEnd, + @Parameter(description = "Number of points in the curve") + @RequestParam(required = false, defaultValue = "100") BigDecimal numCurvePoints, + @Parameter(description="Use log scale for the numerical attribute") + @RequestParam(required = false, defaultValue = "false") Boolean logScale, + @Parameter(description="Sigma stepsize multiplier") + @RequestParam(required = false, defaultValue = "1") BigDecimal sigmaMultiplier, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter, + @Parameter(required = true, description = "Study view filter") + @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter + ) { + // fetch the samples by using the provided study view filter + List filteredSamples = studyViewColumnarService.getFilteredSamples(interceptedStudyViewFilter); + + // remove the numerical clinical data filter from the study view filter. + // this new modified filter is used to fetch sample and patient clinical data. + // this is required to get the complete violin plot data. + // filteredSamples reflects only the original unmodified study view filter. + // we will need to fetch samples again to get the samples corresponding to this modified filter, + // otherwise patient to sample mapping may be incomplete. + if (interceptedStudyViewFilter.getClinicalDataFilters() != null) { + interceptedStudyViewFilter.getClinicalDataFilters().stream() + .filter(f->f.getAttributeId().equals(numericalAttributeId)) + .findAny() + .ifPresent(f->interceptedStudyViewFilter.getClinicalDataFilters().remove(f)); + } + + List combinedClinicalDataList = fetchClinicalDataForXyPlot( + studyViewColumnarService, + interceptedStudyViewFilter, + List.of(numericalAttributeId, categoricalAttributeId), + true // filter out clinical data with empty attribute values due to Clickhouse migration + ); + + // Only mutation count can use log scale + boolean useLogScale = logScale && numericalAttributeId.equals("MUTATION_COUNT"); + + ClinicalViolinPlotData result = violinPlotService.getClinicalViolinPlotData( + combinedClinicalDataList, + filteredSamples, + axisStart, + axisEnd, + numCurvePoints, + useLogScale, + sigmaMultiplier, + interceptedStudyViewFilter + ); + + return new ResponseEntity<>(result, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/genomic-data-counts/fetch", + method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch genomic data counts by GenomicDataCountFilter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenomicDataCountItem.class)))) + public ResponseEntity> fetchGenomicDataCounts( + @Parameter(required = true, description = "Genomic data count filter") @Valid @RequestBody(required = false) GenomicDataCountFilter genomicDataCountFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(required = true, description = "Intercepted Genomic Data Count Filter") + @Valid @RequestAttribute(required = false, value = "interceptedGenomicDataCountFilter") GenomicDataCountFilter interceptedGenomicDataCountFilter + ) throws StudyNotFoundException { + List genomicDataFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters(); + StudyViewFilter studyViewFilter = interceptedGenomicDataCountFilter.getStudyViewFilter(); + // when there is only one filter, it means study view is doing a single chart filter operation + // remove filter from studyViewFilter to return all data counts + // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart + if (genomicDataFilters.size() == 1) { + studyViewFilterUtil.removeSelfFromGenomicDataFilter( + genomicDataFilters.get(0).getHugoGeneSymbol(), + genomicDataFilters.get(0).getProfileType(), + studyViewFilter); + } + + // This endpoint is CNA specific. The name choice of "genomic data" does not imply it support other genomic data types + List result = studyViewColumnarService.getCNACountsByGeneSpecific(studyViewFilter, genomicDataFilters); + + return new ResponseEntity<>(result, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/generic-assay-data-counts/fetch", + method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch generic assay data counts by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenericAssayDataCountItem.class)))) + public ResponseEntity> fetchGenericAssayDataCounts( + @Parameter(required = true, description = "Generic assay data count filter") @Valid @RequestBody(required = false) GenericAssayDataCountFilter genericAssayDataCountFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this + // attribute is needed for the @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedGenericAssayDataCountFilter") GenericAssayDataCountFilter interceptedGenericAssayDataCountFilter) { + + List gaFilters = interceptedGenericAssayDataCountFilter.getGenericAssayDataFilters(); + StudyViewFilter studyViewFilter = interceptedGenericAssayDataCountFilter.getStudyViewFilter(); + // when there is only one filter, it means study view is doing a single chart filter operation + // remove filter from studyViewFilter to return all data counts + // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart + + if (gaFilters.size() == 1) { + studyViewFilterUtil.removeSelfFromGenericAssayFilter(gaFilters.getFirst().getStableId(), studyViewFilter); + } + + return new ResponseEntity<>(studyViewColumnarService.getGenericAssayDataCounts(studyViewFilter, gaFilters), HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/mutation-data-counts/fetch", + method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch mutation data counts by GenomicDataCountFilter") + public ResponseEntity> fetchMutationDataCounts( + @Parameter(description = "Level of detail of the response") + @RequestParam(defaultValue = "SUMMARY") Projection projection, + @Parameter(required = true, description = "Genomic data count filter") + @Valid @RequestBody(required = false) GenomicDataCountFilter genomicDataCountFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @Valid @RequestAttribute(required = false, value = "interceptedGenomicDataCountFilter") GenomicDataCountFilter interceptedGenomicDataCountFilter + ) { + List genomicDataFilters = interceptedGenomicDataCountFilter.getGenomicDataFilters(); + StudyViewFilter studyViewFilter = interceptedGenomicDataCountFilter.getStudyViewFilter(); + // when there is only one filter, it means study view is doing a single chart filter operation + // remove filter from studyViewFilter to return all data counts + // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart + if (genomicDataFilters.size() == 1 && projection == Projection.SUMMARY) { + studyViewFilterUtil.removeSelfFromMutationDataFilter( + genomicDataFilters.get(0).getHugoGeneSymbol(), + genomicDataFilters.get(0).getProfileType(), + MutationOption.MUTATED, + studyViewFilter); + } + + List result = projection == Projection.SUMMARY ? + studyViewColumnarService.getMutationCountsByGeneSpecific(studyViewFilter, genomicDataFilters) : + studyViewColumnarService.getMutationTypeCountsByGeneSpecific(studyViewFilter, genomicDataFilters); + + return new ResponseEntity<>(result, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/clinical-event-type-counts/fetch", + method = RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, + produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Get Counts of Clinical Event Types by Study View Filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = ClinicalEventTypeCount.class)))) + public ResponseEntity> getClinicalEventTypeCounts( + @Parameter(required = true, description = "Study view filter") + @Valid + @RequestBody(required = false) + StudyViewFilter studyViewFilter, + + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") + Collection involvedCancerStudies, + + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid + @RequestAttribute(required = false, value = "interceptedStudyViewFilter") + StudyViewFilter interceptedStudyViewFilter + ) { + return new ResponseEntity<>(studyViewColumnarService.getClinicalEventTypeCounts(interceptedStudyViewFilter), HttpStatus.OK); + } + + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/treatments/patient-counts/fetch", + method = RequestMethod.POST, + produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Get all patient level treatments") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(schema = @Schema(implementation = PatientTreatmentReport.class))) + public ResponseEntity fetchPatientTreatmentCounts( + @Parameter(required = false ) + @RequestParam(name = "tier", required = false, defaultValue = "Agent") + ClinicalEventKeyCode tier, + + @Parameter(required = true, description = "Study view filter") + @Valid + @RequestBody(required = false) + StudyViewFilter studyViewFilter, + + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") + Collection involvedCancerStudies, + + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid + @RequestAttribute(required = false, value = "interceptedStudyViewFilter") + StudyViewFilter interceptedStudyViewFilter + ) { + return new ResponseEntity<>(studyViewColumnarService.getPatientTreatmentReport(interceptedStudyViewFilter), + HttpStatus.OK); + } + + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/treatments/sample-counts/fetch", + method = RequestMethod.POST, + produces = MediaType.APPLICATION_JSON_VALUE) + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(schema = @Schema(implementation = SampleTreatmentReport.class))) + public ResponseEntity fetchSampleTreatmentCounts( + @Parameter(required = false ) + @RequestParam(name = "tier", required = false, defaultValue = "Agent") + ClinicalEventKeyCode tier, + + @Parameter(required = true, description = "Study view filter") + @Valid + @RequestBody(required = false) + StudyViewFilter studyViewFilter, + + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") + Collection involvedCancerStudies, + + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid + @RequestAttribute(required = false, value = "interceptedStudyViewFilter") + StudyViewFilter interceptedStudyViewFilter + ) { + return new ResponseEntity<>(studyViewColumnarService.getSampleTreatmentReport(interceptedStudyViewFilter), + HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/custom-data-counts/fetch", + method=RequestMethod.POST, + consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch custom data counts by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = ClinicalDataCountItem.class)))) + public ResponseEntity> fetchCustomDataCounts( + @Parameter(required = true, description = "Custom data count filter") @Valid @RequestBody(required = false) ClinicalDataCountFilter clinicalDataCountFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui + // interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui + // interface. this attribute is needed for the + // @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedClinicalDataCountFilter") ClinicalDataCountFilter interceptedClinicalDataCountFilter) { + + List attributes = interceptedClinicalDataCountFilter.getAttributes(); + StudyViewFilter studyViewFilter = interceptedClinicalDataCountFilter.getStudyViewFilter(); + if (attributes.size() == 1) { + NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getCustomDataFilters()); + } + + List filteredSampleIdentifiers = studyViewColumnarService.getFilteredSamples(studyViewFilter).stream().map(sample -> studyViewFilterUtil.buildSampleIdentifier(sample.getCancerStudyIdentifier(), sample.getStableId())).toList(); + + if (filteredSampleIdentifiers.isEmpty()) { + return new ResponseEntity<>(new ArrayList<>(), HttpStatus.OK); + } + + final List attributeIds = attributes.stream().map(ClinicalDataFilter::getAttributeId).toList(); + Map customDataSessionsMap = customDataService.getCustomDataSessions(attributeIds); + + List result = customDataFilterUtil.getCustomDataCounts(filteredSampleIdentifiers, customDataSessionsMap); + + return new ResponseEntity<>(result, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/custom-data-bin-counts/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method= RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + @Operation(description = "Fetch custom data bin counts by study view filter") + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = ClinicalDataBin.class)))) + public ResponseEntity> fetchCustomDataBinCounts( + @Parameter(description = "Method for data binning") + @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod, + @Parameter(required = true, description = "Clinical data bin count filter") + @Valid @RequestBody(required = false) ClinicalDataBinCountFilter clinicalDataBinCountFilter, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above. + @Valid @RequestAttribute(required = false, value = "interceptedClinicalDataBinCountFilter") ClinicalDataBinCountFilter interceptedClinicalDataBinCountFilter + ) { + List customDataBins = basicDataBinner.getDataBins( + dataBinMethod, + interceptedClinicalDataBinCountFilter, + true + ); + + return new ResponseEntity<>(customDataBins, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/genomic-data-bin-counts/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenomicDataBin.class)))) + public ResponseEntity> fetchGenomicDataBinCounts( + @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod, + @RequestBody(required = false) GenomicDataBinCountFilter genomicDataBinCountFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedGenomicDataBinCountFilter") GenomicDataBinCountFilter interceptedGenomicDataBinCountFilter + ) { + List genomicDataBins = basicDataBinner.getDataBins( + dataBinMethod, + interceptedGenomicDataBinCountFilter, + true + ); + return new ResponseEntity<>(genomicDataBins, HttpStatus.OK); + } + + @Hidden // should unhide when we remove legacy controller + @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection', T(org.cbioportal.utils.security.AccessLevel).READ)") + @RequestMapping(value = "/column-store/generic-assay-data-bin-counts/fetch", + consumes = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE) + @ApiResponse(responseCode = "200", description = "OK", + content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenericAssayDataBin.class)))) + public ResponseEntity> fetchGenericAssayDataBinCounts( + @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod, + @RequestBody(required = false) GenericAssayDataBinCountFilter genericAssayDataBinCountFilter, + @RequestAttribute(required = false, value = "involvedCancerStudies") Collection involvedCancerStudies, + @RequestAttribute(required = false, value = "interceptedGenericAssayDataBinCountFilter") GenericAssayDataBinCountFilter interceptedGenericAssayDataBinCountFilter + ) { + List genericAssayDataBins = basicDataBinner.getDataBins( + dataBinMethod, + interceptedGenericAssayDataBinCountFilter, + true + ); + return new ResponseEntity<>(genericAssayDataBins, HttpStatus.OK); + } +} diff --git a/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java b/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java new file mode 100644 index 00000000000..aee3a04a485 --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/util/ClinicalDataXyPlotUtil.java @@ -0,0 +1,92 @@ +package org.cbioportal.web.columnar.util; + +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.Sample; +import org.cbioportal.service.StudyViewColumnarService; +import org.cbioportal.web.parameter.StudyViewFilter; + +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +public class ClinicalDataXyPlotUtil { + public static List fetchClinicalDataForXyPlot( + StudyViewColumnarService studyViewColumnarService, + StudyViewFilter studyViewFilter, + List attributeIds, + boolean shouldFilterNonEmptyClinicalData + ) { + List combinedClinicalDataList; + List sampleClinicalDataList = studyViewColumnarService.getSampleClinicalData(studyViewFilter, attributeIds); + List patientClinicalDataList = studyViewColumnarService.getPatientClinicalData(studyViewFilter, attributeIds); + + if (shouldFilterNonEmptyClinicalData) { + sampleClinicalDataList = filterNonEmptyClinicalData(sampleClinicalDataList); + patientClinicalDataList = filterNonEmptyClinicalData(patientClinicalDataList); + } + + if (patientClinicalDataList.isEmpty()) { + combinedClinicalDataList = sampleClinicalDataList; + } else { + // fetch samples for the given study view filter. + // we need this to construct the complete patient to sample map. + List samples = studyViewColumnarService.getFilteredSamples(studyViewFilter); + + combinedClinicalDataList = Stream.concat( + sampleClinicalDataList.stream(), + convertPatientClinicalDataToSampleClinicalData(patientClinicalDataList, samples).stream() + ).toList(); + } + + return combinedClinicalDataList; + } + + public static List filterNonEmptyClinicalData(List clinicalData) { + return clinicalData + .stream() + .filter(data -> !data.getAttrValue().isEmpty()) + .toList(); + } + + public static List convertPatientClinicalDataToSampleClinicalData( + List patientClinicalDataList, + List samplesWithoutNumericalFilter + ) { + List sampleClinicalDataList = new ArrayList<>(); + + Map>> patientToSamples = samplesWithoutNumericalFilter + .stream() + .collect(Collectors.groupingBy( + Sample::getPatientStableId, + Collectors.groupingBy(Sample::getCancerStudyIdentifier) + )); + + // put all clinical data into sample form + for (ClinicalData d: patientClinicalDataList) { + List samplesForPatient = patientToSamples.get(d.getPatientId()).get(d.getStudyId()); + if (samplesForPatient != null) { + for (Sample s: samplesForPatient) { + ClinicalData newData = new ClinicalData(); + + newData.setInternalId(s.getInternalId()); + newData.setAttrId(d.getAttrId()); + newData.setPatientId(d.getPatientId()); + newData.setStudyId(d.getStudyId()); + newData.setAttrValue(d.getAttrValue()); + newData.setSampleId(s.getStableId()); + + sampleClinicalDataList.add(newData); + } + } else { + // TODO ignoring for now rather than throwing an error + // patient has no samples - this shouldn't happen and could affect the integrity + // of the data analysis + // return new ResponseEntity<>(null, HttpStatus.INTERNAL_SERVER_ERROR); + } + } + + return sampleClinicalDataList; + } +} diff --git a/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java b/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java new file mode 100644 index 00000000000..9987bf510c1 --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/util/CustomDataFilterUtil.java @@ -0,0 +1,378 @@ +package org.cbioportal.web.columnar.util; + +import com.google.common.collect.Range; +import org.apache.commons.collections4.CollectionUtils; +import org.apache.commons.collections4.map.MultiKeyMap; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.Patient; +import org.cbioportal.service.CustomDataService; +import org.cbioportal.service.PatientService; +import org.cbioportal.service.util.CustomDataSession; +import org.cbioportal.web.parameter.*; +import org.cbioportal.web.util.CustomDatatype; +import org.cbioportal.web.util.DataBinHelper; +import org.cbioportal.web.util.StudyViewFilterUtil; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.stereotype.Component; + +import java.math.BigDecimal; +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +@Component +public class CustomDataFilterUtil { + private final StudyViewFilterUtil studyViewFilterUtil; + private final CustomDataService customDataService; + private final PatientService patientService; + + @Autowired + public CustomDataFilterUtil(StudyViewFilterUtil studyViewFilterUtil, CustomDataService customDataService, PatientService patientService) { + this.studyViewFilterUtil = studyViewFilterUtil; + this.customDataService = customDataService; + this.patientService = patientService; + } + + public List extractInvolvedCancerStudies(final StudyViewFilter studyViewFilter) { + List involvedCancerStudies; + + if (studyViewFilter.getStudyIds() != null && !studyViewFilter.getStudyIds().isEmpty()) { + involvedCancerStudies = studyViewFilter.getStudyIds(); + } else if (studyViewFilter.getSampleIdentifiers() != null && !studyViewFilter.getSampleIdentifiers().isEmpty()) { + Set studyIdSet = new HashSet<>(); + for (SampleIdentifier sampleIdentifier : studyViewFilter.getSampleIdentifiers()) { + studyIdSet.add(sampleIdentifier.getStudyId()); + } + involvedCancerStudies = studyIdSet.stream().toList(); + } + else { + involvedCancerStudies = Collections.emptyList(); + } + + return involvedCancerStudies; + } + public List extractCustomDataSamples(final StudyViewFilter studyViewFilter) { + if (studyViewFilter == null) { + return null; + } + + if (CollectionUtils.isEmpty(studyViewFilter.getCustomDataFilters())) { + return null; + } + + final List customSamplesFromProperty = studyViewFilter.getCustomDataFilters().stream() + .flatMap(filter -> { + List samples = filter.getSamples(); + return (samples != null) ? samples.stream() : Stream.empty(); + }) + .toList(); + + if (!customSamplesFromProperty.isEmpty()) { + return extractCustomDataSamplesWithoutSession(studyViewFilter, customSamplesFromProperty); + } + else { + return extractCustomDataSamplesWithSession(studyViewFilter); + } + } + + private List extractCustomDataSamplesWithSession(final StudyViewFilter studyViewFilter) { + List customSampleIdentifiers = new ArrayList<>(); + + final List attributeIds = studyViewFilter.getCustomDataFilters().stream() + .map(ClinicalDataFilter::getAttributeId) + .collect(Collectors.toList()); + + final Map customDataSessions = customDataService.getCustomDataSessions(attributeIds); + + Map customDataSessionById = customDataSessions + .values() + .stream() + .collect(Collectors.toMap( + CustomDataSession::getId, + Function.identity() + )); + + MultiKeyMap customDataByStudySampleSession = new MultiKeyMap<>(); + + customDataSessionById.values().forEach(customDataSession -> customDataSession + .getData() + .getData() + .forEach(datum -> { + String value = datum.getValue().toUpperCase(); + if (value.equals("NAN") || value.equals("N/A")) { + value = "NA"; + } + CustomSampleIdentifier customSampleIdentifier = new CustomSampleIdentifier(); + customSampleIdentifier.setStudyId(datum.getStudyId()); + customSampleIdentifier.setSampleId(datum.getSampleId()); + customSampleIdentifiers.add(customSampleIdentifier); + customDataByStudySampleSession.put(datum.getStudyId(), datum.getSampleId(), customDataSession.getId(), value); + }) + ); + + List equalityFilters = new ArrayList<>(); + List intervalFilters = new ArrayList<>(); + + studyViewFilter.getCustomDataFilters().forEach(filter -> { + String attributeId = filter.getAttributeId(); + if (!customDataSessionById.containsKey(attributeId)) { + return; + } + if (customDataSessionById + .get(attributeId) + .getData() + .getDatatype() + .equals(CustomDatatype.STRING.name()) + ) { + equalityFilters.add(filter); + } else { + intervalFilters.add(filter); + } + }); + + List filtered = new ArrayList<>(); + customSampleIdentifiers.forEach(customSampleIdentifier -> { + int equalityFilterCount = studyViewFilterUtil.getFilteredCountByDataEquality(equalityFilters, customDataByStudySampleSession, + customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId(), false); + int intervalFilterCount = getFilteredCountByDataInterval(intervalFilters, customDataByStudySampleSession, + customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId()); + if (equalityFilterCount == equalityFilters.size() + && intervalFilterCount == intervalFilters.size() + ) { + filtered.add(customSampleIdentifier); + } + else { + customSampleIdentifier.setIsFilteredOut(true); + filtered.add(customSampleIdentifier); + } + }); + + return filtered; + } + + private List extractCustomDataSamplesWithoutSession(final StudyViewFilter studyViewFilter, List customSamplesFromProperty) { + List customSampleIdentifiers = new ArrayList<>(customSamplesFromProperty); + + List equalityFilters = new ArrayList<>(); + List intervalFilters = new ArrayList<>(); + + studyViewFilter.getCustomDataFilters().forEach(filter -> { + if (filter.getDatatype() + .equals(CustomDatatype.STRING.name()) + ) { + equalityFilters.add(filter); + } else { + intervalFilters.add(filter); + } + }); + + MultiKeyMap customDataByStudySampleName = new MultiKeyMap<>(); + + studyViewFilter.getCustomDataFilters().stream().forEach(filter -> + filter.getSamples().forEach(datum -> { + String value = datum.getValue().toUpperCase(); + if (value.equals("NAN") || value.equals("N/A")) { + value = "NA"; + } + customDataByStudySampleName.put(datum.getStudyId(), datum.getSampleId(), filter.getDisplayName(), value); + }) + ); + + List filtered = new ArrayList<>(); + customSampleIdentifiers.forEach(customSampleIdentifier -> { + int equalityFilterCount = getFilteredCountByDataEqualityWithStudySampleNameMap(equalityFilters, customDataByStudySampleName, + customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId(), false); + int intervalFilterCount = getFilteredCountByDataIntervalWithStudySampleNameMap(intervalFilters, customDataByStudySampleName, + customSampleIdentifier.getSampleId(), customSampleIdentifier.getStudyId()); + if (equalityFilterCount == equalityFilters.size() + && intervalFilterCount == intervalFilters.size() + ) { + filtered.add(customSampleIdentifier); + } + else { + customSampleIdentifier.setIsFilteredOut(true); + filtered.add(customSampleIdentifier); + } + }); + return filtered; + } + + private Integer getFilteredCountByDataEqualityWithStudySampleNameMap(List attributes, MultiKeyMap clinicalDataMap, + String entityId, String studyId, boolean negateFilters) { + Integer count = 0; + for (ClinicalDataFilter s : attributes) { + List filteredValues = s.getValues() + .stream() + .map(DataFilterValue::getValue) + .collect(Collectors.toList()); + filteredValues.replaceAll(String::toUpperCase); + if (clinicalDataMap.containsKey(studyId, entityId, s.getDisplayName())) { + String value = clinicalDataMap.get(studyId, entityId, s.getDisplayName()); + if (negateFilters ^ filteredValues.contains(value)) { + count++; + } + } else if (negateFilters ^ filteredValues.contains("NA")) { + count++; + } + } + return count; + } + + private Integer getFilteredCountByDataInterval(List attributes, MultiKeyMap clinicalDataMap, + String entityId, String studyId) { + int count = 0; + + for (ClinicalDataFilter filter : attributes) { + if (clinicalDataMap.containsKey(studyId, entityId, filter.getAttributeId())) { + String attrValue = (String) clinicalDataMap.get(studyId, entityId, filter.getAttributeId()); + Range rangeValue = calculateRangeValueForAttr(attrValue); + + // find range filters + List> ranges = filter.getValues().stream() + .map(this::calculateRangeValueForFilter) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + + // find special value filters + List specialValues = filter.getValues().stream() + .filter(f -> f.getValue() != null) + .map(f -> f.getValue().toUpperCase()) + .collect(Collectors.toList()); + + if (rangeValue != null) { + if (ranges.stream().anyMatch(r -> r.encloses(rangeValue))) { + count++; + } + } + else if (specialValues.contains(attrValue.toUpperCase())) { + count++; + } + } else if (containsNA(filter)) { + count++; + } + } + + return count; + } + + private Integer getFilteredCountByDataIntervalWithStudySampleNameMap(List attributes, MultiKeyMap clinicalDataMap, + String entityId, String studyId) { + int count = 0; + + for (ClinicalDataFilter filter : attributes) { + if (clinicalDataMap.containsKey(studyId, entityId, filter.getDisplayName())) { + String attrValue = clinicalDataMap.get(studyId, entityId, filter.getDisplayName()); + Range rangeValue = calculateRangeValueForAttr(attrValue); + + // find range filters + List> ranges = filter.getValues().stream() + .map(this::calculateRangeValueForFilter) + .filter(Objects::nonNull) + .toList(); + + // find special value filters + List specialValues = filter.getValues().stream() + .filter(f -> f.getValue() != null) + .map(f -> f.getValue().toUpperCase()) + .toList(); + + if ((rangeValue != null && ranges.stream().anyMatch(r -> r.encloses(rangeValue))) || + (rangeValue == null && specialValues.contains(attrValue.toUpperCase()))) { + count++; + } + } else if (Boolean.TRUE.equals(containsNA(filter))) { + count++; + } + } + + return count; + } + + private Range calculateRangeValueForAttr(String attrValue) { + if (attrValue == null) { + return null; + } + + BigDecimal min = null; + BigDecimal max = null; + + String value = attrValue.trim(); + + String lte = "<="; + String lt = "<"; + String gte = ">="; + String gt = ">"; + + boolean startInclusive = true; + boolean endInclusive = true; + + try { + if (value.startsWith(lte)) { + max = new BigDecimal(value.substring(lte.length())); + } + else if (value.startsWith(lt)) { + max = new BigDecimal(value.substring(lt.length())); + endInclusive = false; + } + else if (value.startsWith(gte)) { + min = new BigDecimal(value.substring(gte.length())); + } + else if (value.startsWith(gt)) { + min = new BigDecimal(value.substring(gt.length())); + startInclusive = false; + } + else { + min = max = new BigDecimal(attrValue); + } + } catch (Exception e) { + // invalid range -- TODO: also support ranges like 20-30? + return null; + } + + return DataBinHelper.calcRange(min, startInclusive, max, endInclusive); + } + + private Range calculateRangeValueForFilter(DataFilterValue filterValue) { + BigDecimal start = filterValue.getStart(); + BigDecimal end = filterValue.getEnd(); + + // default: (start, end] + boolean startInclusive = false; + boolean endInclusive = true; + + // special case: end == start (both inclusive) + if (end != null && end.equals(start)) { + startInclusive = true; + } + + return DataBinHelper.calcRange(start, startInclusive, end, endInclusive); + } + + private Boolean containsNA(ClinicalDataFilter filter) { + return filter.getValues().stream().anyMatch( + r -> r.getValue() != null && r.getValue().toUpperCase().equals("NA")); + } + + public List getCustomDataCounts(List filteredSampleIdentifiers, Map customDataSessions) { + Map customSamplesMap = filteredSampleIdentifiers.stream() + .collect(Collectors.toMap(sampleIdentifier -> studyViewFilterUtil.getCaseUniqueKey( + sampleIdentifier.getStudyId(), + sampleIdentifier.getSampleId() + ), Function.identity())); + + List studyIds = new ArrayList<>(); + List sampleIds = new ArrayList<>(); + studyViewFilterUtil.extractStudyAndSampleIds(filteredSampleIdentifiers, studyIds, sampleIds); + + long patientCustomDataSessionsCount = customDataSessions.values().stream() + .filter(customDataSession -> customDataSession.getData().getPatientAttribute()).count(); + List patients = new ArrayList<>(); + if (patientCustomDataSessionsCount > 0) { + patients.addAll(patientService.getPatientsOfSamples(studyIds, sampleIds)); + } + + return studyViewFilterUtil.getClinicalDataCountsFromCustomData(customDataSessions.values(), + customSamplesMap, patients); + } +} diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java b/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java new file mode 100644 index 00000000000..df1b9524c6e --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java @@ -0,0 +1,167 @@ +package org.cbioportal.web.columnar.util; + +import org.cbioportal.model.Binnable; +import org.cbioportal.model.ClinicalData; +import org.cbioportal.model.ClinicalDataBin; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.DataBin; +import org.cbioportal.service.util.CustomDataSession; +import org.cbioportal.web.parameter.ClinicalDataBinCountFilter; +import org.cbioportal.web.parameter.ClinicalDataBinFilter; +import org.cbioportal.web.parameter.ClinicalDataType; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.util.DataBinner; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static java.util.Collections.emptyList; + +public class NewClinicalDataBinUtil { + public static StudyViewFilter removeSelfFromFilter(ClinicalDataBinCountFilter dataBinCountFilter) { + List attributes = dataBinCountFilter.getAttributes(); + StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); + + if (attributes.size() == 1) { + NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getClinicalDataFilters()); + } + + return studyViewFilter; + } + + public static StudyViewFilter removeSelfCustomDataFromFilter(ClinicalDataBinCountFilter dataBinCountFilter) { + List attributes = dataBinCountFilter.getAttributes(); + StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); + + if (attributes.size() == 1) { + NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getCustomDataFilters()); + } + + return studyViewFilter; + } + + public static ClinicalDataBin dataBinToClinicalDataBin(ClinicalDataBinFilter attribute, DataBin dataBin) { + ClinicalDataBin clinicalDataBin = new ClinicalDataBin(); + clinicalDataBin.setAttributeId(attribute.getAttributeId()); + clinicalDataBin.setCount(dataBin.getCount()); + if (dataBin.getEnd() != null) { + clinicalDataBin.setEnd(dataBin.getEnd()); + } + if (dataBin.getSpecialValue() != null) { + clinicalDataBin.setSpecialValue(dataBin.getSpecialValue()); + } + if (dataBin.getStart() != null) { + clinicalDataBin.setStart(dataBin.getStart()); + } + return clinicalDataBin; + } + + public static Map toAttributeDatatypeMap( + List sampleAttributeIds, + List patientAttributeIds, + List conflictingPatientAttributeIds + ) { + Map attributeDatatypeMap = new HashMap<>(); + + sampleAttributeIds.forEach(attribute -> { + attributeDatatypeMap.put(attribute, ClinicalDataType.SAMPLE); + }); + patientAttributeIds.forEach(attribute -> { + attributeDatatypeMap.put(attribute, ClinicalDataType.PATIENT); + }); + conflictingPatientAttributeIds.forEach(attribute -> { + attributeDatatypeMap.put(attribute, ClinicalDataType.SAMPLE); + }); + + return attributeDatatypeMap; + } + + public static List calculateStaticDataBins( + DataBinner dataBinner, + List attributes, + Map attributeDatatypeMap, + Map> unfilteredClinicalDataByAttributeId, + Map> filteredClinicalDataByAttributeId + ) { + List clinicalDataBins = new ArrayList<>(); + + for (ClinicalDataBinFilter attribute : attributes) { + if (attributeDatatypeMap.containsKey(attribute.getAttributeId())) { + List dataBins = dataBinner + .calculateClinicalDataBins( + attribute, + filteredClinicalDataByAttributeId.getOrDefault(attribute.getAttributeId(), emptyList()), + unfilteredClinicalDataByAttributeId.getOrDefault(attribute.getAttributeId(), emptyList()) + ) + .stream() + .map(dataBin -> dataBinToClinicalDataBin(attribute, dataBin)) + .toList(); + + clinicalDataBins.addAll(dataBins); + } + } + + return clinicalDataBins; + } + + public static List calculateDynamicDataBins( + DataBinner dataBinner, + List attributes, + Map attributeDatatypeMap, + Map> filteredClinicalDataByAttributeId + ) { + List clinicalDataBins = new ArrayList<>(); + + for (ClinicalDataBinFilter attribute : attributes) { + + // if there is clinical data for requested attribute + if (attributeDatatypeMap.containsKey(attribute.getAttributeId())) { + List dataBins = dataBinner + .calculateDataBins( + attribute, + filteredClinicalDataByAttributeId.getOrDefault(attribute.getAttributeId(), emptyList()) + ) + .stream() + .map(dataBin -> dataBinToClinicalDataBin(attribute, dataBin)) + .toList(); + clinicalDataBins.addAll(dataBins); + } + } + + return clinicalDataBins; + } + + /** + * Generate a list of ClinicalData from the given data count instance. + * Size of the generated list is equal to 'dataCount.count', + * and each ClinicalData in the list contains the same value 'dataCount.value' + * + * This method improves the performance of the data binning because it allows us to fetch only + * the clinical data counts data which is a lot more compact and faster to generated than the actual clinical data. + * We only need the attribute id and the value of the clinical data to generate data bins. + * Constructing the clinical data in memory by using clinical data counts significantly improves the performance, + * and it also allows us to use the exact same SQL used by the clinical data counts endpoint. + * + * @param dataCount ClinicalDataCount instance containing the count and the value + * @return a list of ClinicalData with size 'dataCount.count' and value 'dataCount.value' + */ + public static List generateClinicalDataFromClinicalDataCount(ClinicalDataCount dataCount) + { + List data = new ArrayList<>(dataCount.getCount()); + + for (int i=0; i < dataCount.getCount(); i++) { + ClinicalData d = new ClinicalData(); + d.setAttrId(dataCount.getAttributeId()); + d.setAttrValue(dataCount.getValue()); + data.add(d); + } + + return data; + } + + public static ClinicalDataType getDataType(Map.Entry entry) { + return Boolean.TRUE.equals(entry.getValue().getData().getPatientAttribute()) ? ClinicalDataType.PATIENT : ClinicalDataType.SAMPLE; + } +} diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java b/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java new file mode 100644 index 00000000000..5363802afe2 --- /dev/null +++ b/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java @@ -0,0 +1,15 @@ +package org.cbioportal.web.columnar.util; + + +import org.cbioportal.web.parameter.ClinicalDataFilter; + +import java.util.List; + +public class NewStudyViewFilterUtil { + + public static void removeClinicalDataFilter(String attributeId, List dataFilterList ) { + if (dataFilterList != null) { + dataFilterList.removeIf(f -> f.getAttributeId().equals(attributeId)); + } + } +} diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java b/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java new file mode 100644 index 00000000000..22ce588453e --- /dev/null +++ b/src/main/java/org/cbioportal/web/parameter/CategorizedClinicalDataCountFilter.java @@ -0,0 +1,71 @@ +package org.cbioportal.web.parameter; + +import java.util.List; + +public final class CategorizedClinicalDataCountFilter { + + public static Builder getBuilder() { + return new Builder(); + } + private final List sampleNumericalClinicalDataFilters; + private final List sampleCategoricalClinicalDataFilters; + private final List patientNumericalClinicalDataFilters; + private final List patientCategoricalClinicalDataFilters; + + private CategorizedClinicalDataCountFilter(Builder builder) { + this.sampleCategoricalClinicalDataFilters = builder.sampleCategoricalClinicalDataFilters; + this.sampleNumericalClinicalDataFilters = builder.sampleNumericalClinicalDataFilters; + this.patientCategoricalClinicalDataFilters = builder.patientCategoricalClinicalDataFilters; + this.patientNumericalClinicalDataFilters = builder.patientNumericalClinicalDataFilters; + } + + public List getSampleNumericalClinicalDataFilters() { + return sampleNumericalClinicalDataFilters; + } + + public List getSampleCategoricalClinicalDataFilters() { + return sampleCategoricalClinicalDataFilters; + } + + public List getPatientNumericalClinicalDataFilters() { + return patientNumericalClinicalDataFilters; + } + + public List getPatientCategoricalClinicalDataFilters() { + return patientCategoricalClinicalDataFilters; + } + + public static class Builder { + private List sampleNumericalClinicalDataFilters; + private List sampleCategoricalClinicalDataFilters; + private List patientNumericalClinicalDataFilters; + private List patientCategoricalClinicalDataFilters; + + private Builder(){ + + } + public Builder setSampleCategoricalClinicalDataFilters(List sampleCategoricalClinicalDataFilters) { + this.sampleCategoricalClinicalDataFilters = sampleCategoricalClinicalDataFilters; + return this; + } + + public Builder setSampleNumericalClinicalDataFilters(List sampleNumericalClinicalDataFilters) { + this.sampleNumericalClinicalDataFilters = sampleNumericalClinicalDataFilters; + return this; + } + + public Builder setPatientCategoricalClinicalDataFilters(List patientCategoricalClinicalDataFilters) { + this.patientCategoricalClinicalDataFilters = patientCategoricalClinicalDataFilters; + return this; + } + + public Builder setPatientNumericalClinicalDataFilters(List patientNumericalClinicalDataFilters) { + this.patientNumericalClinicalDataFilters = patientNumericalClinicalDataFilters; + return this; + } + + public CategorizedClinicalDataCountFilter build() { + return new CategorizedClinicalDataCountFilter(this); + } + } +} diff --git a/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java b/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java new file mode 100644 index 00000000000..3d9face92c8 --- /dev/null +++ b/src/main/java/org/cbioportal/web/parameter/CategorizedGenericAssayDataCountFilter.java @@ -0,0 +1,72 @@ +package org.cbioportal.web.parameter; + +import java.util.List; + +public final class CategorizedGenericAssayDataCountFilter { + + public static Builder getBuilder() { + return new Builder(); + } + + private final List sampleNumericalGenericAssayDataFilters; + private final List sampleCategoricalGenericAssayDataFilters; + private final List patientNumericalGenericAssayDataFilters; + private final List patientCategoricalGenericAssayDataFilters; + private CategorizedGenericAssayDataCountFilter(Builder builder) { + this.sampleCategoricalGenericAssayDataFilters = builder.sampleCategoricalGenericAssayDataFilters; + this.sampleNumericalGenericAssayDataFilters = builder.sampleNumericalGenericAssayDataFilters; + this.patientCategoricalGenericAssayDataFilters = builder.patientCategoricalGenericAssayDataFilters; + this.patientNumericalGenericAssayDataFilters = builder.patientNumericalGenericAssayDataFilters; + } + + public List getSampleNumericalGenericAssayDataFilters() { + return sampleNumericalGenericAssayDataFilters; + } + + public List getSampleCategoricalGenericAssayDataFilters() { + return sampleCategoricalGenericAssayDataFilters; + } + + public List getPatientNumericalGenericAssayDataFilters() { + return patientNumericalGenericAssayDataFilters; + } + + public List getPatientCategoricalGenericAssayDataFilters() { + return patientCategoricalGenericAssayDataFilters; + } + + public static class Builder { + private List sampleNumericalGenericAssayDataFilters; + private List sampleCategoricalGenericAssayDataFilters; + private List patientNumericalGenericAssayDataFilters; + private List patientCategoricalGenericAssayDataFilters; + + private Builder(){ + + } + + public Builder setSampleCategoricalGenericAssayDataFilters(List sampleCategoricalGenericAssayDataFilters) { + this.sampleCategoricalGenericAssayDataFilters = sampleCategoricalGenericAssayDataFilters; + return this; + } + + public Builder setSampleNumericalGenericAssayDataFilters(List sampleNumericalGenericAssayDataFilters) { + this.sampleNumericalGenericAssayDataFilters = sampleNumericalGenericAssayDataFilters; + return this; + } + + public Builder setPatientCategoricalGenericAssayDataFilters(List patientCategoricalGenericAssayDataFilters) { + this.patientCategoricalGenericAssayDataFilters = patientCategoricalGenericAssayDataFilters; + return this; + } + + public Builder setPatientNumericalGenericAssayDataFilters(List patientNumericalGenericAssayDataFilters) { + this.patientNumericalGenericAssayDataFilters = patientNumericalGenericAssayDataFilters; + return this; + } + + public CategorizedGenericAssayDataCountFilter build() { + return new CategorizedGenericAssayDataCountFilter(this); + } + } +} diff --git a/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java b/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java index fc9d2bffbf0..1b406b31532 100644 --- a/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java +++ b/src/main/java/org/cbioportal/web/parameter/ClinicalDataFilter.java @@ -1,11 +1,20 @@ package org.cbioportal.web.parameter; +import io.swagger.v3.oas.annotations.Hidden; + import java.io.Serializable; import java.util.List; public class ClinicalDataFilter extends DataFilter implements Serializable { private String attributeId; + + @Hidden + private List samples; + @Hidden + private String datatype; + @Hidden + private String displayName; public String getAttributeId() { return attributeId; @@ -15,4 +24,28 @@ public void setAttributeId(String attributeId) { this.attributeId = attributeId; } + public List getSamples() { + return samples; + } + + public void setSamples(List samples) { + this.samples = samples; + } + + public String getDatatype() { + return datatype; + } + + public void setDatatype(String datatype) { + this.datatype = datatype; + } + + public String getDisplayName() { + return displayName; + } + + public void setDisplayName(String displayName) { + this.displayName = displayName; + } + } diff --git a/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java b/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java new file mode 100644 index 00000000000..9f5f4e0bfe0 --- /dev/null +++ b/src/main/java/org/cbioportal/web/parameter/CustomSampleIdentifier.java @@ -0,0 +1,25 @@ +package org.cbioportal.web.parameter; + +import java.io.Serializable; + +public class CustomSampleIdentifier extends SampleIdentifier implements Serializable { + + private boolean isFilteredOut = false; + private String value; + + public boolean getIsFilteredOut() { + return isFilteredOut; + } + + public void setIsFilteredOut(boolean isFilteredOut) { + this.isFilteredOut = isFilteredOut; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java b/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java index 184aee40f29..af434cfa55d 100644 --- a/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java +++ b/src/main/java/org/cbioportal/web/parameter/DataFilterValue.java @@ -9,6 +9,14 @@ public class DataFilterValue implements Serializable { private BigDecimal end; private String value; + public DataFilterValue() {} + + public DataFilterValue(BigDecimal start, BigDecimal end, String value) { + this.start = start; + this.end = end; + this.value = value; + } + public BigDecimal getStart() { return start; } diff --git a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java b/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java index c4ca1cae155..14dfbf0a46d 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java +++ b/src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java @@ -6,6 +6,13 @@ public class GenericAssayDataFilter extends DataFilter implements Serializable { private String stableId; private String profileType; + public GenericAssayDataFilter() {} + + public GenericAssayDataFilter(String stableId, String profileType) { + this.stableId = stableId; + this.profileType = profileType; + } + public String getStableId() { return stableId; } diff --git a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java b/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java index 5938595e5e7..34aca9c0894 100644 --- a/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java +++ b/src/main/java/org/cbioportal/web/parameter/GenomicDataFilter.java @@ -1,11 +1,25 @@ package org.cbioportal.web.parameter; import java.io.Serializable; +import java.util.List; public class GenomicDataFilter extends DataFilter implements Serializable { private String hugoGeneSymbol; private String profileType; + public GenomicDataFilter() {} + + public GenomicDataFilter(String hugoGeneSymbol, String profileType) { + this.hugoGeneSymbol = hugoGeneSymbol; + this.profileType = profileType; + } + + public GenomicDataFilter(String hugoGeneSymbol, String profileType, List values) { + this.hugoGeneSymbol = hugoGeneSymbol; + this.profileType = profileType; + this.setValues(values); + } + public String getHugoGeneSymbol() { return hugoGeneSymbol; } diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java b/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java index 7928dccaa49..bf90b2de08b 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java +++ b/src/main/java/org/cbioportal/web/util/ClinicalDataBinUtil.java @@ -10,6 +10,7 @@ import org.cbioportal.service.util.CustomAttributeWithData; import org.cbioportal.service.util.CustomDataSession; import org.cbioportal.service.util.CustomDataValue; +import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil; import org.cbioportal.web.parameter.*; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; @@ -41,14 +42,7 @@ public class ClinicalDataBinUtil { private IdPopulator idPopulator; public StudyViewFilter removeSelfFromFilter(ClinicalDataBinCountFilter dataBinCountFilter) { - List attributes = dataBinCountFilter.getAttributes(); - StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); - - if (attributes.size() == 1) { - studyViewFilterUtil.removeSelfFromFilter(attributes.get(0).getAttributeId(), studyViewFilter); - } - - return studyViewFilter; + return NewClinicalDataBinUtil.removeSelfFromFilter(dataBinCountFilter); } public List fetchClinicalDataBinCounts( @@ -335,8 +329,8 @@ public List calculateStaticDataBins( emptyList()), filteredIds, unfilteredIds) .stream() - .map(dataBin -> studyViewFilterUtil.dataBinToClinicalDataBin(attribute, dataBin)) - .collect(toList()); + .map(dataBin -> NewClinicalDataBinUtil.dataBinToClinicalDataBin(attribute, dataBin)) + .toList(); clinicalDataBins.addAll(dataBins); } @@ -369,8 +363,8 @@ public List calculateDynamicDataBins( emptyList()), filteredIds) .stream() - .map(dataBin -> studyViewFilterUtil.dataBinToClinicalDataBin(attribute, dataBin)) - .collect(toList()); + .map(dataBin -> NewClinicalDataBinUtil.dataBinToClinicalDataBin(attribute, dataBin)) + .toList(); clinicalDataBins.addAll(dataBins); } } @@ -389,19 +383,11 @@ public Map toAttributeDatatypeMap( List patientAttributeIds, List conflictingPatientAttributeIds ) { - Map attributeDatatypeMap = new HashMap<>(); - - sampleAttributeIds.forEach(attribute -> { - attributeDatatypeMap.put(attribute, ClinicalDataType.SAMPLE); - }); - patientAttributeIds.forEach(attribute -> { - attributeDatatypeMap.put(attribute, ClinicalDataType.PATIENT); - }); - conflictingPatientAttributeIds.forEach(attribute -> { - attributeDatatypeMap.put(attribute, ClinicalDataType.SAMPLE); - }); - - return attributeDatatypeMap; + return NewClinicalDataBinUtil.toAttributeDatatypeMap( + sampleAttributeIds, + patientAttributeIds, + conflictingPatientAttributeIds + ); } private Map createCustomAttributeDatatypeMap( diff --git a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java b/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java index 0484f024bc7..66d310a2511 100644 --- a/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java +++ b/src/main/java/org/cbioportal/web/util/ClinicalDataIntervalFilterApplier.java @@ -18,9 +18,6 @@ @Component public class ClinicalDataIntervalFilterApplier extends ClinicalDataFilterApplier { - @Autowired - private DataBinHelper dataBinHelper; - @Autowired public ClinicalDataIntervalFilterApplier(PatientService patientService, ClinicalDataService clinicalDataService, @@ -110,7 +107,7 @@ else if (value.startsWith(gt)) { return null; } - return dataBinHelper.calcRange(min, startInclusive, max, endInclusive); + return DataBinHelper.calcRange(min, startInclusive, max, endInclusive); } private Range calculateRangeValueForFilter(DataFilterValue filterValue) { @@ -126,7 +123,7 @@ private Range calculateRangeValueForFilter(DataFilterValue filterVal startInclusive = true; } - return dataBinHelper.calcRange(start, startInclusive, end, endInclusive); + return DataBinHelper.calcRange(start, startInclusive, end, endInclusive); } private Boolean containsNA(ClinicalDataFilter filter) { diff --git a/src/main/java/org/cbioportal/web/util/DataBinHelper.java b/src/main/java/org/cbioportal/web/util/DataBinHelper.java index 6e50f437f5d..9138aef2572 100644 --- a/src/main/java/org/cbioportal/web/util/DataBinHelper.java +++ b/src/main/java/org/cbioportal/web/util/DataBinHelper.java @@ -1,18 +1,21 @@ package org.cbioportal.web.util; import org.cbioportal.model.DataBin; -import org.springframework.stereotype.Component; import com.google.common.collect.Range; import java.math.BigDecimal; import java.math.RoundingMode; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.ListIterator; +import java.util.Map; +import java.util.Set; import java.util.stream.Collectors; import org.springframework.util.Assert; -@Component public class DataBinHelper { - public DataBin calcUpperOutlierBin(List gteValues, List gtValues) { + public static DataBin calcUpperOutlierBin(List gteValues, List gtValues) { BigDecimal gteMin = gteValues.size() > 0 ? Collections.min(gteValues) : null; BigDecimal gtMin = gtValues.size() > 0 ? Collections.min(gtValues) : null; BigDecimal min; @@ -39,7 +42,7 @@ public DataBin calcUpperOutlierBin(List gteValues, List return dataBin; } - public DataBin calcLowerOutlierBin(List lteValues, List ltValues) { + public static DataBin calcLowerOutlierBin(List lteValues, List ltValues) { BigDecimal lteMax = lteValues.size() > 0 ? Collections.max(lteValues) : null; BigDecimal ltMax = ltValues.size() > 0 ? Collections.max(ltValues) : null; BigDecimal max; @@ -65,7 +68,7 @@ public DataBin calcLowerOutlierBin(List lteValues, List return dataBin; } - public List calcQuartileBoundaries(List sortedValues) { + public static List calcQuartileBoundaries(List sortedValues) { // Edge case: some of Q1, Q2, and Q3 are the same value. // Solution: reduce bins to represent unique values only. // Note: cannot use stream.distinct() because BigDecimal does @@ -87,7 +90,7 @@ public List calcQuartileBoundaries(List sortedValues) { return boundaries; } - public Range calcBoxRange(List sortedValues) { + public static Range calcBoxRange(List sortedValues) { if (sortedValues == null || sortedValues.size() == 0) { return null; } @@ -139,7 +142,7 @@ public Range calcBoxRange(List sortedValues) { return Range.closed(minValue, maxValue); } - public Range calcInterquartileRangeApproximation(List sortedValues) { + public static Range calcInterquartileRangeApproximation(List sortedValues) { Range iqr = null; if (sortedValues.size() > 0) { @@ -150,7 +153,7 @@ public Range calcInterquartileRangeApproximation(List so // if iqr == 0 AND max == q3 then recursively try finding a non-zero iqr approximation. if (q1.compareTo(q3) == 0 && max.compareTo(q3) == 0) { // filter out max and try again - iqr = this.calcInterquartileRangeApproximation( + iqr = calcInterquartileRangeApproximation( sortedValues.stream().filter(d -> d.compareTo(max) < 0).collect(Collectors.toList())); } @@ -163,7 +166,7 @@ public Range calcInterquartileRangeApproximation(List so return iqr; } - public BigDecimal calcQ1(List sortedValues) { + public static BigDecimal calcQ1(List sortedValues) { if (sortedValues == null || sortedValues.isEmpty()) { return null; } @@ -172,12 +175,12 @@ public BigDecimal calcQ1(List sortedValues) { return calcMedian(sortedValues, 0, stopIndex); } - public BigDecimal calcMedian(List sortedValues) { + public static BigDecimal calcMedian(List sortedValues) { return (sortedValues == null || sortedValues.isEmpty()) ? null : calcMedian(sortedValues, 0, sortedValues.size() - 1); } - public BigDecimal calcQ3(List sortedValues) { + public static BigDecimal calcQ3(List sortedValues) { if (sortedValues == null || sortedValues.isEmpty()) { return null; } @@ -189,7 +192,7 @@ public BigDecimal calcQ3(List sortedValues) { return calcMedian(sortedValues, startIndex, sortedValues.size() - 1); } - private BigDecimal calcMedian(List sortedValues, int start, int stop) { + private static BigDecimal calcMedian(List sortedValues, int start, int stop) { if (sortedValues == null || sortedValues.isEmpty()) { return null; } @@ -204,24 +207,24 @@ private BigDecimal calcMedian(List sortedValues, int start, int stop } } - public BigDecimal valueCloseToQ1(List sortedValues) { + public static BigDecimal valueCloseToQ1(List sortedValues) { return (sortedValues == null || sortedValues.isEmpty()) ? null : sortedValues.get((int) (sortedValues.size() * 0.25)); } - public BigDecimal valueCloseToQ3(List sortedValues) { + public static BigDecimal valueCloseToQ3(List sortedValues) { return (sortedValues == null || sortedValues.isEmpty()) ? null : sortedValues.get((int) (sortedValues.size() * 0.75)); } - public List filterIntervals(List intervals, BigDecimal lowerOutlier, BigDecimal upperOutlier) { + public static List filterIntervals(List intervals, BigDecimal lowerOutlier, BigDecimal upperOutlier) { // remove values that fall outside the lower and upper outlier limits return intervals.stream() .filter(d -> (lowerOutlier == null || d.compareTo(lowerOutlier) > 0 ) && (upperOutlier == null || d.compareTo(upperOutlier) < 0)) .collect(Collectors.toList()); } - public List initDataBins(List values, + public static List initDataBins(List values, List intervals, BigDecimal lowerOutlier, BigDecimal upperOutlier) { @@ -229,7 +232,7 @@ public List initDataBins(List values, filterIntervals(intervals, lowerOutlier, upperOutlier)); } - public List initDataBins(List values, + public static List initDataBins(List values, List intervals) { List dataBins = initDataBins(intervals); @@ -238,7 +241,7 @@ public List initDataBins(List values, return dataBins; } - public List initDataBins(List intervalValues) { + public static List initDataBins(List intervalValues) { List dataBins = new ArrayList<>(); for (int i = 0; i < intervalValues.size() - 1; i++) { @@ -254,7 +257,7 @@ public List initDataBins(List intervalValues) { return dataBins; } - public List trim(List dataBins) { + public static List trim(List dataBins) { List toRemove = new ArrayList<>(); // find out leading empty bins @@ -285,8 +288,8 @@ public List trim(List dataBins) { return trimmed; } - public void calcCounts(List dataBins, List values) { - Map, DataBin> rangeMap = dataBins.stream().collect(Collectors.toMap(this::calcRange, b -> b)); + public static void calcCounts(List dataBins, List values) { + Map, DataBin> rangeMap = dataBins.stream().collect(Collectors.toMap(DataBinHelper::calcRange, b -> b)); // TODO complexity here is O(n x m), find a better way to do this for (Range range : rangeMap.keySet()) { @@ -300,7 +303,7 @@ public void calcCounts(List dataBins, List values) { } } - public Range calcRange(DataBin dataBin) { + public static Range calcRange(DataBin dataBin) { boolean startInclusive = ">=".equals(dataBin.getSpecialValue()); boolean endInclusive = !"<".equals(dataBin.getSpecialValue()); @@ -312,7 +315,7 @@ public Range calcRange(DataBin dataBin) { return calcRange(dataBin.getStart(), startInclusive, dataBin.getEnd(), endInclusive); } - public Range calcRange(String operator, BigDecimal value) { + public static Range calcRange(String operator, BigDecimal value) { boolean startInclusive = ">=".equals(operator); BigDecimal start = operator.contains(">") ? value : null; boolean endInclusive = !"<".equals(operator); @@ -321,19 +324,19 @@ public Range calcRange(String operator, BigDecimal value) { return calcRange(start, startInclusive, end, endInclusive); } - public boolean isNA(String value) { + public static boolean isNA(String value) { return value.equalsIgnoreCase("NA") || value.equalsIgnoreCase("NAN") || value.equalsIgnoreCase("N/A"); } - public boolean isSmallData(List sortedValues) { + public static boolean isSmallData(List sortedValues) { BigDecimal median = sortedValues.get((int) Math.ceil((sortedValues.size() * (1.0 / 2.0)))); return median.compareTo(new BigDecimal("0.001")) < 0 && median.compareTo(new BigDecimal("-0.001")) > 0 && median.compareTo(new BigDecimal("0")) != 0; } - public String extractOperator(String value) { + public static String extractOperator(String value) { int length = 0; if (value.trim().startsWith(">=") || value.trim().startsWith("<=")) { @@ -345,11 +348,11 @@ public String extractOperator(String value) { return value.trim().substring(0, length); } - public Integer calcExponent(BigDecimal value) { + public static Integer calcExponent(BigDecimal value) { return value.precision() - value.scale() - 1; } - public String stripOperator(String value) { + public static String stripOperator(String value) { int length = 0; if (value.trim().startsWith(">=") || value.trim().startsWith("<=")) { @@ -361,11 +364,11 @@ public String stripOperator(String value) { return value.trim().substring(length); } - public boolean isAgeAttribute(String attributeId) { + public static boolean isAgeAttribute(String attributeId) { return attributeId != null && attributeId.matches("(^AGE$)|(^AGE_.*)|(.*_AGE_.*)|(.*_AGE&)"); } - public Range calcRange(BigDecimal start, boolean startInclusive, BigDecimal end, boolean endInclusive) { + public static Range calcRange(BigDecimal start, boolean startInclusive, BigDecimal end, boolean endInclusive) { // check for invalid filter (no start or end provided) if (start == null && end == null) { return null; @@ -396,19 +399,19 @@ public Range calcRange(BigDecimal start, boolean startInclusive, Big } } - public Set findDistinctValues(DataBin numericalBin, List numericalValues) { + public static Set findDistinctValues(DataBin numericalBin, List numericalValues) { Range range = calcRange(numericalBin); return numericalValues.stream().filter(range::contains).collect(Collectors.toSet()); } - public Set> findDistinctSpecialRanges(DataBin numericalBin, List> rangeValues) { + public static Set> findDistinctSpecialRanges(DataBin numericalBin, List> rangeValues) { Range range = calcRange(numericalBin); return rangeValues.stream().filter(range::encloses).collect(Collectors.toSet()); } - public List convertToDistinctBins( + public static List convertToDistinctBins( List dataBins, List numericalValues, List> rangeValues @@ -416,11 +419,11 @@ public List convertToDistinctBins( List distinctBins = new ArrayList<>(); for (DataBin bin: dataBins) { - Set distinctValues = this.findDistinctValues(bin, numericalValues); - Set> distinctRanges = this.findDistinctSpecialRanges(bin, rangeValues); + Set distinctValues = findDistinctValues(bin, numericalValues); + Set> distinctRanges = findDistinctSpecialRanges(bin, rangeValues); // if the bin contains only one distinct value and no range value then create a distinct bin - if (distinctRanges.size() == 0 && distinctValues.size() == 1 && this.areAllIntegers(distinctValues)) { + if (distinctRanges.size() == 0 && distinctValues.size() == 1 && areAllIntegers(distinctValues)) { BigDecimal distinctValue = distinctValues.iterator().next(); DataBin distinctBin = new DataBin(); @@ -446,7 +449,7 @@ public List convertToDistinctBins( } } - public Boolean areAllDistinctExceptOutliers(List dataBins) { + public static Boolean areAllDistinctExceptOutliers(List dataBins) { return dataBins .stream() .filter(b -> b.getStart() != null && b.getEnd() != null) @@ -455,7 +458,7 @@ public Boolean areAllDistinctExceptOutliers(List dataBins) { .orElse(false); } - public Boolean areAllIntegers(Set uniqueValues) { + public static Boolean areAllIntegers(Set uniqueValues) { return uniqueValues .stream() .map(value -> value.stripTrailingZeros().scale() <= 0) @@ -463,7 +466,7 @@ public Boolean areAllIntegers(Set uniqueValues) { .orElse(false); } - public List generateBins(List sortedNumericalValues, BigDecimal binSize, BigDecimal anchorValue) { + public static List generateBins(List sortedNumericalValues, BigDecimal binSize, BigDecimal anchorValue) { Assert.notNull(sortedNumericalValues, "sortedNumerical values is null!"); Assert.notNull(binSize, "binSize values is null!"); diff --git a/src/main/java/org/cbioportal/web/util/DataBinner.java b/src/main/java/org/cbioportal/web/util/DataBinner.java index 6002f2df9b6..85e21f2e69c 100644 --- a/src/main/java/org/cbioportal/web/util/DataBinner.java +++ b/src/main/java/org/cbioportal/web/util/DataBinner.java @@ -20,8 +20,6 @@ public class DataBinner { private static final Integer DEFAULT_DISTINCT_VALUE_THRESHOLD = 10; - @Autowired - private DataBinHelper dataBinHelper; @Autowired private DiscreteDataBinner discreteDataBinner; @Autowired @@ -31,12 +29,20 @@ public class DataBinner { @Autowired private LogScaleDataBinner logScaleDataBinner; - public List calculateClinicalDataBins(T dataBinFilter, + /** + * This method should only be invoked by legacy endpoints because it requires sample/patient ids. + * + * @deprecated + */ + @Deprecated + public List calculateClinicalDataBins( + T dataBinFilter, ClinicalDataType clinicalDataType, List filteredClinicalData, List unfilteredClinicalData, List filteredIds, - List unfilteredIds) { + List unfilteredIds + ) { // calculate data bins for unfiltered clinical data List dataBins = calculateDataBins( dataBinFilter, clinicalDataType, unfilteredClinicalData, unfilteredIds); @@ -45,10 +51,52 @@ public List calculateClinicalDataBins(T dataB return recalcBinCount(dataBins, clinicalDataType, filteredClinicalData, filteredIds); } - public List recalcBinCount(List dataBins, - ClinicalDataType clinicalDataType, - List clinicalData, - List ids) { + public List calculateClinicalDataBins( + T dataBinFilter, + List filteredClinicalData, + List unfilteredClinicalData + ) { + // calculate data bins for unfiltered clinical data + // we need this additional calculation to know the bins generated for the initial state. + // this allows us to keep the number of bins and bin ranges consistent. + // we only want to update the counts for each bin, we don't want to regenerate the bins for the filtered data. + List dataBins = calculateDataBins( + dataBinFilter, + unfilteredClinicalData + ); + + // recount + return recalcBinCount( + dataBins, + filteredClinicalData, + countNAs(filteredClinicalData) + ); + } + + /** + * This method should only be invoked by legacy endpoints because it requires sample/patient ids. + * + * @deprecated + */ + @Deprecated + public List recalcBinCount( + List dataBins, + ClinicalDataType clinicalDataType, + List clinicalData, + List caseIds + ) { + return recalcBinCount( + dataBins, + clinicalData, + countNAs(clinicalData, clinicalDataType, caseIds) + ); + } + + public List recalcBinCount( + List dataBins, + List clinicalData, + Long naCount + ) { List numericalValues = clinicalData == null ? Collections.emptyList() : filterNumericalValues(clinicalData); List nonNumericalValues = clinicalData == null ? @@ -61,7 +109,7 @@ public List recalcBinCount(List dataBins, dataBin.setCount(0); // calculate range - Range range = dataBinHelper.calcRange(dataBin); + Range range = DataBinHelper.calcRange(dataBin); if (range != null) { for (BigDecimal value : numericalValues) { @@ -83,39 +131,83 @@ public List recalcBinCount(List dataBins, } } if ("NA".equalsIgnoreCase(dataBin.getSpecialValue())) { - dataBin.setCount(countNAs(clinicalData, clinicalDataType, ids).intValue()); + dataBin.setCount(naCount.intValue()); } } return dataBins; } + /** + * This method should only be invoked by legacy endpoints because it requires sample/patient ids. + * + * @deprecated + */ + @Deprecated public List calculateDataBins( T dataBinFilter, ClinicalDataType clinicalDataType, List clinicalData, - List ids + List caseIds ) { return calculateDataBins( dataBinFilter, clinicalDataType, clinicalData, - ids, + caseIds, + DEFAULT_DISTINCT_VALUE_THRESHOLD + ); + } + + public List calculateDataBins( + T dataBinFilter, + List clinicalData + ) { + return calculateDataBins( + dataBinFilter, + clinicalData, DEFAULT_DISTINCT_VALUE_THRESHOLD ); } + public List calculateDataBins( + T dataBinFilter, + List clinicalData, + Integer distinctValueThreshold + ) { + DataBin naDataBin = calcNaDataBin(clinicalData); + + return calculateDataBins(dataBinFilter, clinicalData, naDataBin, distinctValueThreshold); + } + + /** + * This method should only be invoked by legacy endpoints because it requires sample/patient ids. + * + * @deprecated + */ + @Deprecated public List calculateDataBins( T dataBinFilter, ClinicalDataType clinicalDataType, List clinicalData, - List ids, + List caseIds, + Integer distinctValueThreshold + ) { + DataBin naDataBin = calcNaDataBin(clinicalData, clinicalDataType, caseIds); + + return calculateDataBins(dataBinFilter, clinicalData, naDataBin, distinctValueThreshold); + } + + public List calculateDataBins( + T dataBinFilter, + List clinicalData, + DataBin naDataBin, Integer distinctValueThreshold ) { boolean numericalOnly = false; Range range = dataBinFilter.getStart() == null && dataBinFilter.getEnd() == null ? - Range.all() : dataBinHelper.calcRange(dataBinFilter.getStart(), true, dataBinFilter.getEnd(), true); + Range.all() : DataBinHelper.calcRange(dataBinFilter.getStart(), true, dataBinFilter.getEnd(), true); if (range.hasUpperBound()) { clinicalData = filterSmallerThanUpperBound(clinicalData, range.upperEndpoint()); @@ -154,11 +246,11 @@ public List calculateDataBins( } // remove leading and trailing empty bins before adding non numerical ones - dataBins = dataBinHelper.trim(dataBins); + dataBins = DataBinHelper.trim(dataBins); // in some cases every numerical bin actually contains only a single discrete value // convert interval bins to distinct (single value) bins in these cases - dataBins = dataBinHelper.convertToDistinctBins( + dataBins = DataBinHelper.convertToDistinctBins( dataBins, filterNumericalValues(clinicalData), filterSpecialRanges(clinicalData) ); @@ -167,7 +259,6 @@ dataBins, filterNumericalValues(clinicalData), filterSpecialRanges(clinicalData) dataBins.addAll(calcNonNumericalClinicalDataBins(clinicalData)); - DataBin naDataBin = calcNaDataBin(clinicalData, clinicalDataType, ids); if (!naDataBin.getCount().equals(0)) { dataBins.add(naDataBin); } @@ -181,11 +272,11 @@ public List> filterSpecialRanges(List clinicalData) .map(Binnable::getAttrValue) .filter(s -> (s.contains(">") || s.contains("<")) && // ignore any invalid values such as >10PY, <20%, etc. - NumberUtils.isCreatable(dataBinHelper.stripOperator(s))) - .map(v -> dataBinHelper.calcRange( + NumberUtils.isCreatable(DataBinHelper.stripOperator(s))) + .map(v -> DataBinHelper.calcRange( // only use "<" or ">" to make sure that we only generate open ranges - dataBinHelper.extractOperator(v).substring(0, 1), - new BigDecimal(dataBinHelper.stripOperator(v)))) + DataBinHelper.extractOperator(v).substring(0, 1), + new BigDecimal(DataBinHelper.stripOperator(v)))) .collect(Collectors.toList()); } @@ -197,7 +288,7 @@ public List filterNonNumericalValues(List clinicalData) { // filter out numerical values and 'NA's return clinicalData.stream() .map(Binnable::getAttrValue) - .filter(s -> !NumberUtils.isCreatable(dataBinHelper.stripOperator(s)) && !dataBinHelper.isNA(s)) + .filter(s -> !NumberUtils.isCreatable(DataBinHelper.stripOperator(s)) && !DataBinHelper.isNA(s)) .collect(Collectors.toList()); } @@ -282,7 +373,7 @@ public Collection calcNumericalDataBins( List sortedNumericalValues = new ArrayList<>(numericalValues); Collections.sort(sortedNumericalValues); - Range boxRange = dataBinHelper.calcBoxRange(sortedNumericalValues); + Range boxRange = DataBinHelper.calcBoxRange(sortedNumericalValues); // remove initial outliers List withoutOutliers = sortedNumericalValues.stream().filter(isNotOutlier).collect(Collectors.toList()); @@ -303,12 +394,12 @@ public Collection calcNumericalDataBins( customBins = this.adjustCustomBins(customBins, lowerOutlierBin, upperOutlierBin); dataBins = linearDataBinner.calculateDataBins(customBins, numericalValues); } else if (DataBinFilter.BinMethod.GENERATE == binMethod && binsGeneratorConfig != null) { - List bins = this.dataBinHelper.generateBins(sortedNumericalValues, binsGeneratorConfig.getBinSize(), binsGeneratorConfig.getAnchorValue()); + List bins = DataBinHelper.generateBins(sortedNumericalValues, binsGeneratorConfig.getBinSize(), binsGeneratorConfig.getAnchorValue()); dataBins = linearDataBinner.calculateDataBins(bins, numericalValues); } else if (DataBinFilter.BinMethod.MEDIAN == binMethod) { // NOOP - handled later } else if (DataBinFilter.BinMethod.QUARTILE == binMethod) { - List boundaries = this.dataBinHelper.calcQuartileBoundaries(sortedNumericalValues); + List boundaries = DataBinHelper.calcQuartileBoundaries(sortedNumericalValues); dataBins = linearDataBinner.calculateDataBins(boundaries, numericalValues); } else if (boxRange.upperEndpoint().subtract(boxRange.lowerEndpoint()).compareTo(new BigDecimal(1000)) == 1 && (disableLogScale == null || !disableLogScale)) { @@ -317,7 +408,7 @@ public Collection calcNumericalDataBins( withoutOutliers, lowerOutlierBin.getEnd(), upperOutlierBin.getStart()); - } else if (dataBinHelper.isSmallData(sortedNumericalValues)) { + } else if (DataBinHelper.isSmallData(sortedNumericalValues)) { dataBins = scientificSmallDataBinner.calculateDataBins( sortedNumericalValues, withoutOutliers, @@ -329,7 +420,7 @@ public Collection calcNumericalDataBins( boxRange = Range.closed(dataBins.get(0).getStart(), dataBins.get(dataBins.size() - 1).getEnd()); } } else { - Boolean areAllIntegers = this.dataBinHelper.areAllIntegers(uniqueValues); + Boolean areAllIntegers = DataBinHelper.areAllIntegers(uniqueValues); if (areAllIntegers) { boxRange = Range.closed( @@ -355,7 +446,7 @@ public Collection calcNumericalDataBins( // In edge cases all quartile values can be identical (all // values are in the outlier bins). || (DataBinFilter.BinMethod.QUARTILE == binMethod && dataBins.size() == 0)) { - BigDecimal median = this.dataBinHelper.calcMedian(sortedNumericalValues); + BigDecimal median = DataBinHelper.calcMedian(sortedNumericalValues); lowerOutlierBin.setEnd(median); upperOutlierBin.setStart(median); // Covers the situation where there is a single custom boundary (i.e. there are only outlier bins). @@ -453,7 +544,7 @@ public List filterBiggerThanLowerBound(List clinicalData, Bi } public DataBin calcUpperOutlierBin(List clinicalData) { - DataBin dataBin = dataBinHelper.calcUpperOutlierBin( + DataBin dataBin = DataBinHelper.calcUpperOutlierBin( doubleValuesForSpecialOutliers(clinicalData, ">="), doubleValuesForSpecialOutliers(clinicalData, ">")); @@ -464,7 +555,7 @@ public DataBin calcUpperOutlierBin(List clinicalData) { } public DataBin calcLowerOutlierBin(List clinicalData) { - DataBin dataBin = dataBinHelper.calcLowerOutlierBin( + DataBin dataBin = DataBinHelper.calcLowerOutlierBin( doubleValuesForSpecialOutliers(clinicalData, "<="), doubleValuesForSpecialOutliers(clinicalData, "<")); @@ -514,32 +605,58 @@ public List adjustCustomBins( * NA count is: Number of clinical data marked actually as "NA" + Number of patients/samples without clinical data. * Assuming that clinical data is for a single attribute. * + * This method should only be invoked by legacy endpoints because it requires sample/patient ids. + * * @param clinicalData clinical data list for a single attribute - * @param ids sample/patient ids + * @param caseIds sample/patient ids * * @return 'NA' clinical data count as a DataBin instance + * @deprecated */ - public DataBin calcNaDataBin(List clinicalData, - ClinicalDataType clinicalDataType, - List ids) { - DataBin bin = new DataBin(); - - bin.setSpecialValue("NA"); + @Deprecated + public DataBin calcNaDataBin( + List clinicalData, + ClinicalDataType clinicalDataType, + List caseIds + ) { + DataBin bin = initNaDataBin(); + bin.setCount(countNAs(clinicalData, clinicalDataType, caseIds).intValue()); - Long count = countNAs(clinicalData, clinicalDataType, ids); + return bin; + } - bin.setCount(count.intValue()); + /** + * This function assumes that all the NA values are already in the provided clinical data list. + * + * @param clinicalData clinical data list for a single attribute + * + * @return 'NA' clinical data count as a DataBin instance + */ + public DataBin calcNaDataBin( + List clinicalData + ) { + DataBin bin = initNaDataBin(); + bin.setCount(countNAs(clinicalData).intValue()); return bin; } + + public DataBin initNaDataBin() { + DataBin bin = new DataBin(); + bin.setSpecialValue("NA"); + return bin; + } - public Long countNAs(List clinicalData, ClinicalDataType clinicalDataType, List ids) { - // Calculate number of clinical data marked actually as "NA", "NAN", or "N/A" - - Long count = clinicalData == null ? 0 : - clinicalData.stream() - .filter(c -> dataBinHelper.isNA(c.getAttrValue())) - .count(); + /** + * This method should only be invoked by legacy endpoints because it requires sample/patient ids + * + * @deprecated + */ + @Deprecated + public Long countNAs(List clinicalData, ClinicalDataType clinicalDataType, List caseIds) { + // Calculate the number of clinical data marked actually as "NA", "NAN", or "N/A" + + Long count = countNAs(clinicalData); // Calculate number of patients/samples without clinical data @@ -555,7 +672,7 @@ public Long countNAs(List clinicalData, ClinicalDataType clinicalDataT uniqueClinicalDataIds = Collections.emptySet(); } - Set uniqueInputIds = new HashSet<>(ids); + Set uniqueInputIds = new HashSet<>(caseIds); // remove the ids with existing clinical data, // size of the difference (of two sets) is the count we need @@ -565,6 +682,16 @@ public Long countNAs(List clinicalData, ClinicalDataType clinicalDataT return count; } + /** + * Calculate number of clinical data marked actually as "NA", "NAN", or "N/A" + */ + public Long countNAs(List clinicalData) { + return clinicalData == null ? 0 : + clinicalData.stream() + .filter(c -> DataBinHelper.isNA(c.getAttrValue())) + .count(); + } + private String computeUniqueCaseId(Binnable clinicalData, ClinicalDataType clinicalDataType) { return clinicalData.getStudyId() + (clinicalDataType == ClinicalDataType.PATIENT ? clinicalData.getPatientId() diff --git a/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java b/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java new file mode 100644 index 00000000000..47e65543680 --- /dev/null +++ b/src/main/java/org/cbioportal/web/util/DensityPlotParameters.java @@ -0,0 +1,118 @@ +package org.cbioportal.web.util; + +import java.math.BigDecimal; + +public class DensityPlotParameters { + private final Integer xAxisBinCount; + private final Integer yAxisBinCount; + private final BigDecimal xAxisStart; + private final BigDecimal xAxisEnd; + private final BigDecimal yAxisStart; + private final BigDecimal yAxisEnd; + private final Boolean xAxisLogScale; + private final Boolean yAxisLogScale; + private final String xAxisAttributeId; + private final String yAxisAttributeId; + + DensityPlotParameters(Builder builder) { + this.xAxisBinCount = builder.xAxisBinCount; + this.yAxisBinCount = builder.yAxisBinCount; + this.xAxisStart = builder.xAxisStart; + this.xAxisEnd = builder.xAxisEnd; + this.yAxisStart = builder.yAxisStart; + this.yAxisEnd = builder.yAxisEnd; + this.xAxisAttributeId = builder.xAxisAttributeId; + this.yAxisAttributeId = builder.yAxisAttributeId; + this.xAxisLogScale = builder.xAxisLogScale; + this.yAxisLogScale = builder.yAxisLogScale; + } + + public Integer getXAxisBinCount() { + return xAxisBinCount; + } + public Integer getYAxisBinCount() { + return yAxisBinCount; + } + public BigDecimal getXAxisStart() { + return xAxisStart; + } + public BigDecimal getXAxisEnd() { + return xAxisEnd; + } + public BigDecimal getYAxisStart() { + return yAxisStart; + } + public BigDecimal getYAxisEnd() { + return yAxisEnd; + } + public Boolean getXAxisLogScale() { + return xAxisLogScale; + } + public Boolean getYAxisLogScale() { + return yAxisLogScale; + } + public String getXAxisAttributeId() { + return xAxisAttributeId; + } + public String getYAxisAttributeId() { + return yAxisAttributeId; + } + + public static class Builder { + private Integer xAxisBinCount; + private Integer yAxisBinCount; + private BigDecimal xAxisStart; + private BigDecimal xAxisEnd; + private BigDecimal yAxisStart; + private BigDecimal yAxisEnd; + private Boolean xAxisLogScale; + private Boolean yAxisLogScale; + private String xAxisAttributeId; + private String yAxisAttributeId; + + public Builder xAxisBinCount(Integer xAxisBinCount) { + this.xAxisBinCount = xAxisBinCount; + return this; + } + public Builder yAxisBinCount(Integer yAxisBinCount) { + this.yAxisBinCount = yAxisBinCount; + return this; + } + public Builder xAxisStart(BigDecimal xAxisStart) { + this.xAxisStart = xAxisStart; + return this; + } + public Builder xAxisEnd(BigDecimal xAxisEnd) { + this.xAxisEnd = xAxisEnd; + return this; + } + public Builder yAxisStart(BigDecimal yAxisStart) { + this.yAxisStart = yAxisStart; + return this; + } + public Builder yAxisEnd(BigDecimal yAxisEnd) { + this.yAxisEnd = yAxisEnd; + return this; + } + public Builder xAxisLogScale(Boolean xAxisLogScale) { + this.xAxisLogScale = xAxisLogScale; + return this; + } + public Builder yAxisLogScale(Boolean yAxisLogScale) { + this.yAxisLogScale = yAxisLogScale; + return this; + } + public Builder xAxisAttributeId(String xAxisAttributeId) { + this.xAxisAttributeId = xAxisAttributeId; + return this; + } + public Builder yAxisAttributeId(String yAxisAttributeId) { + this.yAxisAttributeId = yAxisAttributeId; + return this; + } + public DensityPlotParameters build() { + return new DensityPlotParameters(this); + + } + } +} diff --git a/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java b/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java index bff1eaf390b..d6eaf334f82 100644 --- a/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java +++ b/src/main/java/org/cbioportal/web/util/DiscreteDataBinner.java @@ -1,7 +1,6 @@ package org.cbioportal.web.util; import org.cbioportal.model.DataBin; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; import java.math.BigDecimal; @@ -12,14 +11,11 @@ @Component public class DiscreteDataBinner { - @Autowired - private DataBinHelper dataBinHelper; - public List calculateDataBins(List values, Set uniqueValues) { List dataBins = initDataBins(uniqueValues); - dataBinHelper.calcCounts(dataBins, values); + DataBinHelper.calcCounts(dataBins, values); return dataBins; } diff --git a/src/main/java/org/cbioportal/web/util/IdPopulator.java b/src/main/java/org/cbioportal/web/util/IdPopulator.java index bfda0b01e95..e7c02227bdf 100644 --- a/src/main/java/org/cbioportal/web/util/IdPopulator.java +++ b/src/main/java/org/cbioportal/web/util/IdPopulator.java @@ -1,14 +1,12 @@ package org.cbioportal.web.util; import org.cbioportal.model.ClinicalAttribute; -import org.cbioportal.service.AttributeByStudyService; import org.cbioportal.service.PatientService; import org.cbioportal.service.util.ClinicalAttributeUtil; import org.cbioportal.web.parameter.SampleIdentifier; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; -import java.util.ArrayList; import java.util.List; @Component diff --git a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java b/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java index 547e50e44ee..e0ee3961f71 100644 --- a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java +++ b/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java @@ -35,6 +35,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import jakarta.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletResponse; +import org.apache.commons.lang3.StringUtils; import org.cbioportal.model.AlterationFilter; import org.cbioportal.model.MolecularProfile; import org.cbioportal.model.MolecularProfileCaseIdentifier; @@ -133,6 +134,8 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept public static final String CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH = "/clinical-event-type-counts/fetch"; public static final String SURVIVAL_DATA_FETCH_PATH = "/survival-data/fetch"; public static final String CLINICAL_EVENT_META_FETCH_PATH = "/clinical-events-meta/fetch"; + public static final String TREATMENTS_PATIENT_COUNT_FETCH_PATH = "/treatments/patient-counts/fetch"; + public static final String TREATMENTS_SAMPLE_COUNT_FETCH_PATH = "/treatments/sample-counts/fetch"; @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) { if (!request.getMethod().equals("POST")) { @@ -142,6 +145,7 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept // reset this to 'String requestPathInfo = request.getPathInfo();' String requestPathInfo = request.getPathInfo() == null? request.getServletPath() : request.getPathInfo(); requestPathInfo = requestPathInfo.replaceFirst("^/api", ""); + requestPathInfo = StringUtils.removeStart(requestPathInfo, "/column-store"); if (requestPathInfo.equals(PATIENT_FETCH_PATH)) { return extractAttributesFromPatientFilter(request); } else if (requestPathInfo.equals(SAMPLE_FETCH_PATH)) { @@ -176,7 +180,8 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept } else if (Arrays.asList(STUDY_VIEW_CLINICAL_DATA_DENSITY_PATH, STUDY_VIEW_CLINICAL_DATA_VIOLIN_PATH, STUDY_VIEW_CNA_GENES, STUDY_VIEW_FILTERED_SAMPLES, STUDY_VIEW_MUTATED_GENES, STUDY_VIEW_STRUCTURAL_VARIANT_GENES, STUDY_VIEW_STRUCTURAL_VARIANT_COUNTS, STUDY_VIEW_SAMPLE_COUNTS, STUDY_VIEW_SAMPLE_LIST_COUNTS_PATH, STUDY_VIEW_CLINICAL_TABLE_DATA_FETCH_PATH, - TREATMENTS_PATIENT_PATH, TREATMENTS_SAMPLE_PATH, STUDY_VIEW_PROFILE_SAMPLE_COUNTS_PATH, CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH + TREATMENTS_PATIENT_PATH, TREATMENTS_SAMPLE_PATH, STUDY_VIEW_PROFILE_SAMPLE_COUNTS_PATH, CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH, + TREATMENTS_PATIENT_COUNT_FETCH_PATH, TREATMENTS_SAMPLE_COUNT_FETCH_PATH ).contains(requestPathInfo)) { return extractAttributesFromStudyViewFilter(request); } else if (requestPathInfo.equals(CLINICAL_DATA_ENRICHMENT_FETCH_PATH)) { diff --git a/src/main/java/org/cbioportal/web/util/LinearDataBinner.java b/src/main/java/org/cbioportal/web/util/LinearDataBinner.java index eb9a0abf281..34bea85d9e4 100644 --- a/src/main/java/org/cbioportal/web/util/LinearDataBinner.java +++ b/src/main/java/org/cbioportal/web/util/LinearDataBinner.java @@ -2,7 +2,6 @@ import com.google.common.collect.Range; import org.cbioportal.model.DataBin; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; import java.math.BigDecimal; @@ -34,9 +33,6 @@ public class LinearDataBinner { public static final Integer DEFAULT_INTERVAL_COUNT = 20; - @Autowired - private DataBinHelper dataBinHelper; - public List calculateDataBins(boolean areAllIntegers, Range boxRange, List values, @@ -50,7 +46,7 @@ public List calculateDataBins(boolean areAllIntegers, // special case for "AGE" attributes if (attributeId.isPresent() && - dataBinHelper.isAgeAttribute(attributeId.get()) && + DataBinHelper.isAgeAttribute(attributeId.get()) && min.doubleValue() < 18 && boxRange.upperEndpoint().subtract(boxRange.lowerEndpoint()).divide(BigDecimal.valueOf(2)).compareTo(BigDecimal.valueOf(18)) == 1 && dataBins.get(0).getEnd().compareTo(BigDecimal.valueOf(18)) == 1) { @@ -58,7 +54,7 @@ public List calculateDataBins(boolean areAllIntegers, dataBins.get(0).setStart(BigDecimal.valueOf(18)); } - dataBinHelper.calcCounts(dataBins, values); + DataBinHelper.calcCounts(dataBins, values); return dataBins; } @@ -66,7 +62,7 @@ public List calculateDataBins(boolean areAllIntegers, public List calculateDataBins(List customBins, List values) { List dataBins = initDataBins(customBins); - dataBinHelper.calcCounts(dataBins, values); + DataBinHelper.calcCounts(dataBins, values); return dataBins; } diff --git a/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java b/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java index 1f6b34d30cf..febeb34ebb8 100644 --- a/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java +++ b/src/main/java/org/cbioportal/web/util/LogScaleDataBinner.java @@ -2,7 +2,6 @@ import com.google.common.collect.Range; import org.cbioportal.model.DataBin; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; import java.math.BigDecimal; @@ -11,8 +10,6 @@ @Component public class LogScaleDataBinner { - @Autowired - private DataBinHelper dataBinHelper; public List calculateDataBins(Range boxRange, List values, @@ -57,7 +54,7 @@ public List calculateDataBins(Range boxRange, } } - return dataBinHelper.initDataBins(values, intervals); + return DataBinHelper.initDataBins(values, intervals); } public BigDecimal calcIntervalValue(BigDecimal exponent) { diff --git a/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java b/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java index 276ab1bb2ba..f3766164ef8 100644 --- a/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java +++ b/src/main/java/org/cbioportal/web/util/ScientificSmallDataBinner.java @@ -2,7 +2,6 @@ import com.google.common.collect.Range; import org.cbioportal.model.DataBin; -import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; import java.math.BigDecimal; @@ -14,22 +13,19 @@ @Component public class ScientificSmallDataBinner { - @Autowired - private DataBinHelper dataBinHelper; - public List calculateDataBins(List sortedNumericalValues, List valuesWithoutOutliers, BigDecimal lowerOutlier, BigDecimal upperOutlier) { List exponents = sortedNumericalValues .stream() - .map(d -> BigDecimal.valueOf(dataBinHelper.calcExponent(d))) + .map(d -> BigDecimal.valueOf(DataBinHelper.calcExponent(d))) .filter(d -> d.compareTo(new BigDecimal("0")) != 0) .collect(Collectors.toList()); Collections.sort(exponents); - Range exponentBoxRange = dataBinHelper.calcBoxRange(exponents); + Range exponentBoxRange = DataBinHelper.calcBoxRange(exponents); List intervals = new ArrayList<>(); @@ -72,6 +68,6 @@ public List calculateDataBins(List sortedNumericalValues, } } - return dataBinHelper.initDataBins(valuesWithoutOutliers, intervals, lowerOutlier, upperOutlier); + return DataBinHelper.initDataBins(valuesWithoutOutliers, intervals, lowerOutlier, upperOutlier); } } diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java index 1684902a437..43980c99f90 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java +++ b/src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java @@ -206,7 +206,7 @@ public List apply(StudyViewFilter studyViewFilter, boolean neg if (!CollectionUtils.isEmpty(clinicalDataIntervalFilters)) { sampleIdentifiers = intervalFilterClinicalData(sampleIdentifiers, clinicalDataIntervalFilters, negateFilters); } - + if (!CollectionUtils.isEmpty(studyViewFilter.getCustomDataFilters())) { sampleIdentifiers = customDataFilterApplier.apply(sampleIdentifiers, studyViewFilter.getCustomDataFilters(), negateFilters); @@ -311,15 +311,24 @@ public List apply(StudyViewFilter studyViewFilter, boolean neg }); }); + List genePanelData = genePanelService .fetchGenePanelDataInMultipleMolecularProfiles(molecularProfileSampleIdentifiers); + // gene panel data is { profileId, sampleId, isProfiled } + // it tells us whether a particular sample is profiled by a given molecularprofile + // we can use the gene panel to find out what genes were profiled for (List profileValues : studyViewFilter.getGenomicProfiles()) { + + // using the profileIds from the filter we get a map, stableId to profile entity Map profileMap = profileValues.stream().flatMap( profileValue -> molecularProfileSet.getOrDefault(profileValue, new ArrayList<>()).stream()) .collect(Collectors.toMap(MolecularProfile::getStableId, Function.identity())); - + Set filteredSampleIdentifiers = new HashSet<>(); + + // for each sample/profile combo, we need to find out whether + // the profileMap contains that profile id genePanelData.forEach(datum -> { if (datum.getProfiled() && profileMap.containsKey(datum.getMolecularProfileId())) { SampleIdentifier sampleIdentifier = @@ -714,7 +723,6 @@ public List getUniqkeyKeys(List studyIds, List caseIds) public List getDataBins( DataBinMethod dataBinMethod, T dataBinCountFilter) { List dataBinFilters = fetchDataBinFilters(dataBinCountFilter); - StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter(); if (dataBinFilters.size() == 1) { @@ -724,6 +732,7 @@ public resultDataBins; List filteredSampleIds = new ArrayList<>(); List filteredStudyIds = new ArrayList<>(); + List filteredData = fetchData(dataBinCountFilter, studyViewFilter, filteredSampleIds, filteredStudyIds); @@ -731,7 +740,7 @@ public > filteredClinicalDataByAttributeId = filteredData.stream() .collect(Collectors.groupingBy(Binnable::getAttrId)); - + if (dataBinMethod == DataBinMethod.STATIC) { StudyViewFilter filter = studyViewFilter == null ? null : new StudyViewFilter(); diff --git a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java b/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java index 7788b88fd72..b44b8bd8a63 100644 --- a/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java +++ b/src/main/java/org/cbioportal/web/util/StudyViewFilterUtil.java @@ -4,12 +4,9 @@ import org.apache.commons.collections4.map.MultiKeyMap; import org.cbioportal.model.Binnable; import org.cbioportal.model.ClinicalData; -import org.cbioportal.model.ClinicalDataBin; import org.cbioportal.model.ClinicalDataCount; import org.cbioportal.model.ClinicalDataCountItem; -import org.cbioportal.model.DataBin; import org.cbioportal.model.Gene; -import org.cbioportal.model.GeneFilterQuery; import org.cbioportal.model.Patient; import org.cbioportal.model.SampleList; import org.cbioportal.model.StructuralVariantFilterQuery; @@ -17,22 +14,7 @@ import org.cbioportal.service.GeneService; import org.cbioportal.service.util.CustomDataSession; import org.cbioportal.service.util.CustomDataValue; -import org.cbioportal.service.util.MolecularProfileUtil; -import org.cbioportal.web.parameter.ClinicalDataBinFilter; -import org.cbioportal.web.parameter.ClinicalDataFilter; -import org.cbioportal.web.parameter.DataBinFilter; -import org.cbioportal.web.parameter.DataFilter; -import org.cbioportal.web.parameter.DataFilterValue; -import org.cbioportal.web.parameter.GeneIdType; -import org.cbioportal.web.parameter.GenericAssayDataBinFilter; -import org.cbioportal.web.parameter.GenericAssayDataFilter; -import org.cbioportal.web.parameter.GenomicDataBinFilter; -import org.cbioportal.web.parameter.GenomicDataFilter; -import org.cbioportal.web.parameter.MutationDataFilter; -import org.cbioportal.web.parameter.MutationOption; -import org.cbioportal.web.parameter.Projection; -import org.cbioportal.web.parameter.SampleIdentifier; -import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.parameter.*; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.stereotype.Component; @@ -46,11 +28,17 @@ @Component public class StudyViewFilterUtil { - @Autowired - private MolecularProfileUtil molecularProfileUtil; + private final GeneService geneService; + @Autowired - private GeneService geneService; + public StudyViewFilterUtil(GeneService geneService) { + this.geneService = geneService; + } + + public StudyViewFilterUtil() { + geneService = null; + } public void extractStudyAndSampleIds( List sampleIdentifiers, @@ -125,22 +113,6 @@ public String getDataBinFilterUniqueKey(S dataBinFilte return null; } - public ClinicalDataBin dataBinToClinicalDataBin(ClinicalDataBinFilter attribute, DataBin dataBin) { - ClinicalDataBin clinicalDataBin = new ClinicalDataBin(); - clinicalDataBin.setAttributeId(attribute.getAttributeId()); - clinicalDataBin.setCount(dataBin.getCount()); - if (dataBin.getEnd() != null) { - clinicalDataBin.setEnd(dataBin.getEnd()); - } - if (dataBin.getSpecialValue() != null) { - clinicalDataBin.setSpecialValue(dataBin.getSpecialValue()); - } - if (dataBin.getStart() != null) { - clinicalDataBin.setStart(dataBin.getStart()); - } - return clinicalDataBin; - } - public Map> categorizeSampleLists(List sampleLists) { return sampleLists.stream().collect(Collectors.groupingBy(sampleList -> { return sampleList.getStableId().replace(sampleList.getCancerStudyIdentifier() + "_", ""); @@ -198,6 +170,7 @@ public List getClinicalDataCountsFromCustomData(Collectio }).distinct().count(); ClinicalDataCount dataCount = new ClinicalDataCount(); + dataCount.setAttributeId(customDataSession.getId()); dataCount.setValue(entry.getKey()); dataCount.setCount(Math.toIntExact(count)); return dataCount; @@ -225,7 +198,16 @@ public List getClinicalDataCountsFromCustomData(Collectio return clinicalDataCountItem; }).collect(Collectors.toList()); } + + public boolean isSingleStudyUnfiltered(StudyViewFilter filter) { + return isSingleStudy(filter) && isUnfilteredQuery(filter); + } + public boolean isSingleStudy(StudyViewFilter filter) { + return filter.getStudyIds() != null && + filter.getStudyIds().size() == 1; + } + public boolean isUnfilteredQuery(StudyViewFilter filter) { return filter.getStudyIds() != null && (filter.getClinicalDataFilters() == null || filter.getClinicalDataFilters().isEmpty()) && @@ -327,24 +309,7 @@ public List filterClinicalData( return combinedResult; } - public List cleanQueryGeneIds(List geneQueries) { - List hugoGeneSymbols = geneQueries - .stream() - .map(GeneFilterQuery::getHugoGeneSymbol) - .collect(Collectors.toList()); - - Map symbolToEntrezGeneId = getStringIntegerMap(hugoGeneSymbols); - - geneQueries.removeIf( - q -> !symbolToEntrezGeneId.containsKey(q.getHugoGeneSymbol()) - ); - geneQueries.stream().forEach( - q -> q.setEntrezGeneId(symbolToEntrezGeneId.get(q.getHugoGeneSymbol())) - ); - - return geneQueries; - } private Map getStringIntegerMap(List hugoGeneSymbols) { Map symbolToEntrezGeneId = geneService @@ -389,15 +354,6 @@ public List resolveEntrezGeneIds(List getHugoToEntrezQueryMap(List hugoGeneSymbols) { - Map symbolToEntrezGeneId = geneService - .fetchGenes(new ArrayList<>(hugoGeneSymbols), - GeneIdType.HUGO_GENE_SYMBOL.name(), Projection.SUMMARY.name()) - .stream() - .collect(Collectors.toMap(Gene::getHugoGeneSymbol, Gene::getEntrezGeneId)); - return symbolToEntrezGeneId; - } - private List filterClinicalDataByStudyAndSampleAndAttribute( List clinicalData, Map sampleToStudyId, diff --git a/src/main/resources/application.properties.EXAMPLE b/src/main/resources/application.properties.EXAMPLE index 77846a3cf60..32a73880501 100644 --- a/src/main/resources/application.properties.EXAMPLE +++ b/src/main/resources/application.properties.EXAMPLE @@ -4,7 +4,20 @@ app.name=cbioportal # Spring Boot Properties 2.7.14 spring.mvc.pathmatch.matching-strategy = ANT_PATH_MATCHER +#Clickhouse Enabled +# Set to True to enable Clickhouse (Warning Experimental Features) +#clickhouse_mode=false + # database +# Properties for when Clickhouse mode is enabled (Warning: Experimental) +#spring.datasource.mysql.url=jdbc:mysql://localhost:3306/cbioportal?useSSL=false +#spring.datasource.mysql.username=cbio +#spring.datasource.mysql.password=P@ssword1 +#spring.datasource.mysql.driver-class-name=com.mysql.jdbc.Driver +#spring.datasource.clickhouse.url=jdbc:ch://localhost:8443/cbioportal +#spring.datasource.clickhouse.username=dummy +#spring.datasource.clickhouse.password=dummy +#spring.datasource.clickhouse.driver-class-name=com.clickhouse.jdbc.ClickHouseDriver spring.datasource.url=jdbc:mysql://localhost:3306/cbioportal?useSSL=false spring.datasource.username=cbio spring.datasource.password=P@ssword1 diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql new file mode 100644 index 00000000000..db311282190 --- /dev/null +++ b/src/main/resources/db-scripts/clickhouse/clickhouse.sql @@ -0,0 +1,402 @@ +DROP TABLE IF EXISTS sample_to_gene_panel_derived; +DROP TABLE IF EXISTS gene_panel_to_gene_derived; +DROP TABLE IF EXISTS sample_derived; +DROP TABLE IF EXISTS genomic_event_derived; +DROP TABLE IF EXISTS clinical_data_derived; +DROP TABLE IF EXISTS clinical_event_derived; +DROP TABLE IF EXISTS genetic_alteration_derived; +DROP TABLE IF EXISTS generic_assay_data_derived; + +CREATE TABLE sample_to_gene_panel_derived +( + sample_unique_id String, + alteration_type LowCardinality(String), + gene_panel_id LowCardinality(String), + cancer_study_identifier LowCardinality(String), + genetic_profile_id LowCardinality(String) +) ENGINE = MergeTree() +ORDER BY (gene_panel_id, alteration_type, genetic_profile_id, sample_unique_id); + +INSERT INTO sample_to_gene_panel_derived +SELECT + concat(cs.cancer_study_identifier, '_', sample.stable_id) AS sample_unique_id, + genetic_alteration_type AS alteration_type, + -- If a mutation is found in a gene that is not in a gene panel we assume Whole Exome Sequencing WES + ifnull(gene_panel.stable_id, 'WES') AS gene_panel_id, + cs.cancer_study_identifier AS cancer_study_identifier, + gp.stable_id AS genetic_profile_id +FROM sample_profile sp + INNER JOIN genetic_profile gp ON sample_profile.genetic_profile_id = gp.genetic_profile_id + LEFT JOIN gene_panel ON sp.panel_id = gene_panel.internal_id + INNER JOIN sample ON sp.sample_id = sample.internal_id + INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id; + +CREATE TABLE gene_panel_to_gene_derived +( + gene_panel_id LowCardinality(String), + gene String +) ENGINE = MergeTree() +ORDER BY (gene_panel_id); + +INSERT INTO gene_panel_to_gene_derived +SELECT + gp.stable_id AS gene_panel_id, + g.hugo_gene_symbol AS gene +FROM gene_panel gp + INNER JOIN gene_panel_list gpl ON gp.internal_id = gpl.internal_id + INNER JOIN gene g ON g.entrez_gene_id = gpl.gene_id +UNION ALL +SELECT + 'WES' AS gene_panel_id, + gene.hugo_gene_symbol AS gene +FROM gene +WHERE gene.entrez_gene_id > 0 AND gene.type = 'protein-coding'; + +CREATE TABLE sample_derived +( + sample_unique_id String, + sample_unique_id_base64 String, + sample_stable_id String, + patient_unique_id String, + patient_unique_id_base64 String, + patient_stable_id String, + cancer_study_identifier LowCardinality(String), + internal_id Int +) + ENGINE = MergeTree + ORDER BY (cancer_study_identifier, sample_unique_id); + +INSERT INTO sample_derived +SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) AS sample_unique_id, + base64Encode(sample.stable_id) AS sample_unique_id_base64, + sample.stable_id AS sample_stable_id, + concat(cs.cancer_study_identifier, '_', p.stable_id) AS patient_unique_id, + base64Encode(p.stable_id) AS patient_unique_id_base64, + p.stable_id AS patient_stable_id, + cs.cancer_study_identifier AS cancer_study_identifier, + sample.internal_id AS internal_id +FROM sample + INNER JOIN patient AS p ON sample.patient_id = p.internal_id + INNER JOIN cancer_study AS cs ON p.cancer_study_id = cs.cancer_study_id; + +CREATE TABLE IF NOT EXISTS genomic_event_derived +( + sample_unique_id String, + hugo_gene_symbol String, + entrez_gene_id Int32, + gene_panel_stable_id LowCardinality(String), + cancer_study_identifier LowCardinality(String), + genetic_profile_stable_id LowCardinality(String), + variant_type LowCardinality(String), + mutation_variant String, + mutation_type LowCardinality(String), + mutation_status LowCardinality(String), + driver_filter LowCardinality(String), + driver_tiers_filter LowCardinality(String), + cna_alteration Nullable(Int8), + cna_cytoband String, + sv_event_info String, + patient_unique_id String +) ENGINE = MergeTree + ORDER BY ( variant_type, entrez_gene_id, hugo_gene_symbol, genetic_profile_stable_id, sample_unique_id); + +INSERT INTO genomic_event_derived +-- Insert Mutations +SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) AS sample_unique_id, + gene.hugo_gene_symbol AS hugo_gene_symbol, + gene.entrez_gene_id AS entrez_gene_id, + ifNull(gp.stable_id, 'WES') AS gene_panel_stable_id, + cs.cancer_study_identifier AS cancer_study_identifier, + g.stable_id AS genetic_profile_stable_id, + 'mutation' AS variant_type, + me.protein_change AS mutation_variant, + me.mutation_type AS mutation_type, + mutation.mutation_status AS mutation_status, + 'NA' AS driver_filter, + 'NA' AS drivet_tiers_filter, + NULL AS cna_alteration, + '' AS cna_cytoband, + '' AS sv_event_info, + concat(cs.cancer_study_identifier, '_', patient.stable_id) AS patient_unique_id +FROM mutation + INNER JOIN mutation_event AS me ON mutation.mutation_event_id = me.mutation_event_id + INNER JOIN sample_profile sp + ON mutation.sample_id = sp.sample_id AND mutation.genetic_profile_id = sp.genetic_profile_id + LEFT JOIN gene_panel gp ON sp.panel_id = gp.internal_id + LEFT JOIN genetic_profile g ON sp.genetic_profile_id = g.genetic_profile_id + INNER JOIN cancer_study cs ON g.cancer_study_id = cs.cancer_study_id + INNER JOIN sample ON mutation.sample_id = sample.internal_id + INNER JOIN patient on sample.patient_id = patient.internal_id + LEFT JOIN gene ON mutation.entrez_gene_id = gene.entrez_gene_id +UNION ALL +-- Insert CNA Genes +SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) AS sample_unique_id, + gene.hugo_gene_symbol AS hugo_gene_symbol, + gene.entrez_gene_id AS entrez_gene_id, + ifNull(gp.stable_id, 'WES') AS gene_panel_stable_id, + cs.cancer_study_identifier AS cancer_study_identifier, + g.stable_id AS genetic_profile_stable_id, + 'cna' AS variant_type, + 'NA' AS mutation_variant, + 'NA' AS mutation_type, + 'NA' AS mutation_status, + 'NA' AS driver_filter, + 'NA' AS drivet_tiers_filter, + ce.alteration AS cna_alteration, + rgg.cytoband AS cna_cytoband, + '' AS sv_event_info, + concat(cs.cancer_study_identifier, '_', patient.stable_id) AS patient_unique_id +FROM cna_event ce + INNER JOIN sample_cna_event sce ON ce.cna_event_id = sce.cna_event_id + INNER JOIN sample_profile sp ON sce.sample_id = sp.sample_id AND sce.genetic_profile_id = sp.genetic_profile_id + LEFT JOIN gene_panel gp ON sp.panel_id = gp.internal_id + INNER JOIN genetic_profile g ON sp.genetic_profile_id = g.genetic_profile_id + INNER JOIN cancer_study cs ON g.cancer_study_id = cs.cancer_study_id + INNER JOIN sample ON sce.sample_id = sample.internal_id + INNER JOIN patient on sample.patient_id = patient.internal_id + INNER JOIN gene ON ce.entrez_gene_id = gene.entrez_gene_id + INNER JOIN reference_genome_gene rgg ON rgg.entrez_gene_id = ce.entrez_gene_id AND rgg.reference_genome_id = cs.reference_genome_id +UNION ALL +-- Insert Structural Variants Site1 +SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) AS sample_unique_id, + gene.hugo_gene_symbol AS hugo_gene_symbol, + gene.entrez_gene_id AS entrez_gene_id, + ifNull(gene_panel.stable_id, 'WES') AS gene_panel_stable_id, + cs.cancer_study_identifier AS cancer_study_identifier, + gp.stable_id AS genetic_profile_stable_id, + 'structural_variant' AS variant_type, + 'NA' AS mutation_variant, + 'NA' AS mutation_type, + 'NA' AS mutation_status, + 'NA' AS driver_filter, + 'NA' AS drivet_tiers_filter, + NULL AS cna_alteration, + '' AS cna_cytoband, + event_info AS sv_event_info, + concat(cs.cancer_study_identifier, '_', patient.stable_id) AS patient_unique_id +FROM structural_variant sv + INNER JOIN genetic_profile gp ON sv.genetic_profile_id = gp.genetic_profile_id + INNER JOIN sample s ON sv.sample_id = s.internal_id + INNER JOIN patient on s.patient_id = patient.internal_id + INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id + INNER JOIN gene ON sv.site1_entrez_gene_id = gene.entrez_gene_id + INNER JOIN sample_profile ON s.internal_id = sample_profile.sample_id AND sample_profile.genetic_profile_id = sv.genetic_profile_id + LEFT JOIN gene_panel ON sample_profile.panel_id = gene_panel.internal_id +UNION ALL +-- Insert Structural Variants Site2 +SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) AS sample_unique_id, + gene.hugo_gene_symbol AS hugo_gene_symbol, + gene.entrez_gene_id AS entrez_gene_id, + ifNull(gene_panel.stable_id, 'WES') AS gene_panel_stable_id, + cs.cancer_study_identifier AS cancer_study_identifier, + gp.stable_id AS genetic_profile_stable_id, + 'structural_variant' AS variant_type, + 'NA' AS mutation_variant, + 'NA' AS mutation_type, + 'NA' AS mutation_status, + 'NA' AS driver_filter, + 'NA' AS drivet_tiers_filter, + NULL AS cna_alteration, + '' AS cna_cytoband, + event_info AS sv_event_info, + concat(cs.cancer_study_identifier, '_', patient.stable_id) AS patient_unique_id +FROM structural_variant sv + INNER JOIN genetic_profile gp ON sv.genetic_profile_id = gp.genetic_profile_id + INNER JOIN sample s ON sv.sample_id = s.internal_id + INNER JOIN patient on s.patient_id = patient.internal_id + INNER JOIN cancer_study cs ON gp.cancer_study_id = cs.cancer_study_id + INNER JOIN gene ON sv.site2_entrez_gene_id = gene.entrez_gene_id + INNER JOIN sample_profile ON s.internal_id = sample_profile.sample_id AND sample_profile.genetic_profile_id = sv.genetic_profile_id + LEFT JOIN gene_panel ON sample_profile.panel_id = gene_panel.internal_id +WHERE + sv.site2_entrez_gene_id != sv.site1_entrez_gene_id + OR sv.site1_entrez_gene_id IS NULL; + +CREATE TABLE IF NOT EXISTS clinical_data_derived +( + internal_id Int, + sample_unique_id String, + patient_unique_id String, + attribute_name LowCardinality(String), + attribute_value String, + cancer_study_identifier LowCardinality(String), + type LowCardinality(String) +) + ENGINE=MergeTree + ORDER BY (type, attribute_name, sample_unique_id); + +-- Insert sample attribute data +INSERT INTO TABLE clinical_data_derived +SELECT sm.internal_id AS internal_id, + sm.sample_unique_id AS sample_unique_id, + sm.patient_unique_id AS patient_unique_id, + cam.attr_id AS attribute_name, + ifNull(csamp.attr_value, '') AS attribute_value, + cs.cancer_study_identifier AS cancer_study_identifier, + 'sample' AS type +FROM sample_derived AS sm + INNER JOIN cancer_study AS cs + ON sm.cancer_study_identifier = cs.cancer_study_identifier + FULL OUTER JOIN clinical_attribute_meta AS cam + ON cs.cancer_study_id = cam.cancer_study_id + FULL OUTER JOIN clinical_sample AS csamp + ON (sm.internal_id = csamp.internal_id) AND (csamp.attr_id = cam.attr_id) +WHERE cam.patient_attribute = 0; + +-- INSERT patient attribute data +INSERT INTO TABLE clinical_data_derived +SELECT p.internal_id AS internal_id, + '' AS sample_unique_id, + concat(cs.cancer_study_identifier, '_', p.stable_id) AS patient_unique_id, + cam.attr_id AS attribute_name, + ifNull(clinpat.attr_value, '') AS attribute_value, + cs.cancer_study_identifier AS cancer_study_identifier, + 'patient' AS type +FROM patient AS p + INNER JOIN cancer_study AS cs ON p.cancer_study_id = cs.cancer_study_id + FULL OUTER JOIN clinical_attribute_meta AS cam + ON cs.cancer_study_id = cam.cancer_study_id + FULL OUTER JOIN clinical_patient AS clinpat + ON (p.internal_id = clinpat.internal_id) AND (clinpat.attr_id = cam.attr_id) +WHERE cam.patient_attribute = 1; + +CREATE TABLE clinical_event_derived +( + patient_unique_id String, + key String, + value String, + start_date Int32, + stop_date Int32 DEFAULT 0, + event_type LowCardinality(String), + cancer_study_identifier LowCardinality(String) +) +ENGINE = MergeTree + ORDER BY (event_type, patient_unique_id, cancer_study_identifier); + +INSERT INTO clinical_event_derived +SELECT + concat(cs.cancer_study_identifier, '_', p.stable_id) AS patient_unique_id, + ced.key AS key, + ced.value AS value, + ce.start_date AS start_date, + ifNull(ce.stop_date, 0) AS stop_date, + ce.event_type AS event_type, + cs.cancer_study_identifier +FROM clinical_event ce + LEFT JOIN clinical_event_data ced ON ce.clinical_event_id = ced.clinical_event_id + INNER JOIN patient p ON ce.patient_id = p.internal_id + INNER JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id; + +CREATE TABLE IF NOT EXISTS genetic_alteration_derived +( + sample_unique_id String, + cancer_study_identifier LowCardinality(String), + hugo_gene_symbol String, + profile_type LowCardinality(String), + alteration_value Nullable(String) + ) + ENGINE = MergeTree() + ORDER BY (cancer_study_identifier, hugo_gene_symbol, profile_type, sample_unique_id); + +INSERT INTO TABLE genetic_alteration_derived +SELECT + sample_unique_id, + cancer_study_identifier, + hugo_gene_symbol, + replaceOne(stable_id, concat(sd.cancer_study_identifier, '_'), '') as profile_type, + alteration_value +FROM + (SELECT + sample_id, + hugo_gene_symbol, + stable_id, + alteration_value + FROM + (SELECT + g.hugo_gene_symbol AS hugo_gene_symbol, + gp.stable_id as stable_id, + arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(substring(ga.values, 1, -1)))) AS alteration_value, + arrayMap(x -> (x = '' ? NULL : toInt32(x)), splitByString(',', assumeNotNull(substring(gps.ordered_sample_list, 1, -1)))) AS sample_id + FROM + genetic_profile gp + JOIN genetic_profile_samples gps ON gp.genetic_profile_id = gps.genetic_profile_id + JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id + JOIN gene g ON ga.genetic_entity_id = g.genetic_entity_id + WHERE + gp.genetic_alteration_type NOT IN ('GENERIC_ASSAY', 'MUTATION_EXTENDED', 'STRUCTURAL_VARIANT')) + ARRAY JOIN alteration_value, sample_id + WHERE alteration_value != 'NA') AS subquery + JOIN sample_derived sd ON sd.internal_id = subquery.sample_id; + +CREATE TABLE IF NOT EXISTS generic_assay_data_derived +( + sample_unique_id String, + patient_unique_id String, + genetic_entity_id String, + value String, + generic_assay_type String, + profile_stable_id String, + entity_stable_id String, + datatype String, + patient_level NUMERIC, + profile_type String +) + ENGINE = MergeTree() + ORDER BY (profile_type, entity_stable_id, patient_unique_id, sample_unique_id); + +INSERT INTO TABLE generic_assay_data_derived +SELECT + sd.sample_unique_id as sample_unique_id, + sd.patient_unique_id as patient_unique_id, + genetic_entity_id, + value, + generic_assay_type, + profile_stable_id, + entity_stable_id, + datatype, + patient_level, + replaceOne(profile_stable_id, concat(cs.cancer_study_identifier, '_'), '') as profile_type +FROM + (SELECT + sample_id, + genetic_entity_id, + value, + cancer_study_id, + generic_assay_type, + genetic_profile_id, + profile_stable_id, + entity_stable_id, + patient_level, + datatype + FROM + (SELECT + sample_id as sample_unique_id, + gp.cancer_study_id AS cancer_study_id, + ga.genetic_entity_id as genetic_entity_id, + gp.genetic_profile_id as genetic_profile_id, + gp.generic_assay_type as generic_assay_type, + gp.stable_id as profile_stable_id, + ge.stable_id as entity_stable_id, + gp.datatype as datatype, + gp.patient_level as patient_level, + arrayMap(x -> (x = '' ? NULL : x), splitByString(',', assumeNotNull(substring(ga.values, 1, -1)))) AS value, + arrayMap(x -> (x = '' ? NULL : toInt64(x)), splitByString(',', assumeNotNull(substring(gps.ordered_sample_list, 1, -1)))) AS sample_id + FROM genetic_profile gp + JOIN genetic_profile_samples gps ON gp.genetic_profile_id = gps.genetic_profile_id + JOIN genetic_alteration ga ON gp.genetic_profile_id = ga.genetic_profile_id + JOIN genetic_entity ge on ga.genetic_entity_id = ge.id + WHERE + gp.generic_assay_type IS NOT NULL + ) + ARRAY JOIN value, sample_id) AS subquery + JOIN cancer_study cs ON cs.cancer_study_id = subquery.cancer_study_id + JOIN sample_derived sd ON sd.internal_id = subquery.sample_id; + +OPTIMIZE TABLE sample_to_gene_panel_derived; +OPTIMIZE TABLE gene_panel_to_gene_derived; +OPTIMIZE TABLE sample_derived; +OPTIMIZE TABLE genomic_event_derived; +OPTIMIZE TABLE clinical_data_derived; +OPTIMIZE TABLE clinical_event_derived; +OPTIMIZE TABLE genetic_alteration_derived; +OPTIMIZE TABLE generic_assay_data_derived; diff --git a/src/main/resources/db-scripts/clickhouse/materialized_views.sql b/src/main/resources/db-scripts/clickhouse/materialized_views.sql new file mode 100644 index 00000000000..0bde005094b --- /dev/null +++ b/src/main/resources/db-scripts/clickhouse/materialized_views.sql @@ -0,0 +1,32 @@ +DROP TABLE IF EXISTS sample_list_columnstore; +DROP VIEW IF EXISTS sample_list_columnstore_mv; + +CREATE TABLE IF NOT EXISTS sample_list_columnstore +( + sample_unique_id VARCHAR(45), + sample_list_stable_id VARCHAR(45), + name VARCHAR(45), + cancer_study_identifier VARCHAR(45) +) + ENGINE = MergeTree + ORDER BY (sample_unique_id, sample_list_stable_id, name, cancer_study_identifier); + +INSERT INTO sample_list_columnstore +SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, + sl.stable_id as sample_list_stable_id, + sl.name as name, + cs.cancer_study_identifier as cancer_study_identifier +FROM sample_list as sl + INNER JOIN sample_list_list AS sll on sll.list_id = sl.list_id + INNER JOIN sample AS s on s.internal_id = sll.sample_id + INNER JOIN cancer_study cs on sl.cancer_study_id = cs.cancer_study_id; + +CREATE MATERIALIZED VIEW sample_list_columnstore_mv TO sample_list_columnstore AS +SELECT concat(cs.cancer_study_identifier, '_', s.stable_id) as sample_unique_id, + sl.stable_id as sample_list_stable_id, + sl.name as name, + cs.cancer_study_identifier as cancer_study_identifier +FROM sample_list as sl + INNER JOIN sample_list_list AS sll on sll.list_id = sl.list_id + INNER JOIN sample AS s on s.internal_id = sll.sample_id + INNER JOIN cancer_study cs on sl.cancer_study_id = cs.cancer_study_id; diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml index f9ff12ee766..828500a579c 100644 --- a/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml +++ b/src/main/resources/org/cbioportal/persistence/mybatis/ClinicalEventMapper.xml @@ -181,7 +181,7 @@ - Group by clinical_event.EVENT_TYPE, patient.STABLE_ID + Group by clinical_event.EVENT_TYPE, patient.INTERNAL_ID + SELECT + internal_id as internalId, + patient_stable_id as patientStableId, + sample_stable_id as stableId, + cancer_study_identifier as cancerStudyIdentifier, + sample_unique_id_base64 as uniqueSampleKey, + patient_unique_id_base64 as uniquePatientKey + FROM sample_derived + + + + + + ORDER BY sample_stable_id ASC + + + + + + + + + + + + + + + + + + + + + + + + + + + ( + WITH clinical_data_query AS ( + SELECT + attribute_name AS attributeId, + upper(attribute_value) AS value, + cast(count(*) AS INTEGER) as count + FROM clinical_data_derived + + type='${type}' + AND + + + + != 'NA' + AND + + + + + + + + + + + + + AND attribute_name IN + + #{attributeId} + + + GROUP BY attribute_name, value ), + clinical_data_sum AS (SELECT attributeId, sum(count) AS sum FROM clinical_data_query GROUP BY attributeId) + + SELECT * FROM clinical_data_query + UNION ALL + SELECT attributeId, + 'NA' AS value, + (( + + + + + + + + + ) - clinical_data_sum.sum) AS count + FROM clinical_data_sum + + count > 0 + + ) + + + + SELECT count(distinct sample_unique_id) as count + FROM sample_derived + WHERE sample_unique_id IN () + + + + SELECT count(distinct patient_unique_id) as count + FROM sample_derived sd + WHERE sample_unique_id IN () + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + SELECT patient_unique_id + FROM sample_derived + + sample_unique_id IN () + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sample_unique_id IN ( ) + + + + + + patient_unique_id in ( + SELECT patient_unique_id + FROM sample_derived + + sample_unique_id IN () + + ) + + + + sample_unique_id IN () + + + + + + multiIf( + -- This condition is to prevent casting non numerical values to float + NOT match(${attribute_value}, '^[><]?=?[-+]?[0-9]*[.,]?[0-9]+$'), + NULL, + (startsWith(${attribute_value}, '<=') OR startsWith(${attribute_value}, '>=')), + cast(substr(${attribute_value}, 3) as float), + startsWith(${attribute_value}, '<'), + cast(substr(${attribute_value}, 2) as float) - exp(-10), + startsWith(${attribute_value}, '>'), + cast(substr(${attribute_value}, 2) as float) + exp(-10), + cast(${attribute_value} as float) + ) + + + + + ${attribute_value}='' + OR upperUTF8(${attribute_value})='NA' + OR upperUTF8(${attribute_value})='NAN' + OR upperUTF8(${attribute_value})='N/A' + + + + multiIf( + + + , + 'NA', + ${attribute_value} + ) + + diff --git a/src/main/resources/templates/index.html b/src/main/resources/templates/index.html index 34cb24cc2f3..3b828ef82bd 100644 --- a/src/main/resources/templates/index.html +++ b/src/main/resources/templates/index.html @@ -32,7 +32,7 @@ window.netlify = localStorage.netlify; if (window.localdev || window.localdist) { - window.frontendConfig.frontendUrl = "//localhost:3000/" + window.frontendConfig.frontendUrl = "https://localhost:3000/" localStorage.setItem("e2etest", "true"); } else if (window.netlify) { window.frontendConfig.frontendUrl = ['//',localStorage.netlify,'.netlify.app','/'].join(''); diff --git a/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java b/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java new file mode 100644 index 00000000000..c2884acab53 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/helper/AlterationFilterHelperTest.java @@ -0,0 +1,167 @@ +package org.cbioportal.persistence.helper; + +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.MutationEventType; +import org.junit.Test; + +import java.util.HashMap; +import java.util.Map; + +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; + +public class AlterationFilterHelperTest { + + @Test + public void build() { + assertNotNull(AlterationFilterHelper.build(null)); + } + + @Test + public void getMutationTypeList() { + // Create AlterationFilter + AlterationFilter alterationFilter = new AlterationFilter(); + Map mutationEventTypeFilterMap = new HashMap<>(); + mutationEventTypeFilterMap.put(MutationEventType.nonsense_mutation, Boolean.TRUE); + mutationEventTypeFilterMap.put(MutationEventType.other, Boolean.FALSE); + alterationFilter.setMutationEventTypes(mutationEventTypeFilterMap); + + AlterationFilterHelper helper = AlterationFilterHelper.build(alterationFilter); + var mutationList = helper.getMutationTypeList(); + assertFalse(mutationList.hasNone()); + assertFalse(mutationList.hasAll()); + assertTrue(mutationList.hasValues()); + + } + + @Test + public void hasDriver() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeDriver(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasDriver()); + } + + @Test + public void hasVUSDriver() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeVUS(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasVUSDriver()); + } + + @Test + public void hasUnknownOncogenicity() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeUnknownOncogenicity(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasUnknownOncogenicity()); + } + + @Test + public void hasGermline() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeGermline(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasGermline()); + } + + @Test + public void hasSomatic() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeSomatic(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasSomatic()); + } + + @Test + public void hasUnknownMutationStatus() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeUnknownStatus(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasUnknownMutationStatus()); + } + + @Test + public void getSelectedTiers() { + AlterationFilter alterationFilter = new AlterationFilter(); + Map tiersMap = new HashMap<>(); + alterationFilter.setTiersBooleanMap(tiersMap); + assertNotNull(AlterationFilterHelper.build(alterationFilter).getSelectedTiers()); + } + + @Test + public void hasUnknownTier() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeUnknownTier(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).hasUnknownTier()); + } + + @Test + public void isAllDriverAnnotationSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeDriver(true); + alterationFilter.setIncludeVUS(true); + alterationFilter.setIncludeUnknownOncogenicity(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).isAllDriverAnnotationSelected()); + } + + @Test + public void isNoDriverAnnotationSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeDriver(false); + alterationFilter.setIncludeVUS(false); + alterationFilter.setIncludeUnknownOncogenicity(false); + assertTrue(AlterationFilterHelper.build(alterationFilter).isNoDriverAnnotationSelected()); + } + + @Test + public void isSomeDriverAnnotationsSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeDriver(true); + alterationFilter.setIncludeVUS(false); + alterationFilter.setIncludeUnknownOncogenicity(false); + assertTrue(AlterationFilterHelper.build(alterationFilter).isSomeDriverAnnotationsSelected()); + } + + @Test + public void isAllMutationStatusSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeGermline(true); + alterationFilter.setIncludeSomatic(true); + alterationFilter.setIncludeUnknownStatus(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).isAllMutationStatusSelected()); + } + + @Test + public void isNoMutationStatusSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeGermline(false); + alterationFilter.setIncludeSomatic(false); + alterationFilter.setIncludeUnknownStatus(false); + assertTrue(AlterationFilterHelper.build(alterationFilter).isNoMutationStatusSelected()); + } + + @Test + public void isSomeMutationStatusSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeGermline(false); + alterationFilter.setIncludeSomatic(true); + alterationFilter.setIncludeUnknownStatus(false); + assertTrue(AlterationFilterHelper.build(alterationFilter).isSomeMutationStatusSelected()); + } + + @Test + public void isAllTierOptionsSelected() { + AlterationFilter alterationFilter = new AlterationFilter(); + Map tiersMap = new HashMap<>(); + alterationFilter.setTiersBooleanMap(tiersMap); + alterationFilter.setIncludeUnknownTier(true); + assertTrue(AlterationFilterHelper.build(alterationFilter).isAllTierOptionsSelected()); + } + + @Test + public void shouldApply() { + AlterationFilter alterationFilter = new AlterationFilter(); + alterationFilter.setIncludeDriver(true); + alterationFilter.setIncludeVUS(false); + alterationFilter.setIncludeUnknownOncogenicity(false); + assertTrue(AlterationFilterHelper.build(alterationFilter).shouldApplyMutationAlterationFilter()); + + } +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java b/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java new file mode 100644 index 00000000000..f9044f09d37 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/helper/StudyViewFilterHelperTest.java @@ -0,0 +1,110 @@ +package org.cbioportal.persistence.helper; + +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.junit.Test; + +import java.math.BigDecimal; +import java.util.ArrayList; +import java.util.List; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNull; + +public class StudyViewFilterHelperTest { + + // (-5, -1], (-1, 3], (3, 7] -> (-5, 7] + @Test + public void testMergeDataFilterNumericalContinuousValues() { + List genomicDataFilters = new ArrayList<>(); + List values = new ArrayList<>(); + values.add(new DataFilterValue(BigDecimal.valueOf(-5), BigDecimal.valueOf(-1), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-1), BigDecimal.valueOf(3), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(3), BigDecimal.valueOf(7), null)); + genomicDataFilters.add(new GenomicDataFilter(null, null, values)); + + List mergedGenomicDataFilters = StudyViewFilterHelper.mergeDataFilters(genomicDataFilters); + List mergedDataFilterValues = mergedGenomicDataFilters.getFirst().getValues(); + BigDecimal start = mergedDataFilterValues.getFirst().getStart(); + BigDecimal end = mergedDataFilterValues.getFirst().getEnd(); + assertEquals(0, BigDecimal.valueOf(-5).compareTo(start)); + assertEquals(0, BigDecimal.valueOf(7).compareTo(end)); + } + + // (-2.5, -2.25], (-2.25, -2], (-1.75, -1.5], (-1.5, -1.25] -> (-2.5, -2], (-1.75, -1.25] + @Test + public void testMergeDataFilterNumericalDiscontinuousValues() { + List genomicDataFilters = new ArrayList<>(); + List values = new ArrayList<>(); + values.add(new DataFilterValue(BigDecimal.valueOf(-2.5), BigDecimal.valueOf(-2.25), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-2.25), BigDecimal.valueOf(-2), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-1.75), BigDecimal.valueOf(-1.5), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-1.5), BigDecimal.valueOf(-1.25), null)); + genomicDataFilters.add(new GenomicDataFilter(null, null, values)); + + List mergedGenomicDataFilters = StudyViewFilterHelper.mergeDataFilters(genomicDataFilters); + List mergedDataFilterValues = mergedGenomicDataFilters.getFirst().getValues(); + BigDecimal firstStart = mergedDataFilterValues.getFirst().getStart(); + BigDecimal firstEnd = mergedDataFilterValues.getFirst().getEnd(); + assertEquals(0, BigDecimal.valueOf(-2.5).compareTo(firstStart)); + assertEquals(0, BigDecimal.valueOf(-2).compareTo(firstEnd)); + + BigDecimal secondStart = mergedDataFilterValues.get(1).getStart(); + BigDecimal secondEnd = mergedDataFilterValues.get(1).getEnd(); + assertEquals(0, BigDecimal.valueOf(-1.75).compareTo(secondStart)); + assertEquals(0, BigDecimal.valueOf(-1.25).compareTo(secondEnd)); + } + + // (null, -2.25], (-2.25, -2], (-2, null] -> (null, null] + @Test + public void testMergeDataFilterNumericalInfiniteValues() { + List genomicDataFilters = new ArrayList<>(); + List values = new ArrayList<>(); + values.add(new DataFilterValue(null, BigDecimal.valueOf(-2.25), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-2.25), BigDecimal.valueOf(-2), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-2), null, null)); + genomicDataFilters.add(new GenomicDataFilter(null, null, values)); + + List mergedGenomicDataFilters = StudyViewFilterHelper.mergeDataFilters(genomicDataFilters); + List mergedDataFilterValues = mergedGenomicDataFilters.getFirst().getValues(); + BigDecimal start = mergedDataFilterValues.getFirst().getStart(); + BigDecimal end = mergedDataFilterValues.getFirst().getEnd(); + assertNull(start); + assertNull(end); + } + + // (-2.5, -2.25], (-2.25, -2], "NA" -> (-2.5, -1.75], "NA" + // This test also ensures the non-numerical values gets moved to the end + @Test + public void testMergeDataFilterNumericalNonNumericalValues() { + List genomicDataFilters = new ArrayList<>(); + List values = new ArrayList<>(); + values.add(new DataFilterValue(BigDecimal.valueOf(-2.5), BigDecimal.valueOf(-2.25), null)); + values.add(new DataFilterValue(BigDecimal.valueOf(-2.25), BigDecimal.valueOf(-2), null)); + values.add(new DataFilterValue(null, null, "NA")); + genomicDataFilters.add(new GenomicDataFilter(null, null, values)); + + List mergedGenomicDataFilters = StudyViewFilterHelper.mergeDataFilters(genomicDataFilters); + List mergedDataFilterValues = mergedGenomicDataFilters.getFirst().getValues(); + BigDecimal start = mergedDataFilterValues.getFirst().getStart(); + BigDecimal end = mergedDataFilterValues.getFirst().getEnd(); + String value = mergedDataFilterValues.get(1).getValue(); + assertEquals(0, BigDecimal.valueOf(-2.5).compareTo(start)); + assertEquals(0, BigDecimal.valueOf(-2).compareTo(end)); + assertEquals("NA", value); + } + + // "NA" -> "NA" + @Test + public void testMergeDataFilterNonNumericalOnlyValues() { + List genomicDataFilters = new ArrayList<>(); + List values = new ArrayList<>(); + values.add(new DataFilterValue(null, null, "NA")); + genomicDataFilters.add(new GenomicDataFilter(null, null, values)); + + List mergedGenomicDataFilters = StudyViewFilterHelper.mergeDataFilters(genomicDataFilters); + List mergedDataFilterValues = mergedGenomicDataFilters.getFirst().getValues(); + String value = mergedDataFilterValues.getFirst().getValue(); + assertEquals("NA", value); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java new file mode 100644 index 00000000000..65708c5a205 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/AbstractTestcontainers.java @@ -0,0 +1,48 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.junit.BeforeClass; + +import org.junit.ClassRule; +import org.springframework.boot.test.util.TestPropertyValues; +import org.springframework.context.ApplicationContextInitializer; +import org.springframework.context.ConfigurableApplicationContext; +import org.testcontainers.clickhouse.ClickHouseContainer; +import org.testcontainers.containers.BindMode; + + +public abstract class AbstractTestcontainers { + @BeforeClass + public static void beforeAll() { + + } + + @ClassRule + public static final ClickHouseContainer clickhouseContainer = + new ClickHouseContainer("clickhouse/clickhouse-server:24.5") + .withUsername("cbio_user") + .withPassword("P@ssword1") + .withClasspathResourceMapping("clickhouse_cgds.sql", "/docker-entrypoint-initdb.d/a_schema.sql", + BindMode.READ_ONLY) + .withClasspathResourceMapping("clickhouse_data.sql", "/docker-entrypoint-initdb.d/b_schema.sql", + BindMode.READ_ONLY) + .withClasspathResourceMapping("clickhouse/clickhouse.sql", "/docker-entrypoint-initdb.d/c_schema.sql", + BindMode.READ_ONLY) + .withClasspathResourceMapping("clickhouse/materialized_views.sql", "/docker-entrypoint-initdb.d/d_schema.sql", + BindMode.READ_ONLY); + + public static class Initializer implements ApplicationContextInitializer { + + @Override + public void initialize(ConfigurableApplicationContext configurableApplicationContext) { + TestPropertyValues values = TestPropertyValues.of( + "spring.datasource.clickhouse.url=" + clickhouseContainer.getJdbcUrl(), + "spring.datasource.clickhouse.password=" + clickhouseContainer.getPassword(), + "spring.datasource.clickhouse.username=" + clickhouseContainer.getUsername(), + "spring.datasource.clickhouse.driver-class-name=com.clickhouse.jdbc.ClickHouseDriver" + ); + values.applyTo(configurableApplicationContext); + } + } + +} + diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java new file mode 100644 index 00000000000..18df4041406 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java @@ -0,0 +1,76 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.CNA; +import org.cbioportal.persistence.helper.AlterationFilterHelper; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class CNAGenesTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getCnaGenes() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + var alterationCountByGenes = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(studyViewFilter.getAlterationFilter())); + assertEquals(3, alterationCountByGenes.size()); + + // Test cna count for akt1 + var testAKT1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "AKT1")) + .mapToInt(c -> c.getTotalCount().intValue()) + .sum(); + assertEquals(3, testAKT1AlterationCount); + } + + @Test + public void getCnaGenesWithAlterationFilter() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + // Create AlterationFilter + AlterationFilter alterationFilter = new AlterationFilter(); + Map cnaEventTypeFilterMap = new HashMap<>(); + cnaEventTypeFilterMap.put(CNA.HOMDEL, false); + cnaEventTypeFilterMap.put(CNA.AMP, true); + alterationFilter.setCopyNumberAlterationEventTypes(cnaEventTypeFilterMap); + + var alterationCountByGenes = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(alterationFilter)); + assertEquals(2, alterationCountByGenes.size()); + + // Test cna count for akt1 filtering for AMP + var testAKT1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "AKT1")) + .mapToInt(c -> c.getTotalCount().intValue()) + .sum(); + assertEquals(2, testAKT1AlterationCount); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java new file mode 100644 index 00000000000..00bf968c29d --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalEventTypeCountsTest.java @@ -0,0 +1,67 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.DataFilter; +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class ClinicalEventTypeCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getClinicalEventTypeCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var clinicalEventTypeCounts = studyViewMapper.getClinicalEventTypeCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + assertEquals(4, clinicalEventTypeCounts.size()); + + var clinicalEventTypeCountOptional = clinicalEventTypeCounts.stream().filter(ce -> ce.getEventType().equals("Treatment")) + .findFirst(); + + assertTrue(clinicalEventTypeCountOptional.isPresent()); + assertEquals(1, clinicalEventTypeCountOptional.get().getCount().intValue()); + + DataFilter dataFilter = new DataFilter(); + DataFilterValue dataFilterValue = new DataFilterValue(); + dataFilterValue.setValue("Treatment"); + dataFilter.setValues(List.of(dataFilterValue)); + studyViewFilter.setClinicalEventFilters(List.of(dataFilter)); + + clinicalEventTypeCounts = studyViewMapper.getClinicalEventTypeCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + assertEquals(3, clinicalEventTypeCounts.size()); + + clinicalEventTypeCountOptional = clinicalEventTypeCounts.stream().filter(ce -> ce.getEventType().equals("status")) + .findFirst(); + + assertFalse(clinicalEventTypeCountOptional.isPresent()); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java new file mode 100644 index 00000000000..d4926855e97 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/FilteredSamplesTest.java @@ -0,0 +1,172 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.web.parameter.CustomSampleIdentifier; +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.math.BigDecimal; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class FilteredSamplesTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_ACC_TCGA = "acc_tcga"; + private static final String STUDY_GENIE_PUB = "study_genie_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getFilteredSamples() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(Arrays.asList(STUDY_TCGA_PUB, STUDY_ACC_TCGA)); + var filteredSamples = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + assertEquals(19, filteredSamples.size()); + + ClinicalDataFilter customDataFilter = new ClinicalDataFilter(); + customDataFilter.setAttributeId("123"); + DataFilterValue value = new DataFilterValue(); + customDataFilter.setValues(List.of(value)); + studyViewFilter.setCustomDataFilters(List.of(customDataFilter)); + var filteredSamples1 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + assertEquals(0, filteredSamples1.size()); + + CustomSampleIdentifier customSampleIdentifier = new CustomSampleIdentifier(); + customSampleIdentifier.setStudyId("acc_tcga"); + customSampleIdentifier.setSampleId("tcga-a1-a0sb-01"); + var filteredSamples2 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, Arrays.asList(customSampleIdentifier), studyViewFilter.getStudyIds())); + assertEquals(1, filteredSamples2.size()); + } + + @Test + public void getSamplesFilteredByClinicalData() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(Arrays.asList(STUDY_GENIE_PUB, STUDY_ACC_TCGA)); + + // samples of patients with AGE <= 20.0 + studyViewFilter.setClinicalDataFilters( + List.of( + newClinicalDataFilter( + "age", List.of( + newDataFilterValue(null, 20.0, null) + ) + ) + ) + ); + var filteredSamples1 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + assertEquals(4, filteredSamples1.size()); + + // samples of patients with AGE <= 20.0 or (80.0, 82.0] + studyViewFilter.setClinicalDataFilters( + List.of( + newClinicalDataFilter( + "age", List.of( + newDataFilterValue(null, 20.0, null), + newDataFilterValue(80.0, 82.0, null) + ) + ) + ) + ); + var filteredSamples2 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + assertEquals(6, filteredSamples2.size()); + + // samples of patients with UNKNOWN AGE + studyViewFilter.setClinicalDataFilters( + List.of( + newClinicalDataFilter( + "age", List.of( + newDataFilterValue(null, null, "Unknown") + ) + ) + ) + ); + var filteredSamples3 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + assertEquals(1, filteredSamples3.size()); + + // samples of patients with AGE <= 20.0 or (80.0, 82.0] or UNKNOWN + // this is a mixed list of filters of both numerical and non-numerical values + studyViewFilter.setClinicalDataFilters( + List.of( + newClinicalDataFilter( + "age", List.of( + newDataFilterValue(null, 20.0, null), + newDataFilterValue(80.0, 82.0, null), + newDataFilterValue(null, null, "unknown") + ) + ) + ) + ); + var filteredSamples4 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + assertEquals(7, filteredSamples4.size()); + + // NA filter + studyViewFilter.setClinicalDataFilters( + List.of( + newClinicalDataFilter( + "age", List.of( + newDataFilterValue(null, null, "NA") + ) + ) + ) + ); + var filteredSamples5 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + // 4 acc_tcga + 7 study_genie_pub samples with "NA" AGE data or no AGE data + assertEquals(11, filteredSamples5.size()); + + // NA + UNKNOWN + studyViewFilter.setClinicalDataFilters( + List.of( + newClinicalDataFilter( + "age", List.of( + newDataFilterValue(null, null, "NA"), + newDataFilterValue(null, null, "UNKNOWN") + ) + ) + ) + ); + var filteredSamples6 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>(), studyViewFilter.getStudyIds())); + // 11 NA + 1 UNKNOWN + assertEquals(12, filteredSamples6.size()); + } + + private DataFilterValue newDataFilterValue(Double start, Double end, String value) { + DataFilterValue dataFilterValue = new DataFilterValue(); + + dataFilterValue.setStart(start == null ? null : new BigDecimal(start)); + dataFilterValue.setEnd(end == null ? null: new BigDecimal(end)); + dataFilterValue.setValue(value); + + return dataFilterValue; + } + + private ClinicalDataFilter newClinicalDataFilter(String attributeId, List values) { + ClinicalDataFilter clinicalDataFilter = new ClinicalDataFilter(); + + clinicalDataFilter.setAttributeId(attributeId); + clinicalDataFilter.setValues(values); + + return clinicalDataFilter; + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java new file mode 100644 index 00000000000..086b18593df --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenericAssayDataCountsTest.java @@ -0,0 +1,87 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.GenericAssayDataCount; +import org.cbioportal.model.GenericAssayDataCountItem; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.GenericAssayDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.assertj.core.api.Assertions.assertThat; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class GenericAssayDataCountsTest extends AbstractTestcontainers { + + private static final String ACC_TCGA = "acc_tcga"; + private static final String STUDY_GENIE_PUB = "study_genie_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getSampleCategoricalGenericAssayDataCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(ACC_TCGA)); + + GenericAssayDataFilter genericAssayDataFilter = new GenericAssayDataFilter("1p_status", "armlevel_cna"); + List actualCounts = studyViewMapper.getGenericAssayDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of(genericAssayDataFilter) + ); + + List expectedCounts = List.of( + new GenericAssayDataCountItem("1p_status", List.of( + new GenericAssayDataCount("Loss", 1), + new GenericAssayDataCount("Gain", 1), + new GenericAssayDataCount("Unchanged", 1), + new GenericAssayDataCount("NA", 1) + )) + ); + + assertThat(actualCounts) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedCounts); + } + + @Test + public void getPatientCategoricalGenericAssayDataCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + GenericAssayDataFilter genericAssayDataFilter = new GenericAssayDataFilter("DMETS_DX_ADRENAL", "distant_mets"); + List actualCounts = studyViewMapper.getGenericAssayDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of(genericAssayDataFilter) + ); + + List expectedCounts = List.of( + new GenericAssayDataCountItem("DMETS_DX_ADRENAL", List.of( + new GenericAssayDataCount("No", 9), + new GenericAssayDataCount("Yes", 1), + new GenericAssayDataCount("NA", 14) + )) + ); + + assertThat(actualCounts) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedCounts); + } +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java new file mode 100644 index 00000000000..9e569b0e4a1 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/GenomicDataCountsTest.java @@ -0,0 +1,73 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.assertj.core.api.Assertions.assertThat; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class GenomicDataCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getCNACounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + GenomicDataFilter genomicDataFilterCNA = new GenomicDataFilter("AKT1", "cna"); + List actualCountsCNA = studyViewMapper.getCNACounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), List.of(genomicDataFilterCNA)); + List expectedCountsCNA = List.of( + new GenomicDataCountItem("AKT1", "cna", List.of( + new GenomicDataCount("Homozygously deleted", "-2", 2), + new GenomicDataCount("Heterozygously deleted", "-1", 2), + new GenomicDataCount("Diploid", "0", 2), + new GenomicDataCount("Gained", "1", 2), + new GenomicDataCount("Amplified", "2", 2), + new GenomicDataCount("NA", "NA", 5) + ))); + assertThat(actualCountsCNA) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedCountsCNA); + + GenomicDataFilter genomicDataFilterGISTIC = new GenomicDataFilter("AKT1", "gistic"); + List actualCountsGISTIC = studyViewMapper.getCNACounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), List.of(genomicDataFilterGISTIC)); + List expectedCountsGISTIC = List.of( + new GenomicDataCountItem("AKT1", "gistic", List.of( + new GenomicDataCount("Homozygously deleted", "-2", 2), + new GenomicDataCount("Heterozygously deleted", "-1", 3), + new GenomicDataCount("Diploid", "0", 3), + new GenomicDataCount("Gained", "1", 3), + new GenomicDataCount("Amplified", "2", 3), + new GenomicDataCount("NA", "NA", 1) + ))); + assertThat(actualCountsGISTIC) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedCountsGISTIC); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java new file mode 100644 index 00000000000..f9748a09110 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MolecularProfileCountTest.java @@ -0,0 +1,119 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; + +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class MolecularProfileCountTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_ACC_TCGA = "acc_tcga"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getMolecularProfileCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var profiles = new ArrayList(Arrays.asList("mutations")); + var profileGroups = new ArrayList>(Arrays.asList(profiles)); + + studyViewFilter.setGenomicProfiles(profileGroups); + + var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + var size = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations")) + .findFirst().get().getCount().intValue(); + assertEquals(11, size); + + } + + @Test + public void getMolecularProfileCountsMultipleStudies() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_ACC_TCGA)); + + var profiles = new ArrayList(Arrays.asList("mutations")); + var profileGroups = new ArrayList>(Arrays.asList(profiles)); + + studyViewFilter.setGenomicProfiles(profileGroups); + + var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + var size = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations")) + .findFirst().get().getCount().intValue(); + assertEquals(11, size); + + } + + @Test + public void getMolecularProfileCountsMultipleProfilesUnion() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var profiles = new ArrayList(Arrays.asList("mutations","mrna")); + var profileGroups = new ArrayList>(Arrays.asList(profiles)); + + studyViewFilter.setGenomicProfiles(profileGroups); + + var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + var sizeMutations = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations")) + .findFirst().get().getCount().intValue(); + assertEquals(11, sizeMutations); + + var sizeMrna = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mrna")) + .findFirst().get().getCount().intValue(); + assertEquals(9, sizeMrna); + + } + + @Test + public void getMolecularProfileCountsMultipleProfilesIntersect() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var profile1 = new ArrayList(Arrays.asList("mutations")); + var profile2 = new ArrayList(Arrays.asList("mrna")); + var profileGroups = new ArrayList>(Arrays.asList(profile1, profile2)); + + studyViewFilter.setGenomicProfiles(profileGroups); + + var molecularProfileCounts = studyViewMapper.getMolecularProfileSampleCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + var sizeMutations = molecularProfileCounts.stream().filter(gc->gc.getValue().equals("mutations")) + .findFirst().get().getCount().intValue(); + assertEquals(10, sizeMutations); + + + + } + + + + +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java new file mode 100644 index 00000000000..dd8001ded6f --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutatedGenesTest.java @@ -0,0 +1,89 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.MutationEventType; +import org.cbioportal.persistence.helper.AlterationFilterHelper; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class MutatedGenesTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getMutatedGenes() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + var alterationCountByGenes = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(studyViewFilter.getAlterationFilter())); + assertEquals(3, alterationCountByGenes.size()); + + var testBrca1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "BRCA1")).findFirst(); + assert (testBrca1AlterationCount.isPresent()); + assertEquals(Integer.valueOf(5), testBrca1AlterationCount.get().getTotalCount()); + } + + @Test + public void getMutatedGenesWithAlterationFilter() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + // Create AlterationFilter + AlterationFilter alterationFilter = new AlterationFilter(); + Map mutationEventTypeFilterMap = new HashMap<>(); + mutationEventTypeFilterMap.put(MutationEventType.nonsense_mutation, Boolean.TRUE); + mutationEventTypeFilterMap.put(MutationEventType.other, Boolean.FALSE); + alterationFilter.setMutationEventTypes(mutationEventTypeFilterMap); + + var alterationCountByGenes = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(alterationFilter)); + assertEquals(2, alterationCountByGenes.size()); + + AlterationFilter onlyMutationStatusFilter = new AlterationFilter(); + onlyMutationStatusFilter.setMutationEventTypes(new HashMap<>()); + onlyMutationStatusFilter.setIncludeGermline(false); + onlyMutationStatusFilter.setIncludeSomatic(false); + onlyMutationStatusFilter.setIncludeUnknownStatus(true); + + var alterationCountByGenes1 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(onlyMutationStatusFilter)); + assertEquals(1, alterationCountByGenes1.size()); + + AlterationFilter mutationTypeAndStatusFilter = new AlterationFilter(); + mutationTypeAndStatusFilter.setMutationEventTypes(mutationEventTypeFilterMap); + mutationTypeAndStatusFilter.setMutationEventTypes(new HashMap<>()); + mutationTypeAndStatusFilter.setIncludeGermline(false); + mutationTypeAndStatusFilter.setIncludeSomatic(false); + mutationTypeAndStatusFilter.setIncludeUnknownStatus(true); + + var alterationCountByGenes2 = studyViewMapper.getMutatedGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(onlyMutationStatusFilter)); + assertEquals(1, alterationCountByGenes2.size()); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java new file mode 100644 index 00000000000..d04adb06575 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java @@ -0,0 +1,72 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import static org.assertj.core.api.Assertions.assertThat; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class MutationDataCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getMutationCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "cna"); + Map actualMutationCounts = studyViewMapper.getMutationCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), genomicDataFilterMutation); + Map expectedMutationCounts = new HashMap<>(); + expectedMutationCounts.put("mutatedCount", 2); + expectedMutationCounts.put("notMutatedCount", 8); + expectedMutationCounts.put("notProfiledCount", 5); + assertThat(actualMutationCounts) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedMutationCounts); + } + + @Test + public void getMutationCountsByType() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + GenomicDataFilter genomicDataFilterMutation = new GenomicDataFilter("AKT1", "mutation"); + List actualMutationCountsByType = studyViewMapper.getMutationCountsByType(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), List.of(genomicDataFilterMutation)); + List expectedMutationCountsByType = List.of( + new GenomicDataCountItem("AKT1", "mutations", List.of( + new GenomicDataCount("nonsense mutation", "nonsense_mutation", 2, 1), + new GenomicDataCount("missense mutation", "missense_mutation", 1, 1) + ))); + assertThat(actualMutationCountsByType) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedMutationCountsByType); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java new file mode 100644 index 00000000000..b23fc8f266f --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/PatientTreatmentCountsTest.java @@ -0,0 +1,67 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.parameter.filter.AndedPatientTreatmentFilters; +import org.cbioportal.web.parameter.filter.OredPatientTreatmentFilters; +import org.cbioportal.web.parameter.filter.PatientTreatmentFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class PatientTreatmentCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getPatientTreatmentReportCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + + var patientTreatmentCounts = studyViewMapper.getPatientTreatmentCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + var patientTreatments = studyViewMapper.getPatientTreatments(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + assertEquals(1, patientTreatmentCounts); + assertEquals("madeupanib", patientTreatments.getFirst().treatment()); + + PatientTreatmentFilter filter = new PatientTreatmentFilter(); + filter.setTreatment("madeupanib"); + + OredPatientTreatmentFilters oredPatientTreatmentFilters = new OredPatientTreatmentFilters(); + oredPatientTreatmentFilters.setFilters(List.of(filter)); + + AndedPatientTreatmentFilters andedPatientTreatmentFilters = new AndedPatientTreatmentFilters(); + andedPatientTreatmentFilters.setFilters(List.of(oredPatientTreatmentFilters)); + studyViewFilter.setPatientTreatmentFilters(andedPatientTreatmentFilters); + + patientTreatmentCounts = studyViewMapper.getPatientTreatmentCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + patientTreatments = studyViewMapper.getPatientTreatments(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + assertEquals(1, patientTreatmentCounts); + assertEquals("madeupanib", patientTreatments.getFirst().treatment()); + + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java new file mode 100644 index 00000000000..aa3e4a12f4f --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProfiledCountsTest.java @@ -0,0 +1,145 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class ProfiledCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_GENIE_PUB = "study_genie_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getTotalProfiledCountsByGene() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + // Testing profiled counts on samples with gene panel data and WES for one study + var totalProfiledCountsForMutationsMap = studyViewMapper.getTotalProfiledCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "MUTATION_EXTENDED", List.of()); + var totalProfiledCountsForCnaMap = studyViewMapper.getTotalProfiledCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "COPY_NUMBER_ALTERATION", List.of()); + var sampleProfiledCountsForMutationsWithoutPanelDataMap = studyViewMapper.getSampleProfileCountWithoutPanelData(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "MUTATION_EXTENDED"); + var sampleProfiledCountsForCnaWithoutPanelDataMap = studyViewMapper.getSampleProfileCountWithoutPanelData(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "COPY_NUMBER_ALTERATION"); + + // Assert the count of genes with profiled cases for mutations + assertEquals(5, totalProfiledCountsForMutationsMap.size()); + // Assert the count of genes with profiled cases for CNA + assertEquals(5, totalProfiledCountsForCnaMap.size()); + // Assert the profiled counts for mutations without panel data (WES) + assertEquals(6, sampleProfiledCountsForMutationsWithoutPanelDataMap); + // Assert the profiled counts for CNA without panel data (WES) + assertEquals(11, sampleProfiledCountsForCnaWithoutPanelDataMap); + + // Assert the profiled counts for AKT2 mutations + // AKT2 is on testpanel2 in STUDY_TCGA_PUB + var akt2TotalProfiledCountsForMutations = totalProfiledCountsForMutationsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2")).findFirst(); + assertTrue(akt2TotalProfiledCountsForMutations.isPresent()); + assertEquals(4, akt2TotalProfiledCountsForMutations.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for BRCA1 mutations + // BRCA1 is on testpanel1 in STUDY_TCGA_PUB + var brca1TotalProfiledCountsForMutations = totalProfiledCountsForMutationsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA1")).findFirst(); + assertTrue(brca1TotalProfiledCountsForMutations.isPresent()); + assertEquals(1, brca1TotalProfiledCountsForMutations.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for AKT1 mutations + // AKT1 is on both testpanel1 and testpanel2 in STUDY_TCGA_PUB + var akt1TotalProfiledCountsForMutations = totalProfiledCountsForMutationsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT1")).findFirst(); + assertTrue(akt1TotalProfiledCountsForMutations.isPresent()); + assertEquals(5, akt1TotalProfiledCountsForMutations.get().getNumberOfProfiledCases().intValue()); + + // Assert the profiled counts for AKT2 CNA + // AKT2 is on testpanel2 in STUDY_TCGA_PUB + var akt2TotalProfiledCountsForCna = totalProfiledCountsForCnaMap.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2")).findFirst(); + assertTrue(akt2TotalProfiledCountsForCna.isPresent()); + assertEquals(6, akt2TotalProfiledCountsForCna.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for BRCA1 CNA + // BRCA1 is on testpanel1 in STUDY_TCGA_PUB + var brca1TotalProfiledCountsForCna = totalProfiledCountsForCnaMap.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA1")).findFirst(); + assertTrue(brca1TotalProfiledCountsForCna.isPresent()); + assertEquals(2, brca1TotalProfiledCountsForCna.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for AKT1 CNA + // AKT1 is on both testpanel1 and testpanel2 in STUDY_TCGA_PUB + var akt1TotalProfiledCountsForCna = totalProfiledCountsForCnaMap.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT1")).findFirst(); + assertTrue(akt1TotalProfiledCountsForCna.isPresent()); + assertEquals(8, akt1TotalProfiledCountsForCna.get().getNumberOfProfiledCases().intValue()); + + // Testing profiled counts on combined studies + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_GENIE_PUB)); + + // Testing profiled counts on samples with gene panel data and WES for a combined study + var totalProfiledCountsForMutationsMap1 = studyViewMapper.getTotalProfiledCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "MUTATION_EXTENDED", List.of()); + var totalProfiledCountsForCnaMap1 = studyViewMapper.getTotalProfiledCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "COPY_NUMBER_ALTERATION", List.of()); + var sampleProfiledCountsForMutationsWithoutPanelDataMap1 = studyViewMapper.getSampleProfileCountWithoutPanelData(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "MUTATION_EXTENDED"); + var sampleProfiledCountsForCnaWithoutPanelDataMap1 = studyViewMapper.getSampleProfileCountWithoutPanelData(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + "COPY_NUMBER_ALTERATION"); + + // Assert the count of genes with profiled cases for mutations in a combined study + assertEquals(8, totalProfiledCountsForMutationsMap1.size()); + // Assert the count of genes with profiled cases for CNA in a combined study + assertEquals(8, totalProfiledCountsForCnaMap1.size()); + // Assert the profiled counts for mutations without panel data (WES) in a combined study + assertEquals(8, sampleProfiledCountsForMutationsWithoutPanelDataMap1); + // Assert the profiled counts for CNA without panel data (WES) in a combined study + assertEquals(12, sampleProfiledCountsForCnaWithoutPanelDataMap1); + + // Assert the profiled counts for BRCA1 mutations + // BRCA1 is on testpanel1 in STUDY_TCGA_PUB + var brca1TotalProfiledCountsForMutations1 = totalProfiledCountsForMutationsMap1.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA1")).findFirst(); + assertTrue(brca1TotalProfiledCountsForMutations1.isPresent()); + assertEquals(1, brca1TotalProfiledCountsForMutations1.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for BRCA2 mutations + // BRCA2 is on testpanel3 and testpanel4 in STUDY_GENIE_PUB + var brca2TotalProfiledCountsForMutations1 = totalProfiledCountsForMutationsMap1.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA2")).findFirst(); + assertTrue(brca2TotalProfiledCountsForMutations1.isPresent()); + assertEquals(2, brca2TotalProfiledCountsForMutations1.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for AKT2 mutations + // AKT2 is on testpanel2 in STUDY_TCGA_PUB and testpanel4 in STUDY_GENIE_PUB + var akt2TotalProfiledCountsForMutations1 = totalProfiledCountsForMutationsMap1.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2")).findFirst(); + assertTrue(akt2TotalProfiledCountsForMutations1.isPresent()); + assertEquals(4, akt2TotalProfiledCountsForMutations1.get().getNumberOfProfiledCases().intValue()); + + // Assert the profiled counts for BRCA1 CNA + // BRCA1 is on testpanel1 in STUDY_TCGA_PUB + var brca1TotalProfiledCountsForCna1 = totalProfiledCountsForCnaMap1.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA1")).findFirst(); + assertTrue(brca1TotalProfiledCountsForCna1.isPresent()); + assertEquals(2, brca1TotalProfiledCountsForCna1.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for BRCA2 CNA + // BRCA2 is on testpanel3 and testpanel4 in STUDY_GENIE_PUB + var brca2TotalProfiledCountsForCna1 = totalProfiledCountsForCnaMap1.stream().filter(c -> c.getHugoGeneSymbol().equals("BRCA2")).findFirst(); + assertTrue(brca2TotalProfiledCountsForCna1.isPresent()); + assertEquals(3, brca2TotalProfiledCountsForCna1.get().getNumberOfProfiledCases().intValue()); + // Assert the profiled counts for AKT2 CNA + // AKT2 is on testpanel2 in STUDY_TCGA_PUB and testpanel4 in STUDY_GENIE_PUB + var akt2TotalProfiledCountsForCna1 = totalProfiledCountsForCnaMap1.stream().filter(c -> c.getHugoGeneSymbol().equals("AKT2")).findFirst(); + assertTrue(akt2TotalProfiledCountsForCna1.isPresent()); + assertEquals(7, akt2TotalProfiledCountsForCna1.get().getNumberOfProfiledCases().intValue()); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java new file mode 100644 index 00000000000..332dff493b4 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/ProteinExpressionCountsTest.java @@ -0,0 +1,99 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.GenomicDataBinFilter; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.assertj.core.api.Assertions.assertThat; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class ProteinExpressionCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_ACC_TCGA = "acc_tcga"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getProteinExpressionCounts() { + // Testing combined study missing samples when one lacks a relevant genomic profile + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_ACC_TCGA)); + + GenomicDataBinFilter genomicDataBinFilterRPPA = new GenomicDataBinFilter(); + genomicDataBinFilterRPPA.setHugoGeneSymbol("AKT1"); + genomicDataBinFilterRPPA.setProfileType("rppa"); + + List actualRPPACounts1 = studyViewMapper.getGenomicDataBinCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), List.of(genomicDataBinFilterRPPA)); + + ClinicalDataCount expectedRPPACount1 = new ClinicalDataCount(); + expectedRPPACount1.setAttributeId("AKT1rppa"); + expectedRPPACount1.setValue("0.7360"); + expectedRPPACount1.setCount(1); + ClinicalDataCount expectedRPPACount2 = new ClinicalDataCount(); + expectedRPPACount2.setAttributeId("AKT1rppa"); + expectedRPPACount2.setValue("-0.8097"); + expectedRPPACount2.setCount(1); + ClinicalDataCount expectedRPPACount3 = new ClinicalDataCount(); + expectedRPPACount3.setAttributeId("AKT1rppa"); + expectedRPPACount3.setValue("-0.1260"); + expectedRPPACount3.setCount(1); + ClinicalDataCount expectedRPPACountNA = new ClinicalDataCount(); + expectedRPPACountNA.setAttributeId("AKT1rppa"); + expectedRPPACountNA.setValue("NA"); + expectedRPPACountNA.setCount(16); + + List expectedRPPACounts1 = List.of( + expectedRPPACount1, expectedRPPACount2, expectedRPPACount3, expectedRPPACountNA + ); + assertThat(actualRPPACounts1) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedRPPACounts1); + + + // Testing NA filtering on combined study missing samples when one lacks a relevant genomic profile + // Make genomic data filter to put in study view filter + GenomicDataFilter genomicDataFilterRPPA = new GenomicDataFilter("AKT1", "rppa"); + DataFilterValue dataFilterValue = new DataFilterValue(); + dataFilterValue.setValue("NA"); + genomicDataFilterRPPA.setValues(List.of(dataFilterValue)); + studyViewFilter.setGenomicDataFilters(List.of(genomicDataFilterRPPA)); + + List actualRPPACounts2 = studyViewMapper.getGenomicDataBinCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), List.of(genomicDataBinFilterRPPA)); + + ClinicalDataCount expectedRPPACount = new ClinicalDataCount(); + expectedRPPACount.setAttributeId("AKT1rppa"); + expectedRPPACount.setValue("NA"); + expectedRPPACount.setCount(16); + + List expectedRPPACounts2 = List.of( + expectedRPPACount + ); + assertThat(actualRPPACounts2) + .usingRecursiveComparison() + .ignoringCollectionOrder() + .isEqualTo(expectedRPPACounts2); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java new file mode 100644 index 00000000000..5baa9149739 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/SampleTreatmentCountsTest.java @@ -0,0 +1,71 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.TemporalRelation; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.cbioportal.web.parameter.filter.AndedSampleTreatmentFilters; +import org.cbioportal.web.parameter.filter.OredSampleTreatmentFilters; +import org.cbioportal.web.parameter.filter.SampleTreatmentFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class SampleTreatmentCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getSampleTreatmentCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + + var totalSampleTreatmentCount = studyViewMapper.getTotalSampleTreatmentCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + var sampleTreatmentCounts = studyViewMapper.getSampleTreatmentCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + assertEquals(1, totalSampleTreatmentCount); + assertEquals("madeupanib", sampleTreatmentCounts.getFirst().treatment()); + assertEquals(1, sampleTreatmentCounts.getFirst().postSampleCount()); + assertEquals(0, sampleTreatmentCounts.getFirst().preSampleCount()); + + SampleTreatmentFilter filter = new SampleTreatmentFilter(); + filter.setTreatment("madeupanib"); + filter.setTime(TemporalRelation.Pre); + + OredSampleTreatmentFilters oredSampleTreatmentFilters = new OredSampleTreatmentFilters(); + oredSampleTreatmentFilters.setFilters(List.of(filter)); + + AndedSampleTreatmentFilters andedSampleTreatmentFilters = new AndedSampleTreatmentFilters(); + andedSampleTreatmentFilters.setFilters(List.of(oredSampleTreatmentFilters)); + studyViewFilter.setSampleTreatmentFilters(andedSampleTreatmentFilters); + + totalSampleTreatmentCount = studyViewMapper.getTotalSampleTreatmentCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + sampleTreatmentCounts = studyViewMapper.getSampleTreatmentCounts(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds())); + + assertEquals(0, totalSampleTreatmentCount); + assertEquals(0, sampleTreatmentCounts.size()); + + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java new file mode 100644 index 00000000000..f3a1dc6db00 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java @@ -0,0 +1,56 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.AlterationFilterHelper; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.List; +import java.util.Objects; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class StructuralVariantGenesTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_ACC_TCGA = "acc_tcga"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getStructuralVariantGenes() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_ACC_TCGA)); + var alterationCountByGenes = studyViewMapper.getStructuralVariantGenes(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + AlterationFilterHelper.build(studyViewFilter.getAlterationFilter())); + assertEquals(8, alterationCountByGenes.size()); + + // Test sv count for eml4 which is in one study + var testeml4AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "eml4")) + .mapToInt(c -> c.getTotalCount().intValue()) + .sum(); + assertEquals(1, testeml4AlterationCount); + + // Test sv count for ncoa4 which is in both studies + var testncoa4AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "ncoa4")) + .mapToInt(c -> c.getTotalCount().intValue()) + .sum(); + assertEquals(3, testncoa4AlterationCount); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java new file mode 100644 index 00000000000..66d72a34a88 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewCaseListSamplesCountsTest.java @@ -0,0 +1,120 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; + +import org.cbioportal.service.util.StudyViewColumnarServiceUtil; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class StudyViewCaseListSamplesCountsTest extends AbstractTestcontainers { + + private static final String STUDY_TCGA_PUB = "study_tcga_pub"; + private static final String STUDY_ACC_TCGA = "acc_tcga"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getMolecularProfileCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var caseList = new ArrayList(Arrays.asList("pub_cna")); + var caseListGroups = new ArrayList(Arrays.asList(caseList)); + + studyViewFilter.setCaseLists(caseListGroups); + + var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()) ); + + var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna")) + .findFirst().get().getCount().intValue(); + assertEquals(7, size); + + } + + @Test + public void getMolecularProfileCountsMultipleListsOr() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var caseList = new ArrayList(Arrays.asList("mrna","pub_cna")); + var caseListGroups = new ArrayList(Arrays.asList(caseList)); + + studyViewFilter.setCaseLists(caseListGroups); + + var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()) ); + + var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna")) + .findFirst().get().getCount().intValue(); + assertEquals(8, size); + + } + + @Test + public void getMolecularProfileCountsMultipleListsAnd() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB)); + + var caseList1 = new ArrayList(Arrays.asList("mrna")); + var caseList2 = new ArrayList(Arrays.asList("pub_cna")); + var caseListGroups = new ArrayList(Arrays.asList(caseList1, caseList2)); + + studyViewFilter.setCaseLists(caseListGroups); + + var sampleListCounts = studyViewMapper.getCaseListDataCountsPerStudy(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()) ); + + var size = sampleListCounts.stream().filter(gc->gc.getValue().equals("mrna")) + .findFirst().get().getCount().intValue(); + assertEquals(7, size); + + } + + @Test + public void getMolecularProfileCountsAcrossStudies() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_ACC_TCGA)); + + var caseList1 = new ArrayList(Arrays.asList("all")); + var caseListGroups = new ArrayList(Arrays.asList(caseList1)); + + studyViewFilter.setCaseLists(caseListGroups); + + var unMergedCounts = studyViewMapper.getCaseListDataCountsPerStudy(StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()) ); + + var caseListCountsMerged = StudyViewColumnarServiceUtil.mergeCaseListCounts( + unMergedCounts + ); + + var sizeUnmerged = unMergedCounts.stream().filter(gc->gc.getValue().equals("all")) + .findFirst().get().getCount().intValue(); + assertEquals(14, sizeUnmerged); + + // now we've combined the "all" from the two studies + var sizeMerged = caseListCountsMerged.stream().filter(gc->gc.getValue().equals("all")) + .findFirst().get().getCount().intValue(); + assertEquals(15, sizeMerged); + + } + +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java new file mode 100644 index 00000000000..a0f5fb67772 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java @@ -0,0 +1,314 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.persistence.helper.StudyViewFilterHelper; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.math.BigDecimal; +import java.util.Collections; +import java.util.List; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class StudyViewMapperClinicalDataCountTest extends AbstractTestcontainers { + private static final String STUDY_ACC_TCGA = "acc_tcga"; + private static final String STUDY_GENIE_PUB = "study_genie_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getMutationCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("mutation_count"), + Collections.emptyList() + ); + + var mutationsCountsOptional = clinicalDataCountItems.stream() + .filter(c -> c.getAttributeId().equals("mutation_count")).findFirst(); + + assertTrue(mutationsCountsOptional.isPresent()); + var mutationsCounts = mutationsCountsOptional.get().getCounts(); + + assertEquals(6, mutationsCounts.size()); + assertEquals(1, findClinicaDataCount(mutationsCounts, "11")); + assertEquals(1, findClinicaDataCount(mutationsCounts, "6")); + assertEquals(2, findClinicaDataCount(mutationsCounts, "4")); + assertEquals(4, findClinicaDataCount(mutationsCounts, "2")); + assertEquals(2, findClinicaDataCount(mutationsCounts, "1")); + // 1 empty string + 1 'NAN' + 15 samples with no data + assertEquals(17, findClinicaDataCount(mutationsCounts, "NA")); + } + + @Test + public void getCenterCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var clinicalDataCounts = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("center"), + Collections.emptyList() + ); + + var categoricalClinicalDataCountsOptional = clinicalDataCounts.stream() + .filter(c -> c.getAttributeId().equals("center")).findFirst(); + + assertTrue(categoricalClinicalDataCountsOptional.isPresent()); + var categoricalClinicalDataCounts = categoricalClinicalDataCountsOptional.get().getCounts(); + + assertEquals(7, categoricalClinicalDataCounts.size()); + assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "MSK")); + assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "DFCI")); + assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "CHOP")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "MDA")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "OHSU")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "UCSF")); + // 1 empty string + 1 'NA' + 12 samples with no data + assertEquals(14, findClinicaDataCount(categoricalClinicalDataCounts, "NA")); + } + + @Test + public void getDeadCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var clinicalDataCounts = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("dead"), + Collections.emptyList() + ); + + var categoricalClinicalDataCountsOptional = clinicalDataCounts.stream() + .filter(c -> c.getAttributeId().equals("dead")).findFirst(); + + assertTrue(categoricalClinicalDataCountsOptional.isPresent()); + var categoricalClinicalDataCounts = categoricalClinicalDataCountsOptional.get().getCounts(); + + assertEquals(6, categoricalClinicalDataCounts.size()); + assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "TRUE")); + assertEquals(4, findClinicaDataCount(categoricalClinicalDataCounts, "FALSE")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "NOT RELEASED")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "NOT COLLECTED")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "UNKNOWN")); + // 1 empty string + 1 'N/A' + 12 samples with no data + assertEquals(14, findClinicaDataCount(categoricalClinicalDataCounts, "NA")); + } + + @Test + public void getMutationAndCenterCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var combinedClinicalDataCounts = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("mutation_count", "center"), + Collections.emptyList() + ); + + assertEquals(2, combinedClinicalDataCounts.size()); + } + + @Test + public void getAgeCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("age"), + Collections.emptyList() + ); + + var ageCountsOptional = clinicalDataCountItems.stream() + .filter(c -> c.getAttributeId().equals("age")).findFirst(); + + assertTrue(ageCountsOptional.isPresent()); + var ageCounts = ageCountsOptional.get().getCounts(); + + assertAgeCounts(ageCounts); + + // 1 empty string + 1 'NAN' + 1 'N/A' + 1 patient without data + assertEquals(4, findClinicaDataCount(ageCounts, "NA")); + } + + @Test + public void getAgeCountsForMultipleStudies() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB, STUDY_ACC_TCGA)); + + var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("age"), + Collections.emptyList() + ); + + var ageCountsOptional = clinicalDataCountItems.stream() + .filter(c -> c.getAttributeId().equals("age")).findFirst(); + + assertTrue(ageCountsOptional.isPresent()); + var ageCounts = ageCountsOptional.get().getCounts(); + + // everything should be exactly the same as single study (STUDY_GENIE_PUB) filter + // except NA counts + assertAgeCounts(ageCounts); + + // 1 empty string + 1 'NAN' + 1 'N/A' + 1 GENIE_PUB patient without data + 4 ACC_TCGA data without data + assertEquals(8, findClinicaDataCount(ageCounts, "NA")); + } + + private void assertAgeCounts(List ageCounts) { + assertEquals(15, ageCounts.size()); + + assertEquals(3, findClinicaDataCount(ageCounts, "<18")); + assertEquals(1, findClinicaDataCount(ageCounts, "18")); + assertEquals(1, findClinicaDataCount(ageCounts, "22")); + assertEquals(2, findClinicaDataCount(ageCounts, "42")); + assertEquals(1, findClinicaDataCount(ageCounts, "66")); + assertEquals(1, findClinicaDataCount(ageCounts, "66")); + assertEquals(1, findClinicaDataCount(ageCounts, "68")); + assertEquals(1, findClinicaDataCount(ageCounts, "77")); + assertEquals(1, findClinicaDataCount(ageCounts, "78")); + assertEquals(1, findClinicaDataCount(ageCounts, "79")); + assertEquals(2, findClinicaDataCount(ageCounts, "80")); + assertEquals(2, findClinicaDataCount(ageCounts, "82")); + assertEquals(1, findClinicaDataCount(ageCounts, "89")); + assertEquals(2, findClinicaDataCount(ageCounts, ">89")); + assertEquals(1, findClinicaDataCount(ageCounts, "UNKNOWN")); + } + + @Test + public void getMutationCountsFilteredByAge() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + // filter patients with age between 20 and 70 + // (there are 5 patients within this range, which are 307..311) + ClinicalDataFilter filter = buildClinicalDataFilter("age", 20, 70); + studyViewFilter.setClinicalDataFilters(List.of(filter)); + + var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("mutation_count"), + Collections.emptyList() + ); + + var mutationsCountsOptional = clinicalDataCountItems.stream() + .filter(c -> c.getAttributeId().equals("mutation_count")).findFirst(); + + assertTrue(mutationsCountsOptional.isPresent()); + var mutationCountsFiltered = mutationsCountsOptional.get().getCounts(); + + assertEquals(3, mutationCountsFiltered.size()); + assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "2")); + assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "1")); + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "NA")); + } + + @Test + public void getMutationCountsFilteredByAgeWithOpenStartValues() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + // filter patients with age less than 20 + // (there are 4 patients within this range, which are 301, 302, 303, and 306) + ClinicalDataFilter filter = buildClinicalDataFilter("age", null, 20); + studyViewFilter.setClinicalDataFilters(List.of(filter)); + + var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("mutation_count"), + Collections.emptyList() + ); + + var mutationsCountsOptional = clinicalDataCountItems.stream() + .filter(c -> c.getAttributeId().equals("mutation_count")).findFirst(); + + assertTrue(mutationsCountsOptional.isPresent()); + var mutationCountsFiltered = mutationsCountsOptional.get().getCounts(); + + assertEquals(4, mutationCountsFiltered.size()); + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301 + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302 + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303 + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306 + + // no patients/samples with NA + assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA")); + } + + @Test + public void getMutationCountsFilteredByAgeWithOpenEndValues() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + // filter patients with age greater than 80 + // (there are 4 patients within this range, which are 317, 318, 319, 304, and 305) + ClinicalDataFilter filter = buildClinicalDataFilter("age", 80, null); + studyViewFilter.setClinicalDataFilters(List.of(filter)); + + var clinicalDataCountItems = studyViewMapper.getClinicalDataCounts( + StudyViewFilterHelper.build(studyViewFilter, null, null, studyViewFilter.getStudyIds()), + List.of("mutation_count"), + Collections.emptyList() + ); + + var mutationsCountsOptional = clinicalDataCountItems.stream() + .filter(c -> c.getAttributeId().equals("mutation_count")).findFirst(); + + assertTrue(mutationsCountsOptional.isPresent()); + var mutationCountsFiltered = mutationsCountsOptional.get().getCounts(); + + assertEquals(3, mutationCountsFiltered.size()); + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 304 + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 305 + + // patients/samples with NA data: 317, 318, and 319 + assertEquals(3, findClinicaDataCount(mutationCountsFiltered, "NA")); + } + + private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer start, Integer end) { + DataFilterValue value = new DataFilterValue(); + if (start != null) { + value.setStart(BigDecimal.valueOf(start)); + } + if (end != null) { + value.setEnd(BigDecimal.valueOf(end)); + } + + ClinicalDataFilter filter = new ClinicalDataFilter(); + filter.setAttributeId(attributeId); + filter.setValues(List.of(value)); + + return filter; + } + + private int findClinicaDataCount(List counts, String attrValue) { + var count = counts.stream().filter(c -> c.getValue().equals(attrValue)).findAny().orElse(null); + + return count == null ? 0 : count.getCount(); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java new file mode 100644 index 00000000000..25d1e098c64 --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java @@ -0,0 +1,48 @@ +package org.cbioportal.persistence.mybatisclickhouse.config; + +import org.mybatis.spring.SqlSessionFactoryBean; +import org.mybatis.spring.annotation.MapperScan; +import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties; +import org.springframework.boot.context.properties.ConfigurationProperties; +import org.springframework.boot.test.context.TestConfiguration; +import org.springframework.context.annotation.Bean; +import org.springframework.core.io.ResourceLoader; + +import javax.sql.DataSource; +import java.io.IOException; + +@TestConfiguration +@MapperScan("org.cbioportal.persistence.mybatisclickhouse") +public class MyBatisConfig { + + @Bean + @ConfigurationProperties("spring.datasource.clickhouse") + public DataSourceProperties clickhouseDatSourceProperties() { + return new DataSourceProperties(); + } + + @Bean + public DataSource dataSource() { + return clickhouseDatSourceProperties() + .initializeDataSourceBuilder() + .build(); + } + + @Bean + public SqlSessionFactoryBean sqlColumnarSessionFactory(ResourceLoader resourceLoader, DataSource dataSource) throws IOException { + SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean(); + sessionFactory.setDataSource(dataSource); + var studyViewMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml") ; + var studyViewFilterMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml"); + var alterationFilterMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml"); + sessionFactory.setMapperLocations( + studyViewMapperResource,studyViewFilterMapperResource, alterationFilterMapperResource + ); + return sessionFactory; + } + + + + + +} diff --git a/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java b/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java index bd2c4955826..45e181d7598 100644 --- a/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java +++ b/src/test/java/org/cbioportal/service/impl/AlterationCountServiceImplTest.java @@ -1,10 +1,19 @@ package org.cbioportal.service.impl; import org.apache.commons.math3.util.Pair; -import org.cbioportal.model.*; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.AlterationCountByStructuralVariant; +import org.cbioportal.model.AlterationFilter; +import org.cbioportal.model.CNA; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.MolecularProfileCaseIdentifier; +import org.cbioportal.model.MutationEventType; import org.cbioportal.model.util.Select; import org.cbioportal.persistence.AlterationRepository; import org.cbioportal.persistence.MolecularProfileRepository; +import org.cbioportal.persistence.StudyViewRepository; +import org.cbioportal.service.SignificantlyMutatedGeneService; import org.cbioportal.service.exception.MolecularProfileNotFoundException; import org.cbioportal.service.util.AlterationEnrichmentUtil; import org.cbioportal.service.util.MolecularProfileUtil; @@ -14,17 +23,25 @@ import org.junit.runner.RunWith; import org.mockito.InjectMocks; import org.mockito.Mock; +import org.mockito.MockitoAnnotations; import org.mockito.Spy; import org.mockito.junit.MockitoJUnitRunner; -import java.util.*; +import java.util.Arrays; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.TreeSet; -import static org.mockito.Mockito.*; +import static org.mockito.Mockito.anyBoolean; +import static org.mockito.Mockito.anyList; +import static org.mockito.Mockito.times; +import static org.mockito.Mockito.verify; +import static org.mockito.Mockito.when; @RunWith(MockitoJUnitRunner.class) public class AlterationCountServiceImplTest extends BaseServiceImplTest { - @InjectMocks private AlterationCountServiceImpl alterationCountService; @Mock private AlterationRepository alterationRepository; @@ -39,6 +56,12 @@ public class AlterationCountServiceImplTest extends BaseServiceImplTest { private MolecularProfileUtil molecularProfileUtil; @Mock private MolecularProfileRepository molecularProfileRepository; + @Mock + private StudyViewRepository studyViewRepository; + @Mock + private SignificantlyMutatedGeneService significantlyMutatedGeneService; + @Mock + private SignificantCopyNumberRegionServiceImpl significantCopyNumberRegionService; List caseIdentifiers = Arrays.asList(new MolecularProfileCaseIdentifier("A", MOLECULAR_PROFILE_ID)); Select mutationEventTypes = Select.byValues(Arrays.asList(MutationEventType.missense_mutation)); @@ -64,6 +87,12 @@ public class AlterationCountServiceImplTest extends BaseServiceImplTest { @Before public void setup() { + MockitoAnnotations.openMocks(this); + + alterationCountService = new AlterationCountServiceImpl(alterationRepository, alterationEnrichmentUtil, + alterationEnrichmentUtilCna, alterationEnrichmentUtilStructVar, molecularProfileRepository, + studyViewRepository, significantlyMutatedGeneService, significantCopyNumberRegionService); + MolecularProfile molecularProfile = new MolecularProfile(); molecularProfile.setStableId(MOLECULAR_PROFILE_ID); molecularProfile.setCancerStudyIdentifier(STUDY_ID); diff --git a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java b/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java index 2403f035f47..2b00e7f2c66 100644 --- a/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java +++ b/src/test/java/org/cbioportal/service/impl/ViolinPlotServiceImplTest.java @@ -4,6 +4,7 @@ import org.cbioportal.model.ClinicalViolinPlotData; import org.cbioportal.model.ClinicalViolinPlotRowData; import org.cbioportal.model.Sample; +import org.cbioportal.web.parameter.StudyViewFilter; import org.junit.Assert; import org.junit.Test; import org.junit.runner.RunWith; @@ -77,7 +78,8 @@ public void getClinicalViolinPlotData() throws Exception { new BigDecimal(1), new BigDecimal(NUM_CURVE_POINTS), false, - new BigDecimal(1) + new BigDecimal(1), + new StudyViewFilter() ); diff --git a/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java b/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java new file mode 100644 index 00000000000..31f09303271 --- /dev/null +++ b/src/test/java/org/cbioportal/service/util/AlterationCountServiceUtilTest.java @@ -0,0 +1,418 @@ +package org.cbioportal.service.util; + +import org.apache.commons.math3.util.Pair; +import org.cbioportal.model.AlterationCountByGene; +import org.cbioportal.model.AlterationCountByStructuralVariant; +import org.cbioportal.model.CopyNumberCountByGene; +import org.cbioportal.model.Gistic; +import org.cbioportal.model.GisticToGene; +import org.cbioportal.model.MolecularProfile; +import org.cbioportal.model.MutSig; +import org.junit.Test; + +import java.math.BigDecimal; +import java.util.Arrays; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + +import static org.junit.Assert.*; + +public class AlterationCountServiceUtilTest { + + @Test + public void testComputeTotalProfiledCount() { + // Test with gene panel data + boolean hasGenePanelData = true; + int alterationsProfiledCount = 5; + int sampleProfileCountWithoutGenePanelData = 10; + int totalProfiledCount = 20; + + int result = AlterationCountServiceUtil.computeTotalProfiledCount( + hasGenePanelData, alterationsProfiledCount, sampleProfileCountWithoutGenePanelData, totalProfiledCount + ); + assertEquals(15, result); + + // Test without gene panel data + hasGenePanelData = false; + result = AlterationCountServiceUtil.computeTotalProfiledCount( + hasGenePanelData, alterationsProfiledCount, sampleProfileCountWithoutGenePanelData, totalProfiledCount + ); + assertEquals(10, result); + + // Test with zero profiled count + hasGenePanelData = true; + alterationsProfiledCount = 0; + sampleProfileCountWithoutGenePanelData = 0; + result = AlterationCountServiceUtil.computeTotalProfiledCount( + hasGenePanelData, alterationsProfiledCount, sampleProfileCountWithoutGenePanelData, totalProfiledCount + ); + assertEquals(20, result); + } + + + @Test + public void testUpdateAlterationCountsWithMutSigQValue() { + AlterationCountByGene count1 = new AlterationCountByGene(); + count1.setHugoGeneSymbol("hugo1"); + + AlterationCountByGene count2 = new AlterationCountByGene(); + count2.setHugoGeneSymbol("hugo2"); + + List counts = Arrays.asList(count1, count2); + + MutSig mutSig1 = new MutSig(); + mutSig1.setHugoGeneSymbol("hugo1"); + mutSig1.setqValue(BigDecimal.valueOf(0.01)); + + Map mutSigs = new HashMap<>(); + mutSigs.put("hugo1", mutSig1); + + List result = AlterationCountServiceUtil.updateAlterationCountsWithMutSigQValue(counts, mutSigs); + + assertEquals(BigDecimal.valueOf(0.01), result.get(0).getqValue()); + assertEquals(null, result.get(1).getqValue()); + } + + + @Test + public void testUpdateAlterationCountsWithCNASigQValue() { + CopyNumberCountByGene count1 = new CopyNumberCountByGene(); + count1.setHugoGeneSymbol("hugo1"); + count1.setAlteration(2); + + CopyNumberCountByGene count2 = new CopyNumberCountByGene(); + count2.setHugoGeneSymbol("hugo2"); + count2.setAlteration(-2); + + List counts = Arrays.asList(count1, count2); + + Gistic gistic1 = new Gistic(); + gistic1.setqValue(BigDecimal.valueOf(0.01)); + + Map, Gistic> gisticMap = new HashMap<>(); + gisticMap.put(Pair.create("hugo1", 2), gistic1); + + List result = AlterationCountServiceUtil.updateAlterationCountsWithCNASigQValue(counts, gisticMap); + + assertEquals(BigDecimal.valueOf(0.01), result.get(0).getqValue()); + assertEquals(null, result.get(1).getqValue()); + } + + + @Test + public void testGetFirstMolecularProfileGroupedByStudy() { + MolecularProfile profile1 = new MolecularProfile(); + profile1.setCancerStudyIdentifier("study1"); + profile1.setMolecularProfileId(1); + + MolecularProfile profile2 = new MolecularProfile(); + profile2.setCancerStudyIdentifier("study1"); + profile2.setMolecularProfileId(2); + + MolecularProfile profile3 = new MolecularProfile(); + profile3.setCancerStudyIdentifier("study2"); + profile3.setMolecularProfileId(3); + + List profiles = Arrays.asList(profile1, profile2, profile3); + + List result = AlterationCountServiceUtil.getFirstMolecularProfileGroupedByStudy(profiles); + + assertEquals(2, result.size()); + + MolecularProfile resultProfile1 = result.stream() + .filter(profile -> profile.getCancerStudyIdentifier().equals("study1")) + .findFirst() + .orElse(null); + assertEquals(Integer.valueOf(1), resultProfile1.getMolecularProfileId()); + + MolecularProfile resultProfile2 = result.stream() + .filter(profile -> profile.getCancerStudyIdentifier().equals("study2")) + .findFirst() + .orElse(null); + assertEquals(Integer.valueOf(3), resultProfile2.getMolecularProfileId()); + } + + + @Test + public void testCombineAlterationCountsWithConflictingHugoSymbols() { + AlterationCountByGene count1 = new AlterationCountByGene(); + count1.setHugoGeneSymbol("hugo1"); + count1.setNumberOfAlteredCases(5); + count1.setTotalCount(10); + + AlterationCountByGene count2 = new AlterationCountByGene(); + count2.setHugoGeneSymbol("hugo1"); + count2.setNumberOfAlteredCases(3); + count2.setTotalCount(6); + + AlterationCountByGene count3 = new AlterationCountByGene(); + count3.setHugoGeneSymbol("hugo2"); + count3.setNumberOfAlteredCases(2); + count3.setTotalCount(4); + + List counts = Arrays.asList(count1, count2, count3); + + List combinedCounts = AlterationCountServiceUtil.combineAlterationCountsWithConflictingHugoSymbols(counts); + + assertEquals(2, combinedCounts.size()); + + AlterationCountByGene combinedCount1 = combinedCounts.stream() + .filter(count -> count.getHugoGeneSymbol().equals("hugo1")) + .findFirst() + .orElse(null); + assertEquals(8, combinedCount1.getNumberOfAlteredCases().intValue()); + assertEquals(16, combinedCount1.getTotalCount().intValue()); + + AlterationCountByGene combinedCount2 = combinedCounts.stream() + .filter(count -> count.getHugoGeneSymbol().equals("hugo2")) + .findFirst() + .orElse(null); + assertEquals(2, combinedCount2.getNumberOfAlteredCases().intValue()); + assertEquals(4, combinedCount2.getTotalCount().intValue()); + } + + + @Test + public void testCombineCopyNumberCountsWithConflictingHugoSymbols() { + CopyNumberCountByGene count1 = new CopyNumberCountByGene(); + count1.setHugoGeneSymbol("hugo1"); + count1.setAlteration(1); + count1.setNumberOfAlteredCases(5); + count1.setTotalCount(10); + + CopyNumberCountByGene count2 = new CopyNumberCountByGene(); + count2.setHugoGeneSymbol("hugo1"); + count2.setAlteration(1); + count2.setNumberOfAlteredCases(3); + count2.setTotalCount(6); + + CopyNumberCountByGene count3 = new CopyNumberCountByGene(); + count3.setHugoGeneSymbol("hugo2"); + count3.setAlteration(2); + count3.setNumberOfAlteredCases(2); + count3.setTotalCount(4); + + List counts = Arrays.asList(count1, count2, count3); + + List result = AlterationCountServiceUtil.combineCopyNumberCountsWithConflictingHugoSymbols(counts); + + assertEquals(2, result.size()); + + CopyNumberCountByGene combinedCount1 = result.stream().filter(c -> c.getHugoGeneSymbol().equals("hugo1")).findFirst().orElse(null); + assertEquals(8, combinedCount1.getNumberOfAlteredCases().intValue()); + assertEquals(16, combinedCount1.getTotalCount().intValue()); + + CopyNumberCountByGene combinedCount2 = result.stream().filter(c -> c.getHugoGeneSymbol().equals("hugo2")).findFirst().orElse(null); + assertEquals(2, combinedCount2.getNumberOfAlteredCases().intValue()); + assertEquals(4, combinedCount2.getTotalCount().intValue()); + } + + + @Test + public void testHasGenePanelData() { + // Test with Whole Exome Sequencing and other panels + Set genePanelIds1 = Set.of("WES", "panel1"); + assertTrue(AlterationCountServiceUtil.hasGenePanelData(genePanelIds1)); + + // Test with only Whole Exome Sequencing + Set genePanelIds2 = Set.of("WES"); + assertFalse(AlterationCountServiceUtil.hasGenePanelData(genePanelIds2)); + + // Test with other panels + Set genePanelIds3 = Set.of("panel1", "panel2"); + assertTrue(AlterationCountServiceUtil.hasGenePanelData(genePanelIds3)); + + // Test with empty set + Set genePanelIds4 = Set.of(); + assertFalse(AlterationCountServiceUtil.hasGenePanelData(genePanelIds4)); + } + + + @Test + public void testSetupGisticMap() { + // Single Gistic with amplification + Gistic gistic1 = new Gistic(); + gistic1.setAmp(true); + gistic1.setqValue(BigDecimal.valueOf(0.01)); + GisticToGene gene1 = new GisticToGene(); + gene1.setHugoGeneSymbol("hugo1"); + gistic1.setGenes(List.of(gene1)); + + // Single Gistic without amplification + Gistic gistic2 = new Gistic(); + gistic2.setAmp(false); + gistic2.setqValue(BigDecimal.valueOf(0.02)); + GisticToGene gene2 = new GisticToGene(); + gene2.setHugoGeneSymbol("hugo2"); + gistic2.setGenes(List.of(gene2)); + + // Multiple Gistics for the same gene with different qValues + Gistic gistic3 = new Gistic(); + gistic3.setAmp(true); + gistic3.setqValue(BigDecimal.valueOf(0.03)); + GisticToGene gene3 = new GisticToGene(); + gene3.setHugoGeneSymbol("hugo1"); + gistic3.setGenes(List.of(gene3)); + + List gisticList = List.of(gistic1, gistic2, gistic3); + Map, Gistic> gisticMap = new HashMap<>(); + + AlterationCountServiceUtil.setupGisticMap(gisticList, gisticMap); + + assertEquals(2, gisticMap.size()); + assertTrue(gisticMap.containsKey(Pair.create("hugo1", 2))); + assertTrue(gisticMap.containsKey(Pair.create("hugo2", -2))); + assertEquals(gistic1, gisticMap.get(Pair.create("hugo1", 2))); // gistic1 should be chosen over gistic3 due to lower qValue + assertEquals(gistic2, gisticMap.get(Pair.create("hugo2", -2))); + } + + + @Test + public void testSetupAlterationGeneCountsMapWithAlterationCountByGene() { + AlterationCountByGene datum1 = new AlterationCountByGene(); + datum1.setHugoGeneSymbol("hugo1"); + datum1.setTotalCount(1); + datum1.setNumberOfAlteredCases(1); + datum1.setNumberOfProfiledCases(1); + datum1.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel1"))); + + AlterationCountByGene datum2 = new AlterationCountByGene(); + datum2.setHugoGeneSymbol("hugo1"); + datum2.setTotalCount(2); + datum2.setNumberOfAlteredCases(2); + datum2.setNumberOfProfiledCases(2); + datum2.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel2"))); + + AlterationCountByGene datum3 = new AlterationCountByGene(); + datum3.setHugoGeneSymbol("hugo2"); + datum3.setTotalCount(3); + datum3.setNumberOfAlteredCases(3); + datum3.setNumberOfProfiledCases(3); + datum3.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel3"))); + + List studyAlterationCountByGenes = Arrays.asList(datum1, datum2, datum3); + Map totalResult = new HashMap<>(); + + AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult); + + assertEquals(2, totalResult.size()); + assertTrue(totalResult.containsKey("hugo1")); + assertTrue(totalResult.containsKey("hugo2")); + + AlterationCountByGene result1 = totalResult.get("hugo1"); + assertEquals(3L, (long) result1.getTotalCount()); + assertEquals(3L, (long) result1.getNumberOfAlteredCases()); + assertEquals(3L, (long) result1.getNumberOfProfiledCases()); + assertTrue(result1.getMatchingGenePanelIds().contains("panel1")); + assertTrue(result1.getMatchingGenePanelIds().contains("panel2")); + + AlterationCountByGene result2 = totalResult.get("hugo2"); + assertEquals(3L, (long) result2.getTotalCount()); + assertEquals(3L, (long) result2.getNumberOfAlteredCases()); + assertEquals(3L, (long) result2.getNumberOfProfiledCases()); + assertTrue(result2.getMatchingGenePanelIds().contains("panel3")); + } + + @Test + public void testSetupAlterationGeneCountsMapWithAlterationCountByStructuralVariant() { + AlterationCountByStructuralVariant datum1 = new AlterationCountByStructuralVariant(); + datum1.setGene1HugoGeneSymbol("hugo1"); + datum1.setGene2HugoGeneSymbol("hugo2"); + datum1.setTotalCount(1); + datum1.setNumberOfAlteredCases(1); + datum1.setNumberOfProfiledCases(1); + datum1.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel1"))); + + AlterationCountByStructuralVariant datum2 = new AlterationCountByStructuralVariant(); + datum2.setGene1HugoGeneSymbol("hugo1"); + datum2.setGene2HugoGeneSymbol("hugo2"); + datum2.setTotalCount(2); + datum2.setNumberOfAlteredCases(2); + datum2.setNumberOfProfiledCases(2); + datum2.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel2"))); + + AlterationCountByStructuralVariant datum3 = new AlterationCountByStructuralVariant(); + datum3.setGene1HugoGeneSymbol("hugo3"); + datum3.setGene2HugoGeneSymbol("hugo4"); + datum3.setTotalCount(3); + datum3.setNumberOfAlteredCases(3); + datum3.setNumberOfProfiledCases(3); + datum3.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel3"))); + + List studyAlterationCountByGenes = Arrays.asList(datum1, datum2, datum3); + Map totalResult = new HashMap<>(); + + AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult); + + assertEquals(2, totalResult.size()); + assertTrue(totalResult.containsKey("hugo1::hugo2")); + assertTrue(totalResult.containsKey("hugo3::hugo4")); + + AlterationCountByStructuralVariant result1 = totalResult.get("hugo1::hugo2"); + assertEquals(3L, (long) result1.getTotalCount()); + assertEquals(3L, (long) result1.getNumberOfAlteredCases()); + assertEquals(3L, (long) result1.getNumberOfProfiledCases()); + assertTrue(result1.getMatchingGenePanelIds().contains("panel1")); + assertTrue(result1.getMatchingGenePanelIds().contains("panel2")); + + AlterationCountByStructuralVariant result2 = totalResult.get("hugo3::hugo4"); + assertEquals(3L, (long) result2.getTotalCount()); + assertEquals(3L, (long) result2.getNumberOfAlteredCases()); + assertEquals(3L, (long) result2.getNumberOfProfiledCases()); + assertTrue(result2.getMatchingGenePanelIds().contains("panel3")); + } + + @Test + public void testSetupAlterationGeneCountsMapWithCopyNumberCountByGene() { + CopyNumberCountByGene datum1 = new CopyNumberCountByGene(); + datum1.setEntrezGeneId(1); + datum1.setAlteration(2); + datum1.setTotalCount(1); + datum1.setNumberOfAlteredCases(1); + datum1.setNumberOfProfiledCases(1); + datum1.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel1"))); + + CopyNumberCountByGene datum2 = new CopyNumberCountByGene(); + datum2.setEntrezGeneId(1); + datum2.setAlteration(2); + datum2.setTotalCount(2); + datum2.setNumberOfAlteredCases(2); + datum2.setNumberOfProfiledCases(2); + datum2.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel2"))); + + CopyNumberCountByGene datum3 = new CopyNumberCountByGene(); + datum3.setEntrezGeneId(2); + datum3.setAlteration(-2); + datum3.setTotalCount(3); + datum3.setNumberOfAlteredCases(3); + datum3.setNumberOfProfiledCases(3); + datum3.setMatchingGenePanelIds(new HashSet<>(Arrays.asList("panel3"))); + + List studyAlterationCountByGenes = Arrays.asList(datum1, datum2, datum3); + Map totalResult = new HashMap<>(); + + AlterationCountServiceUtil.setupAlterationGeneCountsMap(studyAlterationCountByGenes, totalResult); + + assertEquals(2, totalResult.size()); + assertTrue(totalResult.containsKey("12")); + assertTrue(totalResult.containsKey("2-2")); + + CopyNumberCountByGene result1 = totalResult.get("12"); + assertEquals(3L, (long) result1.getTotalCount()); + assertEquals(3L, (long) result1.getNumberOfAlteredCases()); + assertEquals(3L, (long) result1.getNumberOfProfiledCases()); + assertTrue(result1.getMatchingGenePanelIds().contains("panel1")); + assertTrue(result1.getMatchingGenePanelIds().contains("panel2")); + + CopyNumberCountByGene result2 = totalResult.get("2-2"); + assertEquals(3L, (long) result2.getTotalCount()); + assertEquals(3L, (long) result2.getNumberOfAlteredCases()); + assertEquals(3L, (long) result2.getNumberOfProfiledCases()); + assertTrue(result2.getMatchingGenePanelIds().contains("panel3")); + } + + +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java b/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java new file mode 100644 index 00000000000..0c9687d6e59 --- /dev/null +++ b/src/test/java/org/cbioportal/service/util/StudyViewColumnarServiceUtilTest.java @@ -0,0 +1,346 @@ +package org.cbioportal.service.util; + +import org.cbioportal.model.CaseListDataCount; +import org.cbioportal.model.ClinicalAttribute; +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.model.ClinicalDataCountItem; +import org.cbioportal.model.GenomicDataCount; +import org.cbioportal.model.GenomicDataCountItem; +import org.cbioportal.web.parameter.GenomicDataFilter; +import org.junit.Assert; +import org.junit.Test; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.Map; +import java.util.Optional; + +import static org.junit.Assert.*; + +public class StudyViewColumnarServiceUtilTest { + + @Test + public void testMergeClinicalDataCounts() { + + // first two counts are for same value (value1) and so should be + // merged + + ClinicalDataCount count1 = new ClinicalDataCount(); + count1.setAttributeId("attr1"); + count1.setValue("value1"); + count1.setCount(1); + + ClinicalDataCount count2 = new ClinicalDataCount(); + count2.setAttributeId("attr1"); + count2.setValue("value1"); + count2.setCount(2); + + ClinicalDataCount count3 = new ClinicalDataCount(); + count3.setAttributeId("attr1"); + count3.setValue("value3"); + count3.setCount(6); + + ClinicalDataCount count4 = new ClinicalDataCount(); + count4.setAttributeId("attr1"); + count4.setValue("value3"); + count4.setCount(4); + + ClinicalDataCount count5 = new ClinicalDataCount(); + count5.setAttributeId("attr1"); + count5.setValue("value2"); + count5.setCount(4); + + ClinicalDataCountItem item = new ClinicalDataCountItem(); + item.setAttributeId("attr1"); + item.setCounts(Arrays.asList(count1, count2, count3, count4, count5)); + + List items = Collections.singletonList(item); + + // Call the method under test + List mergedItems = StudyViewColumnarServiceUtil.mergeClinicalDataCounts(items); + + // it merged three count items to 2 + Optional mergedCount=mergedItems.get(0).getCounts().stream() + .filter(count->count.getValue().equals("value1")).findFirst(); + Assert.assertEquals(3, mergedCount.get().getCount().intValue()); + + Optional mergedCount2=mergedItems.get(0).getCounts().stream() + .filter(count->count.getValue().equals("value2")).findFirst(); + Assert.assertEquals(4, mergedCount2.get().getCount().intValue()); + + Optional mergedCount3=mergedItems.get(0).getCounts().stream() + .filter(count->count.getValue().equals("value3")).findFirst(); + Assert.assertEquals(10, mergedCount3.get().getCount().intValue()); + + } + + + @Test + public void testAddClinicalDataCountsForMissingAttributes() { + ClinicalDataCountItem existingItem = new ClinicalDataCountItem(); + existingItem.setAttributeId("attr1"); + ClinicalDataCount existingCount = new ClinicalDataCount(); + existingCount.setCount(5); + existingCount.setValue("value1"); + existingCount.setAttributeId("attr1"); + existingItem.setCounts(Collections.singletonList(existingCount)); + + List counts = Collections.singletonList(existingItem); + + // we're gonna create two attributes which will not be represented in the passed result set + // test whether addClinicalDataCountsForMissingAttributes restores them + + ClinicalAttribute missingAttributeSample = new ClinicalAttribute(); + missingAttributeSample.setAttrId("attr2"); + missingAttributeSample.setPatientAttribute(false); + + ClinicalAttribute missingAttributePatient = new ClinicalAttribute(); + missingAttributePatient.setAttrId("attr3"); + missingAttributePatient.setPatientAttribute(true); + + List attributes = Arrays.asList(missingAttributeSample, missingAttributePatient); + + List result = StudyViewColumnarServiceUtil.addClinicalDataCountsForMissingAttributes( + counts, attributes, 10, 20 + ); + + assertEquals(3, result.size()); + + Optional addedItemSample = result.stream() + .filter(item -> item.getAttributeId().equals("attr2")) + .findFirst(); + + assertTrue(addedItemSample.isPresent()); + assertEquals(1, addedItemSample.get().getCounts().size()); + assertEquals("NA", addedItemSample.get().getCounts().get(0).getValue()); + assertEquals(10, addedItemSample.get().getCounts().get(0).getCount().intValue()); + + Optional addedItemPatient = result.stream() + .filter(item -> item.getAttributeId().equals("attr3")) + .findFirst(); + + assertTrue(addedItemPatient.isPresent()); + assertEquals(1, addedItemPatient.get().getCounts().size()); + assertEquals("NA", addedItemPatient.get().getCounts().get(0).getValue()); + assertEquals(20, addedItemPatient.get().getCounts().get(0).getCount().intValue()); + + + } + + + @Test + public void testMergeGenomicDataCounts() { + GenomicDataCount count1 = new GenomicDataCount(); + count1.setValue("value1"); + count1.setLabel("label1"); + count1.setCount(1); + + GenomicDataCount count2 = new GenomicDataCount(); + count2.setValue("value1"); + count2.setLabel("label1"); + count2.setCount(2); + + GenomicDataCount count3 = new GenomicDataCount(); + count3.setValue("value2"); + count3.setLabel("label2"); + count3.setCount(3); + + List counts = Arrays.asList(count1, count2, count3); + + List mergedCounts = StudyViewColumnarServiceUtil.mergeGenomicDataCounts(counts); + + assertEquals(2, mergedCounts.size()); + + GenomicDataCount mergedCount1 = mergedCounts.stream() + .filter(count -> count.getValue().equals("value1")) + .findFirst() + .orElse(null); + assertEquals(3, mergedCount1.getCount().intValue()); + assertEquals("label1", mergedCount1.getLabel()); + + GenomicDataCount mergedCount2 = mergedCounts.stream() + .filter(count -> count.getValue().equals("value2")) + .findFirst() + .orElse(null); + assertEquals(3, mergedCount2.getCount().intValue()); + assertEquals("label2", mergedCount2.getLabel()); + } + + + @Test + public void testMergeCaseListCounts() { + CaseListDataCount count1 = new CaseListDataCount(); + count1.setValue("value1"); + count1.setLabel("label1"); + count1.setCount(1); + + CaseListDataCount count2 = new CaseListDataCount(); + count2.setValue("value1"); + count2.setLabel("label1"); + count2.setCount(2); + + CaseListDataCount count3 = new CaseListDataCount(); + count3.setValue("value2"); + count3.setLabel("label2"); + count3.setCount(3); + + List counts = Arrays.asList(count1, count2, count3); + + List mergedCounts = StudyViewColumnarServiceUtil.mergeCaseListCounts(counts); + + assertEquals(2, mergedCounts.size()); + + CaseListDataCount mergedCount1 = mergedCounts.stream() + .filter(count -> count.getValue().equals("value1")) + .findFirst() + .orElse(null); + assertEquals(3, mergedCount1.getCount().intValue()); + assertEquals("label1", mergedCount1.getLabel()); + + CaseListDataCount mergedCount2 = mergedCounts.stream() + .filter(count -> count.getValue().equals("value2")) + .findFirst() + .orElse(null); + assertEquals(3, mergedCount2.getCount().intValue()); + assertEquals("label2", mergedCount2.getLabel()); + } + + + @Test + public void testNormalizeDataCounts() { + ClinicalDataCount count1 = new ClinicalDataCount(); + count1.setAttributeId("attr1"); + count1.setValue("TRUE"); + count1.setCount(1); + + ClinicalDataCount count2 = new ClinicalDataCount(); + count2.setAttributeId("attr1"); + count2.setValue("True"); + count2.setCount(2); + + ClinicalDataCount count3 = new ClinicalDataCount(); + count3.setAttributeId("attr1"); + count3.setValue("true"); + count3.setCount(3); + + ClinicalDataCount count4 = new ClinicalDataCount(); + count4.setAttributeId("attr1"); + count4.setValue("FALSE"); + count4.setCount(4); + + ClinicalDataCount count5 = new ClinicalDataCount(); + count5.setAttributeId("attr1"); + count5.setValue("False"); + count5.setCount(5); + + List dataCounts = Arrays.asList(count1, count2, count3, count4, count5); + + List normalizedDataCounts = StudyViewColumnarServiceUtil.normalizeDataCounts(dataCounts); + + assertEquals(2, normalizedDataCounts.size()); + + // should be null because it prioritizes lower case over upper case + ClinicalDataCount trueCountNullCheck = normalizedDataCounts.stream() + .filter(count -> count.getValue().equals("True")) + .findFirst() + .orElse(null); + assertEquals(null, trueCountNullCheck); + + ClinicalDataCount trueCount = normalizedDataCounts.stream() + .filter(count -> count.getValue().equals("true")) + .findFirst() + .orElse(null); + assertEquals(6, trueCount.getCount().intValue()); + + // should be null because it prioritizes lower case over upper case + ClinicalDataCount falseCountNullCheck = normalizedDataCounts.stream() + .filter(count -> count.getValue().equals("FALSE")) + .findFirst() + .orElse(null); + assertEquals(null, falseCountNullCheck); + + ClinicalDataCount falseCount = normalizedDataCounts.stream() + .filter(count -> count.getValue().equals("False")) + .findFirst() + .orElse(null); + assertEquals(9, falseCount.getCount().intValue()); + } + + + @Test + public void testCreateGenomicDataCountItemFromMutationCounts() { + GenomicDataFilter genomicDataFilter = new GenomicDataFilter(); + genomicDataFilter.setHugoGeneSymbol("hugo1"); + + Map counts1 = Map.of( + "mutatedCount", 5, + "notMutatedCount", 10, + "notProfiledCount", 15 + ); + + GenomicDataCountItem item1 = StudyViewColumnarServiceUtil.createGenomicDataCountItemFromMutationCounts(genomicDataFilter, counts1); + + assertEquals("hugo1", item1.getHugoGeneSymbol()); + assertEquals("mutations", item1.getProfileType()); + + assertEquals(3, item1.getCounts().size()); + + GenomicDataCount mutatedCount1 = item1.getCounts().stream() + .filter(count -> count.getValue().equals("MUTATED")) + .findFirst() + .orElse(null); + assertNotNull(mutatedCount1); + assertEquals(5, mutatedCount1.getCount().intValue()); + + GenomicDataCount notMutatedCount1 = item1.getCounts().stream() + .filter(count -> count.getValue().equals("NOT_MUTATED")) + .findFirst() + .orElse(null); + assertNotNull(notMutatedCount1); + assertEquals(10, notMutatedCount1.getCount().intValue()); + + GenomicDataCount notProfiledCount1 = item1.getCounts().stream() + .filter(count -> count.getValue().equals("NOT_PROFILED")) + .findFirst() + .orElse(null); + assertNotNull(notProfiledCount1); + assertEquals(15, notProfiledCount1.getCount().intValue()); + + // Test case where a count equals 0 + Map counts2 = Map.of( + "mutatedCount", 5, + "notMutatedCount", 0, + "notProfiledCount", 5 + ); + + GenomicDataCountItem item2 = StudyViewColumnarServiceUtil.createGenomicDataCountItemFromMutationCounts(genomicDataFilter, counts2); + + assertEquals("hugo1", item2.getHugoGeneSymbol()); + assertEquals("mutations", item2.getProfileType()); + + assertEquals(2, item2.getCounts().size()); + + GenomicDataCount mutatedCount2 = item2.getCounts().stream() + .filter(count -> count.getValue().equals("MUTATED")) + .findFirst() + .orElse(null); + assertNotNull(mutatedCount2); + assertEquals(5, mutatedCount2.getCount().intValue()); + + GenomicDataCount notMutatedCount2 = item2.getCounts().stream() + .filter(count -> count.getValue().equals("NOT_MUTATED")) + .findFirst() + .orElse(null); + assertNull(notMutatedCount2); + + GenomicDataCount notProfiledCount2 = item2.getCounts().stream() + .filter(count -> count.getValue().equals("NOT_PROFILED")) + .findFirst() + .orElse(null); + assertNotNull(notProfiledCount2); + assertEquals(5, notProfiledCount2.getCount().intValue()); + } + + +} \ No newline at end of file diff --git a/src/test/java/org/cbioportal/test/integration/MysqlInitializer.java b/src/test/java/org/cbioportal/test/integration/DatabaseInitializer.java similarity index 67% rename from src/test/java/org/cbioportal/test/integration/MysqlInitializer.java rename to src/test/java/org/cbioportal/test/integration/DatabaseInitializer.java index a4b60e3c741..049bb54d70e 100644 --- a/src/test/java/org/cbioportal/test/integration/MysqlInitializer.java +++ b/src/test/java/org/cbioportal/test/integration/DatabaseInitializer.java @@ -5,7 +5,7 @@ import org.springframework.context.ConfigurableApplicationContext; import org.testcontainers.containers.MySQLContainer; -public abstract class MysqlInitializer implements +public abstract class DatabaseInitializer implements ApplicationContextInitializer { public void initializeImpl(ConfigurableApplicationContext configurableApplicationContext, @@ -13,7 +13,12 @@ public void initializeImpl(ConfigurableApplicationContext configurableApplicatio TestPropertyValues values = TestPropertyValues.of( String.format("spring.datasource.url=%s?useSSL=false&allowPublicKeyRetrieval=true", mysqlContainer.getJdbcUrl()), String.format("spring.datasource.username=%s", mysqlContainer.getUsername()), - String.format("spring.datasource.password=%s", mysqlContainer.getPassword()) + String.format("spring.datasource.password=%s", mysqlContainer.getPassword()), + "spring.datasource.driver-class-name=com.mysql.jdbc.Driver", + "spring.datasource.clickhouse.url=jdbc:ch://localhost:8443/cbioportal", + "spring.datasource.clickhouse.username=dummy", + "spring.datasource.clickhouse.password=dummy", + "spring.datasource.clickhouse.driver-class-name=com.clickhouse.jdbc.ClickHouseDriver" ); values.applyTo(configurableApplicationContext); } diff --git a/src/test/java/org/cbioportal/test/integration/security/ContainerConfig.java b/src/test/java/org/cbioportal/test/integration/security/ContainerConfig.java index b74ff9c542d..ccdb3a58d7e 100644 --- a/src/test/java/org/cbioportal/test/integration/security/ContainerConfig.java +++ b/src/test/java/org/cbioportal/test/integration/security/ContainerConfig.java @@ -1,7 +1,7 @@ package org.cbioportal.test.integration.security; import dasniko.testcontainers.keycloak.KeycloakContainer; -import org.cbioportal.test.integration.MysqlInitializer; +import org.cbioportal.test.integration.DatabaseInitializer; import org.cbioportal.test.integration.OAuth2KeycloakInitializer; import org.cbioportal.test.integration.OAuth2ResourceServerKeycloakInitializer; import org.cbioportal.test.integration.SamlKeycloakInitializer; @@ -119,7 +119,7 @@ public void initialize( } // Update application properties with connection info on Mysql container - public static class MyMysqlInitializer extends MysqlInitializer { + public static class MyMysqlInitializer extends DatabaseInitializer { @Override public void initialize( ConfigurableApplicationContext configurableApplicationContext) { diff --git a/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java b/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java index 83383756a04..b25def51f5b 100644 --- a/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java +++ b/src/test/java/org/cbioportal/web/util/ClinicalDataBinUtilTest.java @@ -12,13 +12,9 @@ import org.cbioportal.service.PatientService; import org.cbioportal.service.impl.CustomDataServiceImpl; import org.cbioportal.service.util.ClinicalAttributeUtil; -import org.cbioportal.service.util.CustomAttributeWithData; -import org.cbioportal.service.util.CustomDataSession; -import org.cbioportal.service.util.CustomDataValue; import org.cbioportal.service.util.SessionServiceRequestHandler; import org.cbioportal.web.parameter.*; import org.junit.Before; -import org.junit.Ignore; import org.junit.Test; import org.junit.runner.RunWith; @@ -74,6 +70,7 @@ public class ClinicalDataBinUtilTest { @Spy @InjectMocks private DataBinner dataBinner; + @Spy @InjectMocks private DiscreteDataBinner discreteDataBinner; diff --git a/src/test/java/org/cbioportal/web/util/DataBinnerTest.java b/src/test/java/org/cbioportal/web/util/DataBinnerTest.java index b6fe1f81688..5ed86de169b 100644 --- a/src/test/java/org/cbioportal/web/util/DataBinnerTest.java +++ b/src/test/java/org/cbioportal/web/util/DataBinnerTest.java @@ -31,11 +31,7 @@ import org.springframework.boot.test.mock.mockito.MockBean; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; -import org.mockito.InjectMocks; -import org.mockito.MockitoAnnotations; -import org.mockito.Spy; import org.mockito.internal.matchers.apachecommons.ReflectionEquals; -import org.mockito.junit.MockitoJUnitRunner; @RunWith(SpringJUnit4ClassRunner.class) @SpringBootTest diff --git a/src/test/resources/clickhouse_cgds.sql b/src/test/resources/clickhouse_cgds.sql new file mode 100644 index 00000000000..05548ba80c7 --- /dev/null +++ b/src/test/resources/clickhouse_cgds.sql @@ -0,0 +1,602 @@ +DROP TABLE IF EXISTS info; +DROP TABLE IF EXISTS clinical_event_data; +DROP TABLE IF EXISTS clinical_event; +DROP TABLE IF EXISTS cosmic_mutation; +DROP TABLE IF EXISTS copy_number_seg_file; +DROP TABLE IF EXISTS copy_number_seg; +DROP TABLE IF EXISTS sample_cna_event; +DROP TABLE IF EXISTS cna_event; +DROP TABLE IF EXISTS gistic_to_gene; +DROP TABLE IF EXISTS gistic; +DROP TABLE IF EXISTS mut_sig; +DROP TABLE IF EXISTS clinical_attribute_meta; +DROP TABLE IF EXISTS clinical_sample; +DROP TABLE IF EXISTS clinical_patient; +DROP TABLE IF EXISTS resource_definition; +DROP TABLE IF EXISTS resource_sample; +DROP TABLE IF EXISTS resource_patient; +DROP TABLE IF EXISTS resource_study; +DROP TABLE IF EXISTS mutation_count_by_keyword; +DROP TABLE IF EXISTS allele_specific_copy_number; +DROP TABLE IF EXISTS mutation; +DROP TABLE IF EXISTS mutation_event; +DROP TABLE IF EXISTS structural_variant; +DROP TABLE IF EXISTS sample_profile; +DROP TABLE IF EXISTS gene_panel_list; +DROP TABLE IF EXISTS gene_panel; +DROP TABLE IF EXISTS genetic_profile_samples; +DROP TABLE IF EXISTS genetic_alteration; +DROP TABLE IF EXISTS genetic_profile_link; +DROP TABLE IF EXISTS alteration_driver_annotation; +DROP TABLE IF EXISTS genetic_profile; +DROP TABLE IF EXISTS gene_alias; +DROP TABLE IF EXISTS geneset_gene; +DROP TABLE IF EXISTS reference_genome_gene; +DROP TABLE IF EXISTS gene; +DROP TABLE IF EXISTS sample_list_list; +DROP TABLE IF EXISTS sample_list; +DROP TABLE IF EXISTS sample; +DROP TABLE IF EXISTS patient; +DROP TABLE IF EXISTS authorities; +DROP TABLE IF EXISTS data_access_tokens; +DROP TABLE IF EXISTS users; +DROP TABLE IF EXISTS cancer_study_tags; +DROP TABLE IF EXISTS cancer_study; +DROP TABLE IF EXISTS type_of_cancer; +DROP TABLE IF EXISTS geneset_hierarchy_leaf; +DROP TABLE IF EXISTS geneset_hierarchy_node; +DROP TABLE IF EXISTS geneset; +DROP TABLE IF EXISTS generic_entity_properties; +DROP TABLE IF EXISTS genetic_entity; +DROP TABLE IF EXISTS reference_genome; + +-- -------------------------------------------------------- +CREATE TABLE generic_entity_properties +( + id Int32, + genetic_entity_id Int32, + name String, + value String +) ENGINE = MergeTree() ORDER BY id; + +-- -------------------------------------------------------- +CREATE TABLE geneset +( + id Int32, + genetic_entity_id Int32, + external_id String, + name String, + description Nullable(String), + ref_link String +) ENGINE = MergeTree() ORDER BY id; + +CREATE TABLE geneset_gene +( + geneset_id Int32, + entrez_gene_id Int32 +) ENGINE = MergeTree() ORDER BY geneset_id; +-- -------------------------------------------------------- +CREATE TABLE geneset_hierarchy_node +( + node_id Int32, + node_name String, + parent_id Nullable(Int32) +) ENGINE = MergeTree() ORDER BY node_id; + +-- -------------------------------------------------------- +CREATE TABLE geneset_hierarchy_leaf +( + node_id Int32, + geneset_id Nullable(Int32) +) ENGINE = MergeTree() ORDER BY node_id; + +-- -------------------------------------------------------- +CREATE TABLE type_of_cancer +( + type_of_cancer_id String, + name String, + dedicated_color String, + short_name Nullable(String), + parent Nullable(String) +) ENGINE = MergeTree() ORDER BY type_of_cancer_id; + +-- -------------------------------------------------------- +CREATE TABLE cancer_study +( + cancer_study_id Int32, + cancer_study_identifier String, + type_of_cancer_id String, + name String, + description String, + public UInt8, + pmid Nullable(String), + citation Nullable(String), + groups Nullable(String), + status Nullable(Int8), + import_date Nullable(DateTime), + reference_genome_id Int32 DEFAULT 1 +) ENGINE = MergeTree() ORDER BY cancer_study_id; + +-- -------------------------------------------------------- +CREATE TABLE cancer_study_tags +( + cancer_study_id Int32, + tags String +) ENGINE = MergeTree() ORDER BY cancer_study_id; + +-- -------------------------------------------------------- +CREATE TABLE users +( + email String, + name String, + enabled UInt8 +) ENGINE = MergeTree() ORDER BY email; + +-- -------------------------------------------------------- +CREATE TABLE authorities +( + email String, + authority String +) ENGINE = MergeTree() ORDER BY email; + +-- -------------------------------------------------------- +CREATE TABLE patient +( + internal_id Int32, + stable_id String, + cancer_study_id Int32 +) ENGINE = MergeTree() ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE sample +( + internal_id Int32, + stable_id String, + sample_type String, + patient_id Int32 +) ENGINE = MergeTree() ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE sample_list +( + list_id Int32, + stable_id String, + category String, + cancer_study_id Int32, + name String, + description Nullable(String) +) ENGINE = MergeTree() ORDER BY list_id; + +-- -------------------------------------------------------- +CREATE TABLE sample_list_list +( + list_id Int32, + sample_id Int32 +) ENGINE = MergeTree() ORDER BY list_id; + +-- -------------------------------------------------------- +CREATE TABLE genetic_entity +( + id Int32, + entity_type String, + stable_id Nullable(String) +) ENGINE = MergeTree() ORDER BY id; + +-- -------------------------------------------------------- +CREATE TABLE alteration_driver_annotation ( + alteration_event_id Int32, + genetic_profile_id Int32, + sample_id Int32, + driver_filter String, + driver_filter_annotation String, + driver_tiers_filter String, + driver_tiers_filter_annotation String +) ENGINE = MergeTree() ORDER BY (alteration_event_id, genetic_profile_id, sample_id); + +-- -------------------------------------------------------- +CREATE TABLE genetic_profile +( + genetic_profile_id Int32, + stable_id String, + genetic_alteration_type String, + genomic_build String, + genetic_alteration_identifier String, + name String, + datatype String, + description String, + show_profile_in_analysis_tab Int32, + generic_assay_type Nullable(String), + cancer_study_id Int32, + patient_level Nullable(Int32), +) ENGINE = MergeTree() ORDER BY genetic_profile_id; + +-- -------------------------------------------------------- +CREATE TABLE genetic_profile_link +( + genetic_profile_id Int32, + genetic_entity_id Int32 +) ENGINE = MergeTree() ORDER BY genetic_profile_id; + +-- -------------------------------------------------------- +CREATE TABLE genetic_alteration +( + genetic_profile_id Int32, + genetic_entity_id Int32, + values String +) ENGINE = MergeTree() ORDER BY genetic_profile_id; + +-- -------------------------------------------------------- +CREATE TABLE genetic_profile_samples +( + genetic_profile_id Int32, + ordered_sample_list String +) ENGINE = MergeTree() ORDER BY genetic_profile_id; + +-- -------------------------------------------------------- +CREATE TABLE gene_panel +( + internal_id Int32, + stable_id Nullable(String), + name Nullable(String), + description Nullable(String) +) ENGINE = MergeTree() ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE gene_panel_list +( + internal_id Int32, + gene_id Int32 +) ENGINE = MergeTree() ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE sample_profile +( + panel_id Nullable(Int32), + sample_id Int32, + genetic_profile_id Int32 +) ENGINE = MergeTree() ORDER BY sample_id; + +-- -------------------------------------------------------- +CREATE TABLE structural_variant +( + internal_id Int32, + genetic_profile_id Int32, + sample_id Int32, + site1_entrez_gene_id Nullable(Int32), + site1_ensembl_transcript_id Nullable(String), + site1_chromosome Nullable(String), + site1_region Nullable(String), + site1_region_number Nullable(Int32), + site1_contig Nullable(String), + site1_position Nullable(Int32), + site1_description Nullable(String), + site2_entrez_gene_id Nullable(Int32), + site2_ensembl_transcript_id Nullable(String), + site2_chromosome Nullable(String), + site2_region Nullable(String), + site2_region_number Nullable(Int32), + site2_contig Nullable(String), + site2_position Nullable(Int32), + site2_description Nullable(String), + site2_effect_on_frame Nullable(String), + ncbi_build Nullable(String), + dna_support Nullable(String), + rna_support Nullable(String), + normal_read_count Nullable(Int32), + tumor_read_count Nullable(Int32), + normal_variant_count Nullable(Int32), + tumor_variant_count Nullable(Int32), + normal_paired_end_read_count Nullable(Int32), + tumor_paired_end_read_count Nullable(Int32), + normal_split_read_count Nullable(Int32), + tumor_split_read_count Nullable(Int32), + annotation Nullable(String), + breakpoint_type Nullable(String), + connection_type Nullable(String), + event_info Nullable(String), + class Nullable(String), + length Nullable(Int32), + comments Nullable(String), + sv_status Enum8('GERMLINE' = 0, 'SOMATIC' = 1) DEFAULT 'SOMATIC', + annotation_json Nullable(String) +) ENGINE = MergeTree() + ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE mutation_event +( + mutation_event_id Int32, + entrez_gene_id Int32, + chr Nullable(String), + start_position Nullable(Int64), + end_position Nullable(Int64), + reference_allele Nullable(String), + tumor_seq_allele Nullable(String), + protein_change String, + mutation_type String, + ncbi_build Nullable(String), + strand Nullable(String), + variant_type Nullable(String), + db_snp_rs Nullable(String), + db_snp_val_status Nullable(String), + refseq_mrna_id Nullable(String), + codon_change Nullable(String), + uniprot_accession Nullable(String), + protein_pos_start Nullable(Int32), + protein_pos_end Nullable(Int32), + canonical_transcript Nullable(UInt8), + functional_impact_score String, + fis_value String, + link_xvar String, + link_pdb String, + link_msa String, + keyword Nullable(String) DEFAULT NULL COMMENT 'e.g. truncating, V200 Missense, E338del' +) ENGINE = MergeTree() ORDER BY mutation_event_id; + +-- -------------------------------------------------------- +CREATE TABLE mutation ( + mutation_event_id Int32, + genetic_profile_id Int32, + sample_id Int32, + entrez_gene_id Int32, + center String, + sequencer String, + mutation_status String COMMENT 'Germline, Somatic or LOH.', + validation_status String, + tumor_seq_allele1 String, + tumor_seq_allele2 String, + matched_norm_sample_barcode String, + match_norm_seq_allele1 String, + match_norm_seq_allele2 String, + tumor_validation_allele1 String, + tumor_validation_allele2 String, + match_norm_validation_allele1 String, + match_norm_validation_allele2 String, + verification_status String, + sequencing_phase String, + sequence_source String, + validation_method String, + score String, + bam_file String, + tumor_alt_count Int32, + tumor_ref_count Int32, + normal_alt_count Int32, + normal_ref_count Int32, + amino_acid_change String, + annotation_json String +) ENGINE = MergeTree() ORDER BY (mutation_event_id, genetic_profile_id, sample_id); + +-- -------------------------------------------------------- +CREATE TABLE allele_specific_copy_number ( + mutation_event_id Int32, + genetic_profile_id Int32, + sample_id Int32, + ascn_integer_copy_number Nullable(Int32), + ascn_method String, + ccf_expected_copies_upper Nullable(Float32), + ccf_expected_copies Nullable(Float32), + clonal Nullable(String), + minor_copy_number Nullable(Int32), + expected_alt_copies Nullable(Int32), + total_copy_number Nullable(Int32) +) ENGINE = MergeTree() + ORDER BY (mutation_event_id, genetic_profile_id, sample_id); + +-- -------------------------------------------------------- +CREATE TABLE mutation_count_by_keyword +( + genetic_profile_id Int32, + entrez_gene_id Int32, + mutation_id Int32, + keyword String, + keyword_count Int32, + gene_count Int32 +) ENGINE = MergeTree() ORDER BY genetic_profile_id; + +-- -------------------------------------------------------- +CREATE TABLE resource_study +( + resource_id Int32, + study_id Int32 +) ENGINE = MergeTree() ORDER BY resource_id; + +-- -------------------------------------------------------- +CREATE TABLE resource_patient +( + resource_id Int32, + patient_id Int32 +) ENGINE = MergeTree() ORDER BY resource_id; + +-- -------------------------------------------------------- +CREATE TABLE resource_sample +( + resource_id Int32, + sample_id Int32 +) ENGINE = MergeTree() ORDER BY resource_id; + +-- -------------------------------------------------------- +CREATE TABLE resource_definition +( + resource_id Int32, + definition String +) ENGINE = MergeTree() ORDER BY resource_id; + +-- -------------------------------------------------------- +CREATE TABLE clinical_patient +( + internal_id Int32, + attr_id Nullable(String), + attr_value Nullable(String) +) ENGINE = MergeTree() ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE clinical_sample +( + internal_id Int32, + attr_id Nullable(String), + attr_value Nullable(String) +) ENGINE = MergeTree() ORDER BY internal_id; + +-- -------------------------------------------------------- +CREATE TABLE clinical_attribute_meta +( + attr_id String, + display_name Nullable(String), + description Nullable(String), + datatype Nullable(String), + patient_attribute Nullable(Int32), + priority Nullable(String), + cancer_study_id Nullable(Int32) +) ENGINE = MergeTree() ORDER BY attr_id; + +-- -------------------------------------------------------- +CREATE TABLE mut_sig +( + cancer_study_id Int32, + entrez_gene_id Int32, + rank Int32, + numbasescovered Int32, + nummutations Int32, + p_value Float32, + q_value Float32 +) ENGINE = MergeTree() + ORDER BY (cancer_study_id, entrez_gene_id); + +-- -------------------------------------------------------- +CREATE TABLE gistic +( + gistic_roi_id Int32, + cancer_study_id Nullable(Int32), + chromosome Int32, + cytoband Nullable(Float32), + wide_peak_start Nullable(Float32), + wide_peak_end Nullable(Float32), + q_value Float32, + amp tinyint +) ENGINE = MergeTree() ORDER BY gistic_roi_id; + +-- -------------------------------------------------------- +CREATE TABLE gistic_to_gene +( + gistic_roi_id Int32, + entrez_gene_id Nullable(Int32) +) ENGINE = MergeTree() ORDER BY gistic_roi_id; + +-- -------------------------------------------------------- +CREATE TABLE cna_event +( + cna_event_id Int32, + entrez_gene_id Nullable(Int32), + alteration Int32 + +) ENGINE = MergeTree() ORDER BY cna_event_id; + +-- -------------------------------------------------------- +CREATE TABLE sample_cna_event +( + cna_event_id Int32, + sample_id Int32, + genetic_profile_id Int32, + annotation_json String +) ENGINE = MergeTree() ORDER BY cna_event_id; + +-- -------------------------------------------------------- +CREATE TABLE copy_number_seg +( + seg_id Int32, + sample_id Int32, + genetic_profile_id Int32, + cancer_study_id Int32, + chr String, + segment_mean Nullable(Float32), + num_probes Int32, + start Int64, + end Int64 +) ENGINE = MergeTree() ORDER BY seg_id; + +-- -------------------------------------------------------- +CREATE TABLE copy_number_seg_file +( + seg_file_id Int32, + copy_number_profile_id Int32, + file_path String, + file_md5sum String, + imported_datetime Nullable(DateTime) +) ENGINE = MergeTree() ORDER BY seg_file_id; + +-- -------------------------------------------------------- +CREATE TABLE cosmic_mutation +( + cosmic_mutation_id String, + chr Nullable(String), + start_position Nullable(Int64), + reference_allele Nullable(String), + tumor_seq_allele Nullable(String), + strand Nullable(String), + codon_change Nullable(String), + entrez_gene_id Int32, + protein_change String, + count Int32, + keyword Nullable(String) +) ENGINE = MergeTree() ORDER BY cosmic_mutation_id; + +-- -------------------------------------------------------- +CREATE TABLE clinical_event +( + clinical_event_id Int32, + patient_id Int, + event_type String, + start_date Int32 default 0, + stop_date Int32 default 0 +) ENGINE = MergeTree() ORDER BY clinical_event_id; + +-- -------------------------------------------------------- +CREATE TABLE clinical_event_data +( + clinical_event_id Int32, + key String, + value String +) ENGINE = MergeTree() ORDER BY clinical_event_id; + +-- -------------------------------------------------------- +CREATE TABLE info +( + table_id String, + description String +) ENGINE = MergeTree() ORDER BY table_id; + +-- -------------------------------------------------------- +CREATE TABLE reference_genome +( + reference_genome_id Int32, + species String, + name String, + build_name String, + genome_size Nullable(Int64), + url String, + release_date Nullable(DateTime) +) ENGINE = MergeTree() ORDER BY reference_genome_id; + +CREATE TABLE gene +( + entrez_gene_id Int32, + hugo_gene_symbol String, + genetic_entity_id Int32, + type Nullable(String) +) ENGINE = MergeTree() ORDER BY entrez_gene_id; + +CREATE TABLE gene_alias +( + entrez_gene_id Int32, + gene_alias String +) ENGINE MergeTree() ORDER BY entrez_gene_id; + +CREATE TABLE reference_genome_gene +( + entrez_gene_id Int32, + reference_genome_id Int32, + chr varchar(5), + cytoband String, + start BIGINT, + end BIGINT +) ENGINE MergeTree() ORDER BY entrez_gene_id; \ No newline at end of file diff --git a/src/test/resources/clickhouse_data.sql b/src/test/resources/clickhouse_data.sql new file mode 100644 index 00000000000..20b0da393dd --- /dev/null +++ b/src/test/resources/clickhouse_data.sql @@ -0,0 +1,668 @@ +insert into type_of_cancer (type_of_cancer_id,name,dedicated_color,short_name,parent) values ('brca','breast invasive carcinoma','hotpink','breast','tissue'); +insert into type_of_cancer (type_of_cancer_id,name,dedicated_color,short_name,parent) values ('acc','adrenocortical carcinoma','purple','acc','adrenal_gland'); + +insert into `reference_genome` values (1, 'human', 'hg19', 'grch37', null, 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigzips', '2009-02-01 00:00:00'); +insert into `reference_genome` values (2, 'human', 'hg38', 'grch38', null, 'http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigzips', '2013-12-01 00:00:00'); + +insert into cancer_study (cancer_study_id,cancer_study_identifier,type_of_cancer_id,name,description,public,pmid,citation,groups,status,import_date,reference_genome_id) values(1,'study_tcga_pub','brca','breast invasive carcinoma (tcga, nature 2012)','the cancer genome atlas (tcga) breast invasive carcinoma project. 825 cases.
nature 2012. raw data via the tcga data portal.',1,'23000897,26451490','tcga, nature 2012, ...','su2c-pi3k;public;gdac',0,'2011-12-18 13:17:17+00:00',1); +insert into cancer_study (cancer_study_id,cancer_study_identifier,type_of_cancer_id,name,description,public,pmid,citation,groups,status,import_date,reference_genome_id) values(2,'acc_tcga','acc','adrenocortical carcinoma (tcga, provisional)','tcga adrenocortical carcinoma; raw data at the nci.',1,'23000897','tcga, nature 2012','su2c-pi3k;public;gdac',0,'2013-10-12 11:11:15+00:00',1); +insert into cancer_study (cancer_study_id,cancer_study_identifier,type_of_cancer_id,name,description,public,pmid,citation,groups,status,import_date,reference_genome_id) values(3,'study_genie_pub','mixed','GENIE Cohort public','GENIE public','1','','','GENIEPUB;GENIE',0,'2024-04-03 20:12:24.000000',1); + +insert into cancer_study_tags (cancer_study_id,tags) values(1,'{"analyst": {"name": "jack", "email": "jack@something.com"}, "load id": 35}'); +insert into cancer_study_tags (cancer_study_id,tags) values(2,'{"load id": 36}'); + +insert into genetic_entity (id,entity_type,stable_id) values (1,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (2,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (3,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (4,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (5,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (6,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (7,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (8,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (9,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (10,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (11,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (12,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (13,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (14,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (15,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (16,'gene', null); +insert into genetic_entity (id,entity_type,stable_id) values (17,'geneset', null); +insert into genetic_entity (id,entity_type,stable_id) values (18,'geneset', null); +insert into genetic_entity (id,entity_type,stable_id) values (19,'generic_assay','17-aag'); +insert into genetic_entity (id,entity_type,stable_id) values (20,'generic_assay','aew541'); +-- add genes, genetic entities and structural variants for structural_variant +insert into genetic_entity (id,entity_type) values(21,'gene'); +insert into genetic_entity (id,entity_type) values(22,'gene'); +insert into genetic_entity (id,entity_type) values(23,'gene'); +insert into genetic_entity (id,entity_type) values(24,'gene'); +insert into genetic_entity (id,entity_type) values(25,'gene'); +insert into genetic_entity (id,entity_type) values(26,'gene'); +insert into genetic_entity (id,entity_type) values(27,'gene'); +insert into genetic_entity (id,entity_type,stable_id) values (28,'generic_assay','mean_1'); +insert into genetic_entity (id,entity_type,stable_id) values (29,'generic_assay','mean_2'); +insert into genetic_entity (id,entity_type,stable_id) values (30,'GENERIC_ASSAY','1p_status'); +insert into genetic_entity (id,entity_type,stable_id) values (31,'GENERIC_ASSAY','DMETS_DX_ADRENAL'); + +-- hugo_gene_symbol should be UPPERCASE +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(207,'AKT1',1,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(208,'AKT2',2,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(10000,'AKT3',3,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(369,'ARAF',4,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(472,'ATM',5,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(673,'BRAF',6,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(672,'BRCA1',7,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(675,'BRCA2',8,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(3265,'HRAS',9,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(3845,'KRAS',10,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(4893,'NRAS',11,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(79501,'OR4F5',12,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(148398,'SAMD11',13,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(26155,'NOC2L',14,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2064,'ERBB2',15,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2886,'GRB7',16,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(57670,'kiaa1549',21,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(8031,'ncoa4',22,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(5979,'ret',23,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(27436,'eml4',24,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(238,'alk',25,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(7113,'tmprss2',26,'protein-coding'); +insert into gene (entrez_gene_id,hugo_gene_symbol,genetic_entity_id,type) values(2078,'erg',27,'protein-coding'); + +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(3677745,'d45a',79501,1,'OR4F5 d45 missense'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(426644,'g145c',79501,1,'OR4F5 g145 missense'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(460103,'p23p',148398,1,'SAMD11 p23 silent'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(4010395,'s146s',26155,1,'NOC2L s146 silent'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(1290240,'m1t',26155,1,'NOC2L truncating'); +insert into cosmic_mutation (cosmic_mutation_id,protein_change,entrez_gene_id,count,keyword) values(4010425,'q197*',26155,1,'NOC2L truncating'); + +insert into gene_alias (entrez_gene_id,gene_alias) values (207,'akt alias'); +insert into gene_alias (entrez_gene_id,gene_alias) values (207,'akt alias2'); +insert into gene_alias (entrez_gene_id,gene_alias) values (675,'BRCA1 alias'); + +insert into reference_genome_gene (entrez_gene_id,cytoband,start,end,chr,reference_genome_id) values(207,'14q32.33',105235686,105262088,14,1); +insert into reference_genome_gene (entrez_gene_id,cytoband,start,end,chr,reference_genome_id) values(207,'14q32.33',104769349,104795751,14,2); +insert into reference_genome_gene (entrez_gene_id,cytoband,start,end,chr,reference_genome_id) values(208,'19q13.2', 40736224, 40791443,19,1); +insert into reference_genome_gene (entrez_gene_id,cytoband,start,end,chr,reference_genome_id) values(208,'19q13.2', 40230317, 40285536,19,2); + +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (2,'study_tcga_pub_gistic',1,'COPY_NUMBER_ALTERATION','discrete','putative copy-number alterations from gistic','putative copy-number from gistic 2.0. values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (3,'study_tcga_pub_mrna',1,'mrna_expression','z-score','mrna expression (microarray)','expression levels (agilent microarray).',0); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (10,'study_tcga_pub_m_na',1,'mrna_expression','z-score','mrna expression (microarray)','expression levels (agilent microarray).',0); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (4,'study_tcga_pub_log2cna',1,'COPY_NUMBER_ALTERATION','log2-value','log2 copy-number values','log2 copy-number valuesfor each gene (from affymetrix snp6).',0); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (5,'study_tcga_pub_methylation_hm27',1,'methylation','continuous','methylation (hm27)','methylation beta-values (hm27 platform). for genes with multiple methylation probes, the probe least correlated with expression is selected.',0); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (6,'study_tcga_pub_mutations',1,'MUTATION_EXTENDED','maf','mutations','mutation data from whole exome sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (7,'study_tcga_pub_sv',1,'structural_variant','sv','structural variants','structural variants detected by illumina hiseq sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (8,'acc_tcga_mutations',2,'MUTATION_EXTENDED','maf','mutations','mutation data from whole exome sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (13,'acc_tcga_sv',2,'structural_variant','sv','structural variants','structural variants detected by illumina hiseq sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (9,'study_tcga_pub_gsva_scores',1,'geneset_score','gsva-score','gsva scores','gsva scores for oncogenic signature gene sets from msigdb calculated with gsva version 1.22.4, r version 3.3.2.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab,generic_assay_type) values (11,'study_tcga_pub_treatment_ic50',1,'generic_assay','ic50','treatment ic50 values','treatment response ic50 values',1,'treatment_response'); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab,generic_assay_type) values (12,'study_tcga_pub_mutational_signature',1,'generic_assay','limit-value','mutational_signature values','mutational_signature values',1,'mutational_signature'); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (14,'study_tcga_pub_cna',1,'COPY_NUMBER_ALTERATION','discrete','Copy-number alterations','Copy number alterations (amplifications and deletions) from targeted sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (15,'study_tcga_pub_rppa',1,'PROTEIN_LEVEL','log2-value','Protein expression (RPPA)','Protein expression measured by reverse-phase protein array',0); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (16,'genie_public_mutations',3,'MUTATION_EXTENDED','maf','Somatic mutations','Somatic mutations from targeted sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab) values (17,'genie_public_cna',3,'COPY_NUMBER_ALTERATION','discrete','Copy-number alterations','Copy number alterations (amplifications and deletions) from targeted sequencing.',1); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab,generic_assay_type) values (18,'acc_tcga_armlevel_cna',2,'GENERIC_ASSAY','CATEGORICAL','Putative arm-level copy-number from GISTIC','Putative arm-level copy-number from GISTIC 2.0.',1,'ARMLEVEL_CNA'); +insert into genetic_profile (genetic_profile_id,stable_id,cancer_study_id,genetic_alteration_type,datatype,name,description,show_profile_in_analysis_tab,generic_assay_type,patient_level) values (19,'study_genie_pub_distant_mets',3,'GENERIC_ASSAY','CATEGORICAL','Patient-level information on distant mets','Patient-level information on distant mets from GENIE BPC NSCLC Public',1,'DISTANT_METS',1); + +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (2,'1,2,3,4,5,6,7,8,9,10,11,12,13,14,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (3,'2,3,6,8,9,10,12,13,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (4,'1,2,3,4,5,6,7,8,9,10,11,12,13,14,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (5,'2,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (11,'1,2,3,4,5,6,7,8,9,10,11,12,13,14,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (14,'1,2,3,4,5,6,7,8,9,10,11,12,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values (15,'1,2,3,4,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values(10,'1,2,3,4,5,6,7,8,9,10,11,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values(18,'15,16,17,19,'); +insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values(19,'301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,'); + +insert into patient (internal_id,stable_id,cancer_study_id) values (1,'tcga-a1-a0sb',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (2,'tcga-a1-a0sd',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (3,'tcga-a1-a0se',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (4,'tcga-a1-a0sf',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (5,'tcga-a1-a0sg',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (6,'tcga-a1-a0sh',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (7,'tcga-a1-a0si',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (8,'tcga-a1-a0sj',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (9,'tcga-a1-a0sk',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (10,'tcga-a1-a0sm',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (11,'tcga-a1-a0sn',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (12,'tcga-a1-a0so',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (13,'tcga-a1-a0sp',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (14,'tcga-a1-a0sq',1); +insert into patient (internal_id,stable_id,cancer_study_id) values (15,'tcga-a1-b0so',2); +insert into patient (internal_id,stable_id,cancer_study_id) values (16,'tcga-a1-b0sp',2); +insert into patient (internal_id,stable_id,cancer_study_id) values (17,'tcga-a1-b0sq',2); +insert into patient (internal_id,stable_id,cancer_study_id) values (18,'tcga-a1-a0sb',2); +insert into patient (internal_id,stable_id,cancer_study_id) values (301,'GENIE-TEST-301',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (302,'GENIE-TEST-302',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (303,'GENIE-TEST-303',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (304,'GENIE-TEST-304',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (305,'GENIE-TEST-305',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (306,'GENIE-TEST-306',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (307,'GENIE-TEST-307',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (308,'GENIE-TEST-308',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (309,'GENIE-TEST-309',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (310,'GENIE-TEST-310',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (311,'GENIE-TEST-311',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (312,'GENIE-TEST-312',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (313,'GENIE-TEST-313',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (314,'GENIE-TEST-314',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (315,'GENIE-TEST-315',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (316,'GENIE-TEST-316',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (317,'GENIE-TEST-317',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (318,'GENIE-TEST-318',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (319,'GENIE-TEST-319',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (320,'GENIE-TEST-320',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (321,'GENIE-TEST-321',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (322,'GENIE-TEST-322',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (323,'GENIE-TEST-323',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (324,'GENIE-TEST-324',3); + +insert into sample (internal_id,stable_id,sample_type,patient_id) values (1,'tcga-a1-a0sb-01','primary solid tumor',1); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (18,'tcga-a1-a0sb-02','primary solid tumor',1); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (2,'tcga-a1-a0sd-01','primary solid tumor',2); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (3,'tcga-a1-a0se-01','primary solid tumor',3); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (4,'tcga-a1-a0sf-01','primary solid tumor',4); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (5,'tcga-a1-a0sg-01','primary solid tumor',5); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (6,'tcga-a1-a0sh-01','primary solid tumor',6); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (7,'tcga-a1-a0si-01','primary solid tumor',7); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (8,'tcga-a1-a0sj-01','primary solid tumor',8); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (9,'tcga-a1-a0sk-01','primary solid tumor',9); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (10,'tcga-a1-a0sm-01','primary solid tumor',10); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (11,'tcga-a1-a0sn-01','primary solid tumor',11); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (12,'tcga-a1-a0so-01','primary solid tumor',12); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (13,'tcga-a1-a0sp-01','primary solid tumor',13); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (14,'tcga-a1-a0sq-01','primary solid tumor',14); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (15,'tcga-a1-b0so-01','primary solid tumor',15); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (16,'tcga-a1-b0sp-01','primary solid tumor',16); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (17,'tcga-a1-b0sq-01','primary solid tumor',17); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (19,'tcga-a1-a0sb-01','primary solid tumor',18); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (301,'GENIE-TEST-301-01','primary solid tumor',301); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (302,'GENIE-TEST-302-01','primary solid tumor',302); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (303,'GENIE-TEST-303-01','primary solid tumor',303); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (304,'GENIE-TEST-304-01','primary solid tumor',304); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (305,'GENIE-TEST-305-01','primary solid tumor',305); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (306,'GENIE-TEST-306-01','primary solid tumor',306); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (307,'GENIE-TEST-307-01','primary solid tumor',307); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (308,'GENIE-TEST-308-01','primary solid tumor',308); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (309,'GENIE-TEST-309-01','primary solid tumor',309); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (310,'GENIE-TEST-310-01','primary solid tumor',310); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (311,'GENIE-TEST-311-01','primary solid tumor',311); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (312,'GENIE-TEST-312-01','primary solid tumor',312); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (313,'GENIE-TEST-313-01','primary solid tumor',313); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (314,'GENIE-TEST-314-01','primary solid tumor',314); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (315,'GENIE-TEST-315-01','primary solid tumor',315); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (316,'GENIE-TEST-316-01','primary solid tumor',316); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (317,'GENIE-TEST-317-01','primary solid tumor',317); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (318,'GENIE-TEST-318-01','primary solid tumor',318); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (319,'GENIE-TEST-319-01','primary solid tumor',319); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (320,'GENIE-TEST-320-01','primary solid tumor',320); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (321,'GENIE-TEST-321-01','primary solid tumor',321); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (322,'GENIE-TEST-322-01','primary solid tumor',322); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (323,'GENIE-TEST-323-01','primary solid tumor',323); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (324,'GENIE-TEST-324-01','primary solid tumor',324); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (325,'GENIE-TEST-321-02','primary solid tumor',321); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (326,'GENIE-TEST-322-02','primary solid tumor',322); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (327,'GENIE-TEST-323-02','primary solid tumor',323); + +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2038,672,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'BRCA1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (22604,672,'17',41258504,41258504,'a','c','c61g','missense_mutation','37','+','snp','rs28897672','bycluster','nm_007294','c.(181-183)tgt>ggt','p38398',61,61,1,'BRCA1 c61 missense'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2039,672,'17',41276033,41276033,'c','t','c27_splice','splice_site','37','+','snp','rs80358010','bycluster','nm_007294','c.e2+1','na',-1,-1,1,'BRCA1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2040,207,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'BRCA1 truncating'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2041,207,'17',41258504,41258504,'a','c','c61g','missense_mutation','37','+','snp','rs28897672','bycluster','nm_007294','c.(181-183)tgt>ggt','p38398',61,61,1,'BRCA1 c61 missense'); +insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2042,208,'17',41276033,41276033,'c','t','c27_splice','splice_site','37','+','snp','rs80358010','bycluster','nm_007294','c.e2+1','na',-1,-1,1,'BRCA1 truncating'); + +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2038,6,6, 'putative_driver', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (22604,6,6, 'putative_passenger', 'pathogenic', 'tier 2', 'potentially actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2039,6,12, 'putative_passenger', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2038,6,7, 'putative_driver', 'pathogenic', 'tier 2', 'potentially actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2039,6,13, 'putative_driver', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2040,6,1, 'putative_driver', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2041,6,2, 'putative_passenger', 'pathogenic', 'tier 2', 'potentially actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2042,6,3, 'putative_passenger', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (2042,8,15, 'putative_driver', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (1,7,1, 'putative_passenger', 'pathogenic', 'tier 1', 'potentially actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (3,7,1, 'putative_driver', 'pathogenic', 'class 2', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (5,7,2, 'putative_driver', 'pathogenic', 'class 3', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (1,2,1, 'putative_driver', 'pathogenic', 'tier 1', 'highly actionable'); +insert into alteration_driver_annotation (alteration_event_id,genetic_profile_id,sample_id, driver_filter, driver_filter_annotation, driver_tiers_filter, driver_tiers_filter_annotation) values (3,2,2, 'putative_passenger', 'pathogenic', 'tier 2', 'potentially actionable'); + +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2038,6,6,672,'genome.wustl.edu','illuminagaiix','na','unknown','g','a','tcga-a1-a0sh-10a-03d-a099-09','g','a','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',1,0,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (22604,6,6,672,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','a','c','tcga-a1-a0sh-10a-03d-a099-09','a','c','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2039,6,12,672,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','t','t','tcga-a1-a0so-10a-03d-a099-09','t','t','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2038,6,7,672,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','g','a','tcga-a1-a0sh-10a-03d-a099-09','g','a','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2039,6,13,672,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','t','t','tcga-a1-a0so-10a-03d-a099-09','t','t','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2040,6,1,207,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','g','a','tcga-a1-a0sh-10a-03d-a099-09','g','a','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2041,6,2,207,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','a','c','tcga-a1-a0sh-10a-03d-a099-09','a','c','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',0,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2042,6,3,208,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','t','t','tcga-a1-a0so-10a-03d-a099-09','t','t','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); +insert into mutation (mutation_event_id,genetic_profile_id,sample_id,entrez_gene_id,center,sequencer,mutation_status,validation_status,tumor_seq_allele1,tumor_seq_allele2,matched_norm_sample_barcode,match_norm_seq_allele1,match_norm_seq_allele2,tumor_validation_allele1,tumor_validation_allele2,match_norm_validation_allele1,match_norm_validation_allele2,verification_status,sequencing_phase,sequence_source,validation_method,score,bam_file,tumor_alt_count,tumor_ref_count,normal_alt_count,normal_ref_count,amino_acid_change,annotation_json) values (2042,8,15,208,'genome.wustl.edu','illuminagaiix','GERMLINE','unknown','t','t','tcga-a1-a0so-10a-03d-a099-09','t','t','na','na','na','na','unknown','phase_iv','capture','na','1','dbgap',-1,-1,-1,-1,'cyclases/protein','{"zygosity":{"status": "heterozygous"}}'); + +insert into gene_panel (internal_id,stable_id,description) values (1,'testpanel1','a test panel consisting of a few genes'); +insert into gene_panel (internal_id,stable_id,description) values (2,'testpanel2','another test panel consisting of a few genes'); +insert into gene_panel (internal_id,stable_id,description) values (3,'testpanel3','third test panel consisting of a few genes'); +insert into gene_panel (internal_id,stable_id,description) values (4,'testpanel4','fourth test panel consisting of a few genes'); + +insert into gene_panel_list (internal_id,gene_id) values (1,207); +insert into gene_panel_list (internal_id,gene_id) values (1,369); +insert into gene_panel_list (internal_id,gene_id) values (1,672); +insert into gene_panel_list (internal_id,gene_id) values (2,207); +insert into gene_panel_list (internal_id,gene_id) values (2,208); +insert into gene_panel_list (internal_id,gene_id) values (2,4893); +insert into gene_panel_list (internal_id,gene_id) values (3,472); +insert into gene_panel_list (internal_id,gene_id) values (3,673); +insert into gene_panel_list (internal_id,gene_id) values (3,675); +insert into gene_panel_list (internal_id,gene_id) values (4,208); +insert into gene_panel_list (internal_id,gene_id) values (4,673); +insert into gene_panel_list (internal_id,gene_id) values (4,675); + +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,2,1); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,3,1); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,6,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,6,1); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,7,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,2,1); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,2,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,3,1); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,4,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,5,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,6,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (3,2,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (3,3,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (3,4,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (3,6,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (4,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (4,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (5,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (5,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (6,2,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (6,3,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (6,4,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (6,6,2); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (7,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (7,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (7,6,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (8,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (8,3,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (8,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (8,6,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (9,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (9,3,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (9,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (9,6,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (10,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (10,3,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (10,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (10,6,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (11,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (11,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (12,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (12,3,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (12,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (12,6,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (13,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (13,3,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (13,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (13,6,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (14,2,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (14,4,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (15,13,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (301,16,3); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (301,17,3); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (302,16,3); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (303,17,3); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (304,17,4); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (305,16,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (306,16,null); +insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (306,17,null); + +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (1,'study_tcga_pub_all','other',1,'all tumors','all tumor samples'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (2,'study_tcga_pub_acgh','other',1,'tumors acgh','all tumors with acgh data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (3,'study_tcga_pub_cnaseq','other',1,'tumors with sequencing and acgh data','all tumor samples that have cna and sequencing data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (4,'study_tcga_pub_complete','other',1,'complete samples (mutations, copy-number, expression)','samples with complete data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (5,'study_tcga_pub_log2cna','other',1,'tumors log2 copy-number','all tumors with log2 copy-number data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (6,'study_tcga_pub_methylation_hm27','all_cases_with_mutation_data',1,'tumors with methylation data','all samples with methylation (hm27) data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (7,'study_tcga_pub_mrna','other',1,'tumors with mrna data (agilent microarray)','all samples with mrna expression data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (8,'study_tcga_pub_sequenced','other',1,'sequenced tumors','all sequenced samples'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (9,'study_tcga_pub_cna','other',1,'tumor samples with cna data','all tumors with cna data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (10,'study_tcga_pub_rna_seq_v2_mrna','other',1,'tumor samples with mrna data (rna seq v2)','all samples with mrna expression data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (11,'study_tcga_pub_microrna','other',1,'tumors with microrna data (microrna-seq)','all samples with microrna data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (12,'study_tcga_pub_rppa','other',1,'tumor samples with rppa data','tumors with reverse phase protein array (rppa) data for about 200 antibodies'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (13,'study_tcga_pub_3way_complete','other',1,'all complete tumors','all tumor samples that have mrna,cna and sequencing data'); +insert into sample_list (list_id,stable_id,category,cancer_study_id,name,description) values (14,'acc_tcga_all','other',2,'all tumors','all tumor samples'); + +insert into sample_list_list (list_id,sample_id) values (1,1); +insert into sample_list_list (list_id,sample_id) values (1,2); +insert into sample_list_list (list_id,sample_id) values (1,3); +insert into sample_list_list (list_id,sample_id) values (1,4); +insert into sample_list_list (list_id,sample_id) values (1,5); +insert into sample_list_list (list_id,sample_id) values (1,6); +insert into sample_list_list (list_id,sample_id) values (1,7); +insert into sample_list_list (list_id,sample_id) values (1,8); +insert into sample_list_list (list_id,sample_id) values (1,9); +insert into sample_list_list (list_id,sample_id) values (1,10); +insert into sample_list_list (list_id,sample_id) values (1,11); +insert into sample_list_list (list_id,sample_id) values (1,12); +insert into sample_list_list (list_id,sample_id) values (1,13); +insert into sample_list_list (list_id,sample_id) values (1,14); +insert into sample_list_list (list_id,sample_id) values (2,1); +insert into sample_list_list (list_id,sample_id) values (2,2); +insert into sample_list_list (list_id,sample_id) values (2,3); +insert into sample_list_list (list_id,sample_id) values (2,4); +insert into sample_list_list (list_id,sample_id) values (2,5); +insert into sample_list_list (list_id,sample_id) values (2,6); +insert into sample_list_list (list_id,sample_id) values (2,7); +insert into sample_list_list (list_id,sample_id) values (2,8); +insert into sample_list_list (list_id,sample_id) values (2,9); +insert into sample_list_list (list_id,sample_id) values (2,10); +insert into sample_list_list (list_id,sample_id) values (2,11); +insert into sample_list_list (list_id,sample_id) values (2,12); +insert into sample_list_list (list_id,sample_id) values (2,13); +insert into sample_list_list (list_id,sample_id) values (2,14); +insert into sample_list_list (list_id,sample_id) values (3,2); +insert into sample_list_list (list_id,sample_id) values (3,3); +insert into sample_list_list (list_id,sample_id) values (3,6); +insert into sample_list_list (list_id,sample_id) values (3,8); +insert into sample_list_list (list_id,sample_id) values (3,9); +insert into sample_list_list (list_id,sample_id) values (3,10); +insert into sample_list_list (list_id,sample_id) values (3,12); +insert into sample_list_list (list_id,sample_id) values (4,2); +insert into sample_list_list (list_id,sample_id) values (4,3); +insert into sample_list_list (list_id,sample_id) values (4,6); +insert into sample_list_list (list_id,sample_id) values (4,8); +insert into sample_list_list (list_id,sample_id) values (4,9); +insert into sample_list_list (list_id,sample_id) values (4,10); +insert into sample_list_list (list_id,sample_id) values (4,12); +insert into sample_list_list (list_id,sample_id) values (5,1); +insert into sample_list_list (list_id,sample_id) values (5,2); +insert into sample_list_list (list_id,sample_id) values (5,3); +insert into sample_list_list (list_id,sample_id) values (5,4); +insert into sample_list_list (list_id,sample_id) values (5,5); +insert into sample_list_list (list_id,sample_id) values (5,6); +insert into sample_list_list (list_id,sample_id) values (5,7); +insert into sample_list_list (list_id,sample_id) values (5,8); +insert into sample_list_list (list_id,sample_id) values (5,9); +insert into sample_list_list (list_id,sample_id) values (5,10); +insert into sample_list_list (list_id,sample_id) values (5,11); +insert into sample_list_list (list_id,sample_id) values (5,12); +insert into sample_list_list (list_id,sample_id) values (5,13); +insert into sample_list_list (list_id,sample_id) values (5,14); +insert into sample_list_list (list_id,sample_id) values (6,2); +insert into sample_list_list (list_id,sample_id) values (7,2); +insert into sample_list_list (list_id,sample_id) values (7,3); +insert into sample_list_list (list_id,sample_id) values (7,6); +insert into sample_list_list (list_id,sample_id) values (7,8); +insert into sample_list_list (list_id,sample_id) values (7,9); +insert into sample_list_list (list_id,sample_id) values (7,10); +insert into sample_list_list (list_id,sample_id) values (7,12); +insert into sample_list_list (list_id,sample_id) values (7,13); +insert into sample_list_list (list_id,sample_id) values (8,2); +insert into sample_list_list (list_id,sample_id) values (8,3); +insert into sample_list_list (list_id,sample_id) values (8,6); +insert into sample_list_list (list_id,sample_id) values (8,8); +insert into sample_list_list (list_id,sample_id) values (8,9); +insert into sample_list_list (list_id,sample_id) values (8,10); +insert into sample_list_list (list_id,sample_id) values (8,12); +insert into sample_list_list (list_id,sample_id) values (9,2); +insert into sample_list_list (list_id,sample_id) values (9,3); +insert into sample_list_list (list_id,sample_id) values (9,6); +insert into sample_list_list (list_id,sample_id) values (9,8); +insert into sample_list_list (list_id,sample_id) values (9,9); +insert into sample_list_list (list_id,sample_id) values (9,10); +insert into sample_list_list (list_id,sample_id) values (9,12); +insert into sample_list_list (list_id,sample_id) values (10,2); +insert into sample_list_list (list_id,sample_id) values (10,3); +insert into sample_list_list (list_id,sample_id) values (10,6); +insert into sample_list_list (list_id,sample_id) values (10,8); +insert into sample_list_list (list_id,sample_id) values (10,9); +insert into sample_list_list (list_id,sample_id) values (10,10); +insert into sample_list_list (list_id,sample_id) values (10,12); +insert into sample_list_list (list_id,sample_id) values (13,2); +insert into sample_list_list (list_id,sample_id) values (13,3); +insert into sample_list_list (list_id,sample_id) values (13,6); +insert into sample_list_list (list_id,sample_id) values (13,8); +insert into sample_list_list (list_id,sample_id) values (13,9); +insert into sample_list_list (list_id,sample_id) values (13,10); +insert into sample_list_list (list_id,sample_id) values (13,12); +insert into sample_list_list (list_id,sample_id) values (14,15); + +insert into copy_number_seg (seg_id,cancer_study_id,sample_id,chr,start,end,num_probes,segment_mean) values (50236594,1,1,'1',324556,180057677,291,0.0519); +insert into copy_number_seg (seg_id,cancer_study_id,sample_id,chr,start,end,num_probes,segment_mean) values (50236595,1,1,'2',224556,327677,391,0.0219); +insert into copy_number_seg (seg_id,cancer_study_id,sample_id,chr,start,end,num_probes,segment_mean) values (50236593,1,2, '2',1402650,190262486,207,0.0265); +insert into copy_number_seg (seg_id,cancer_study_id,sample_id,chr,start,end,num_probes,segment_mean) values (50236592,1,3, '3',1449872,194238390,341,0.0347); +insert into copy_number_seg (seg_id,cancer_study_id,sample_id,chr,start,end,num_probes,segment_mean) values (50236500,2,15, '2',14492,19423390,41,0.047); + +insert into clinical_patient (internal_id,attr_id,attr_value) values (1,'retrospective_collection','no'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (1,'form_completion_date','2013-12-5'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (1,'other_patient_id','286cf147-b7f7-4a05-8e41-7fbd3717ad71'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (2,'prospective_collection','yes'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'dfs_months','5.72'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'dfs_status','1:recurred/progressed'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'os_months','12.3'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'os_status','0:living'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (18,'retrospective_collection','no'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (301,'center','msk'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (302,'center','msk'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (303,'center','msk'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (304,'center','dfci'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (305,'center','dfci'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (306,'center','chop'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (307,'center','chop'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (308,'center','mda'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (309,'center','ohsu'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (310,'center','ucsf'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (311,'center','NA'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (312,'center',''); +insert into clinical_patient (internal_id,attr_id,attr_value) values (301,'dead','True'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (302,'dead','false'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (303,'dead','TRUE'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (304,'dead','False'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (305,'dead','FALSE'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (306,'dead','true'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (307,'dead','Not Released'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (308,'dead','Not Collected'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (309,'dead','FALSE'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (310,'dead','Unknown'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (311,'dead','N/A'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (312,'dead',''); +insert into clinical_patient (internal_id,attr_id,attr_value) values (301,'age','<18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (302,'age','<18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (303,'age','<18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (304,'age','>89'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (305,'age','>89'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (306,'age','18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (307,'age','22'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (308,'age','42'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (309,'age','42'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (310,'age','66'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (311,'age','68'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (312,'age','77'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (313,'age','78'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (314,'age','79'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (315,'age','80'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (316,'age','80'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (317,'age','82'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (318,'age','82'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (319,'age','89'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (320,'age','N/A'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (321,'age',''); +insert into clinical_patient (internal_id,attr_id,attr_value) values (322,'age','NAN'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (324,'age','UNKNOWN'); + +insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'other_sample_id','5c631ce8-f96a-4c35-a459-556fc4ab21e1'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'days_to_collection','276'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'is_ffpe','no'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'sample_type','secondary tumor'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (2,'oct_embedded','false'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (2,'days_to_collection','277'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (2,'pathology_report_file_name','tcga-gc-a3bm.f3408556-9259-4700-b9a0-f41e516b420c.pdf'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (2,'sample_type','primary tumor'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (15,'other_sample_id','91e7f41c-17b3-4724-96ef-d3c207b964e1'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (15,'days_to_collection','111'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (19,'days_to_collection','111'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (301,'mutation_count','11'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (302,'mutation_count','6'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (303,'mutation_count','4'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (304,'mutation_count','4'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (305,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (306,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (307,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (308,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (309,'mutation_count','1'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (310,'mutation_count','1'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (311,'mutation_count','NAN'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (312,'mutation_count',''); + +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('retrospective_collection','tissue retrospective collection indicator','text indicator for the time frame of tissue procurement,indicating that the tissue was obtained and stored prior to the initiation of the project.','string',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('prospective_collection','tissue prospective collection indicator','text indicator for the time frame of tissue procurement,indicating that the tissue was procured in parallel to the project.','string',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('form_completion_date','form completion date','form completion date','string',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('other_patient_id','other patient id','legacy dmp patient identifier (dmpnnnn)','string',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('dfs_months','disease free (months)','disease free (months) since initial treatment.','number',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('dfs_status','disease free status','disease free status since initial treatment.','string',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('os_months','overall survival (months)','overall survival in months since initial diagonosis.','number',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('os_status','overall survival status','overall patient survival status.','string',1,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('other_sample_id','other sample id','legacy dmp sample identifier (dmpnnnn)','string',0,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('days_to_collection','days to sample collection.','days to sample collection.','string',0,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('is_ffpe','is ffpe','if the sample is from ffpe','string',0,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('oct_embedded','oct embedded','oct embedded','string',0,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('pathology_report_file_name','pathology report file name','pathology report file name','string',0,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('sample_type','sample type','the type of sample (i.e.,normal,primary,met,recurrence).','string',0,'1',1); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('retrospective_collection','tissue retrospective collection indicator','text indicator for the time frame of tissue procurement,indicating that the tissue was obtained and stored prior to the initiation of the project.','string',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('prospective_collection','tissue prospective collection indicator','text indicator for the time frame of tissue procurement,indicating that the tissue was procured in parallel to the project.','string',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('form_completion_date','form completion date','form completion date','string',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('other_patient_id','other patient id','legacy dmp patient identifier (dmpnnnn)','string',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('dfs_months','disease free (months)','disease free (months) since initial treatment.','number',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('dfs_status','disease free status','disease free status since initial treatment.','string',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('os_months','overall survival (months)','overall survival in months since initial diagonosis.','number',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('os_status','overall survival status','overall patient survival status.','string',1,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('other_sample_id','other sample id','legacy dmp sample identifier (dmpnnnn)','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('days_to_collection','days to sample collection.','days to sample collection.','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('is_ffpe','is ffpe','if the sample is from ffpe','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('oct_embedded','oct embedded','oct embedded','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('pathology_report_file_name','pathology report file name','pathology report file name','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('sample_type','sample type','the type of sample (i.e.,normal,primary,met,recurrence).','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('mutation_count','mutaiton count','mutation count','number',0,'30',3); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('age','age at metastatic diagnosis (years)','age at metastatic diagnosis (years)','number',1,'3',3); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('center','center','center of sequencing','string',1,'1',3); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('dead','vital status','is this patient known to be deceased','string',1,'1',3); + +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,1,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,2,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','GERMLINE'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,1,8031,'enst00000344348','10','exon',-1,'q13.4',51582939,'ncoa4-ret.n7r12_1',5979,'enst00000340058','10','exon',-1,'p13.1',43612031,'ncoa4-ret.n7r12_2','grch37','no','yes',100001,80000,'ncoa4-ret.n7r1','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,1,27436,'enst00000318522','2','exon',-1,'q13.4',42492091,'eml4-alk.e6ba20.ab374362_1',238,'enst00000389048','2','exon',-1,'p13.1',29446394,'eml4-alk.e6ba20.ab374362_2','grch37','no','yes',100002,70000,'eml4-alk.e6ba20.ab374362','fusion','gain-of-function','GERMLINE'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,2,27436,'enst00000318522','2','exon',-1,'q13.4',42492091,'eml4-alk.e6ba20.ab374362_1',238,'enst00000389048','2','exon',-1,'p13.1',29446394,'eml4-alk.e6ba20.ab374362_2','grch37','no','yes',100002,70000,'eml4-alk.e6ba20.ab374362-2','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,1,7113,'enst00000332149','21','exon',-1,'q13.4',42880007,'tmprss2-erg.t1e2.cosf23.1_1',2078,'enst00000442448','21','exon',-1,'p13.1',39956869,'tmprss2-erg.t1e2.cosf23.1_2','grch37','no','yes',100003,60000,'tmprss2-erg.t1e2.cosf23.1','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(7,2,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(13,15,57670,'enst00000242365','7','exon',-1,'q13.4',138536968,'kiaa1549-BRAF.k16b10.cosf509_1',673,'enst00000288602','7','exon',-1,'p13.1',140482957,'kiaa1549-BRAF.k16b10.cosf509_2','grch37','no','yes',100000,90000,'kiaa1549-BRAF.k16b10.cosf509','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(13,15,8031,'enst00000344348','10','exon',-1,'q13.4',51582939,'ncoa4-ret.n7r12_1',5979,'enst00000340058','10','exon',-1,'p13.1',43612031,'ncoa4-ret.n7r12_2','grch37','no','yes',100001,80000,'ncoa4-ret.n7r1-2','fusion','gain-of-function','SOMATIC'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(13,15,7113,'enst00000332149','21','exon',-1,'q13.4',42880007,'tmprss2-erg.t1e2.cosf23.1_1',2078,'enst00000442448','21','exon',-1,'p13.1',39956869,'tmprss2-erg.t1e2.cosf23.1_2','grch37','no','yes',100003,60000,'tmprss2-erg.t1e2.cosf23.1','fusion','gain-of-function','GERMLINE'); +insert into structural_variant (genetic_profile_id,sample_id,site1_entrez_gene_id,site1_ensembl_transcript_id,site1_chromosome,site1_region,site1_region_number,site1_contig,site1_position,site1_description,site2_entrez_gene_id,site2_ensembl_transcript_id,site2_chromosome,site2_region,site2_region_number,site2_contig,site2_position,site2_description,ncbi_build,dna_support,rna_support,tumor_read_count,tumor_variant_count,annotation,event_info,comments,sv_status) +values(13,15,8031,'enst00000344348','10','exon',-1,'q13.4',51582939,'ncoa4-null',null,'enst00000340058_null','10','exon',-1,'p13.1',43612031,'ncoa4-null','grch37','no','yes',100001,80000,'ncoa4-null','fusion','gain-of-function','SOMATIC'); + +insert into mut_sig (cancer_study_id,entrez_gene_id,rank,numbasescovered,nummutations,p_value,q_value) values (1,207,1,998421,17,0.00000315,0.00233); +insert into mut_sig (cancer_study_id,entrez_gene_id,rank,numbasescovered,nummutations,p_value,q_value) values (1,208,2,3200341,351,0.000000012,0.00000000000212); + +-- gistic values (genetic_profile_id = 2) should only be {-2, -1, 0, 1, 2} +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (2,1,'-1,2,0,1,-2,2,-1,0,1,-2,2,0,1,-1,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (4,2,'1.4146,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1146,0.3498,0.0349,0.4927,-0.8665,-0.4754,-0.7221,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (3,2,'-0.8097,0.7360,-1.0225,-0.8922,0.7247,0.3537,1.2702,-0.1419,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (9,17,'-0.0670,-0.6270,-1.2266,-1.2079,-1.2262,0.6962,-0.3338,-0.1260,0.7559,-1.1267,-0.5893,-1.1506,-1.0027,-1.3157,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (9,18,'1.0106,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1106,0.3098,0.0309,0.0927,-0.8665,-0.0750,-0.7221,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (11,19,'-0.0670,-0.6270,-1.2266,-1.2079,-1.2262,0.6962,-0.3338,-0.1260,0.7559,-1.1267,-0.5893,-1.1506,-1.0027,-1.3157,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (11,20,'1.0106,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1106,0.3098,0.0309,0.0927,-0.8665,-0.0750,-0.7221,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (12,28,'-0.0670,-0.6270,-1.2266,-1.2079,-1.2262,0.6962,-0.3338,-0.1260,0.7559,-1.1267,-0.5893,-1.1506,-1.0027,-1.3157,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (12,29,'1.0106,-0.0662,-0.8585,-1.6576,-0.3552,-0.8306,0.8102,0.1106,0.3098,0.0309,0.0927,-0.8665,-0.0750,-0.7221,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (14,1,'1,-1,NA,2,0,-2,1,NA,-1,0,2,-2,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (15,1,'-0.8097,0.7360,-0.1260,NA,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (18,30,'Loss,Gain,Unchanged,NA,'); +insert into genetic_alteration (genetic_profile_id,genetic_entity_id,`values`) values (19,31,'No,NA,NA,NA,NA,NA,No,NA,NA,NA,No,No,NA,NA,NA,NA,NA,No,NA,No,No,NA,No,No,Yes,NA,No,'); + +insert into cna_event (cna_event_id,entrez_gene_id,alteration) values (1,207,-2); +insert into cna_event (cna_event_id,entrez_gene_id,alteration) values (2,208,2); +insert into cna_event (cna_event_id,entrez_gene_id,alteration) values (3,207,2); + +insert into sample_cna_event (cna_event_id,sample_id,genetic_profile_id, annotation_json) values (1,1,2, '{"columnname":{"fieldname":"fieldvalue"}}'); +insert into sample_cna_event (cna_event_id,sample_id,genetic_profile_id, annotation_json) values (2,1,2, '{"columnname":{"fieldname":"fieldvalue"}}'); +insert into sample_cna_event (cna_event_id,sample_id,genetic_profile_id, annotation_json) values (3,2,2, '{"columnname":{"fieldname":"fieldvalue"}}'); + +insert into gistic (gistic_roi_id,cancer_study_id,chromosome,cytoband,wide_peak_start,wide_peak_end,q_value,amp) values (1,1,1,'1q32.32',123,136,0.0208839997649193,0); +insert into gistic (gistic_roi_id,cancer_study_id,chromosome,cytoband,wide_peak_start,wide_peak_end,q_value,amp) values (2,1,2,'2q30.32',324234,324280,0.000323799991747364,1); +insert into gistic (gistic_roi_id,cancer_study_id,chromosome,cytoband,wide_peak_start,wide_peak_end,q_value,amp) values (3,2,1,'1q3.32',123,136,0.000000129710002738648,0); + +insert into gistic_to_gene (gistic_roi_id,entrez_gene_id) values (1,207); +insert into gistic_to_gene (gistic_roi_id,entrez_gene_id) values (1,208); +insert into gistic_to_gene (gistic_roi_id,entrez_gene_id) values (2,207); +insert into gistic_to_gene (gistic_roi_id,entrez_gene_id) values (3,208); + +insert into clinical_event (clinical_event_id,patient_id,start_date,stop_date,event_type) values (1,1,123,0,'status'); +insert into clinical_event (clinical_event_id,patient_id,start_date,stop_date,event_type) values (2,2,233,345,'SPECIMEN'); +insert into clinical_event (clinical_event_id,patient_id,start_date,stop_date,event_type) values (3,2,213,445,'Treatment'); +insert into clinical_event (clinical_event_id,patient_id,start_date,stop_date,event_type) values (4,2,211,441,'Seqencing'); + +insert into clinical_event_data (clinical_event_id,key,value) values (1,'status','radiographic_progression'); +insert into clinical_event_data (clinical_event_id,key,value) values (1,'SAMPLE_ID','tcga-a1-a0sb-01'); +insert into clinical_event_data (clinical_event_id,key,value) values (2,'surgery','oa ii initial'); +insert into clinical_event_data (clinical_event_id,key,value) values (2,'SAMPLE_ID','tcga-a1-a0sd-01'); +insert into clinical_event_data (clinical_event_id,key,value) values (3,'event_type_detailed','aa iii recurrence1'); +insert into clinical_event_data (clinical_event_id,key,value) values (3,'AGENT','madeupanib'); +insert into clinical_event_data (clinical_event_id,key,value) values (3,'agent_target','directly to forehead, elbow'); +insert into clinical_event_data (clinical_event_id,key,value) values (3,'SAMPLE_ID','tcga-a1-a0sd-01'); +insert into clinical_event_data (clinical_event_id,key,value) values (4,'SAMPLE_ID','tcga-a1-a0sd-01'); + +insert into geneset (id,genetic_entity_id,external_id,name,description,ref_link) values (1,17,'morf_atrx','morf atrx name','morf description','https://morf_link'); +insert into geneset (id,genetic_entity_id,external_id,name,description,ref_link) values (2,18,'hinata_nfkb_matrix','hinata nfkb matrix name','hinata description','https://hinata_link'); + +insert into geneset_gene (geneset_id,entrez_gene_id) values (1,207); +insert into geneset_gene (geneset_id,entrez_gene_id) values (1,208); +insert into geneset_gene (geneset_id,entrez_gene_id) values (1,10000); +insert into geneset_gene (geneset_id,entrez_gene_id) values (2,369); +insert into geneset_gene (geneset_id,entrez_gene_id) values (2,472); + +-- root node -> sub node a -> parent node 1 -> morf_atrx +-- " " " -> hinata_nfkb_matrix +-- " " -> parent node 2 -> hinata_nfkb_matrix +-- root node -> sub node b -> x (dead branch) +insert into geneset_hierarchy_node (node_id,node_name,parent_id) values (1,'root node',null); +insert into geneset_hierarchy_node (node_id,node_name,parent_id) values (2,'sub node a',1); +insert into geneset_hierarchy_node (node_id,node_name,parent_id) values (3,'sub node b',1); +insert into geneset_hierarchy_node (node_id,node_name,parent_id) values (4,'parent node 1',2); +insert into geneset_hierarchy_node (node_id,node_name,parent_id) values (5,'parent node 2',2); + +insert into geneset_hierarchy_leaf (node_id,geneset_id) values (4,1); +insert into geneset_hierarchy_leaf (node_id,geneset_id) values (4,2); +insert into geneset_hierarchy_leaf (node_id,geneset_id) values (5,2); + +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'AKT1 truncating', 207, 54, 64); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, null, 207, 21, 22); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'ARAF g1513 missense', 369, 1, 2); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (6, 'ARAF g1514 missense', 369, 4, 7); +insert into mutation_count_by_keyword (genetic_profile_id,keyword,entrez_gene_id,keyword_count,gene_count) values (8, 'NOC2L truncating', 26155, 1, 3); + + +-- treatment test data +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (1,19,'name','tanespimycin'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (2,19,'description','hsp90 inhibitor'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (3,19,'url','https://en.wikipedia.org/wiki/tanespimycin'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (4,20,'name','larotrectinib'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (5,20,'description','trka/b/c inhibitor'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (6,20,'url','https://en.wikipedia.org/wiki/larotrectinib'); +-- generic assay test data +-- mutational signature test data +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (7,28,'name','mean_1'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (8,28,'description','description of mean_1'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (9,29,'name','mean_2'); +insert into generic_entity_properties (id,genetic_entity_id,name,value) values (10,29,'description','description of mean_2'); + +-- allele specific copy number data +insert into allele_specific_copy_number (mutation_event_id, genetic_profile_id, sample_id, ascn_integer_copy_number, ascn_method, ccf_expected_copies_upper, ccf_expected_copies, clonal, minor_copy_number, expected_alt_copies, total_copy_number) values (2040, 6, 1, 3, 'facets', 1.25, 1.75, 'clonal', 2, 1, 4); +insert into allele_specific_copy_number (mutation_event_id, genetic_profile_id, sample_id, ascn_integer_copy_number, ascn_method, ccf_expected_copies_upper, ccf_expected_copies, clonal, minor_copy_number, expected_alt_copies, total_copy_number) values (2038, 6, 6, 1, 'facets', 1.25, 1.75, 'subclonal', 1, 1, 2); \ No newline at end of file diff --git a/src/test/resources/logback.xml b/src/test/resources/logback.xml index 9d21a927c45..d243e7dfa34 100644 --- a/src/test/resources/logback.xml +++ b/src/test/resources/logback.xml @@ -1,24 +1,5 @@ + - - - - %d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n - - - - - - - - - - - \ No newline at end of file + + + diff --git a/src/test/resources/testContextDatabase.xml b/src/test/resources/testContextDatabase.xml deleted file mode 100644 index 1c9c4183da2..00000000000 --- a/src/test/resources/testContextDatabase.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - - - - - - - - - - - mysql - h2 - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/test/api-e2e/mergeJson.js b/test/api-e2e/mergeJson.js new file mode 100644 index 00000000000..08e8c0a4309 --- /dev/null +++ b/test/api-e2e/mergeJson.js @@ -0,0 +1,28 @@ +const fsProm = require('fs/promises'); +const path = require('path'); + +async function mergeApiTestJson() { + const files = (await fsProm.readdir('./api-e2e/specs')).map(fileName => { + return path.join('./api-e2e/specs', fileName); + }); + + const jsons = files.map(path => { + return fsProm.readFile(path).then(data => { + try { + const json = JSON.parse(data); + return { file: path, suites: json }; + } catch (ex) { + console.log('invalid apiTest json spec'); + return []; + } + }); + }); + + Promise.all(jsons) + .then(d => { + fsProm.writeFile('./api-e2e/merged-tests.json', JSON.stringify(d)); + }) + .then(r => console.log('merged-tests.json written')); +} + +exports.mergeApiTestJson = mergeApiTestJson; diff --git a/test/api-e2e/specs/clinical-data-filters.json b/test/api-e2e/specs/clinical-data-filters.json new file mode 100644 index 00000000000..b11a6ae46b8 --- /dev/null +++ b/test/api-e2e/specs/clinical-data-filters.json @@ -0,0 +1,3686 @@ +[ + { + "name":"Range start comparison", + "note":"Range boundaries must be cast to floats in order to evaluate properly", + "studies":["cesc_tcga_pan_can_atlas_2018"], + "tests":[ + {"hash":50301331,"filterString":"Fraction Genome Altered: < x ≤ 0.30.35","data":{"clinicalDataFilters":[{"attributeId":"FRACTION_GENOME_ALTERED","values":[{"end":0.35,"start":0.3}]}],"studyIds":["cesc_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["cesc_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=cesc_tcga_pan_can_atlas_2018#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"FRACTION_GENOME_ALTERED\",\"values\":[{\"end\":0.35,\"start\":0.3}]}],\"studyIds\":[\"cesc_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"} + ] + }, + { + "name": "Age at Which Sequencing was Reported <= 25", + "note": "Filter result should include patients/samples with special age value of '<18'", + "studies": [ + "genie_public" + ], + "filterUrl": "/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}", + "filterText": "Age at Which Sequencing was Reported:≤ 25", + "tests": [ + { + "hash": 22663238, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + "attributes": [ + { + "attributeId": "AGE_AT_SEQ_REPORT", + "disableLogScale": false, + "showNA": false + } + ], + "studyViewFilter": { + "studyIds": [ + "genie_public" + ], + "alterationFilter": { + "copyNumberAlterationEventTypes": { + "AMP": true, + "HOMDEL": true + }, + "mutationEventTypes": { + "any": true + }, + "structuralVariants": null, + "includeDriver": true, + "includeVUS": true, + "includeUnknownOncogenicity": true, + "includeUnknownTier": true, + "includeGermline": true, + "includeSomatic": true, + "includeUnknownStatus": true, + "tiersBooleanMap": {} + } + } + }, + "url": "/api/column-store/clinical-data-bin-counts/fetch?dataBinMethod=STATIC&", + "label": "ClinicalDataBin", + "studies": [ + "genie_public" + ], + "filterUrl": "/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}" + }, + { + "hash": 1521321988, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + "clinicalDataFilters": [ + { + "attributeId": "AGE_AT_SEQ_REPORT", + "values": [ + { + "end": 25 + } + ] + } + ], + "studyIds": [ + "genie_public" + ], + "alterationFilter": { + "copyNumberAlterationEventTypes": { + "AMP": true, + "HOMDEL": true + }, + "mutationEventTypes": { + "any": true + }, + "structuralVariants": null, + "includeDriver": true, + "includeVUS": true, + "includeUnknownOncogenicity": true, + "includeUnknownTier": true, + "includeGermline": true, + "includeSomatic": true, + "includeUnknownStatus": true, + "tiersBooleanMap": {} + } + }, + "url": "/api/column-store/filtered-samples/fetch?", + "label": "FilteredSamples", + "studies": [ + "genie_public" + ], + "filterUrl": "/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}" + }, + { + "hash": 1565039040, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + 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"/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}" + }, + { + "hash": 1753439688, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + "clinicalDataFilters": [ + { + "attributeId": "AGE_AT_SEQ_REPORT", + "values": [ + { + "end": 25 + } + ] + } + ], + "studyIds": [ + "genie_public" + ], + "alterationFilter": { + "copyNumberAlterationEventTypes": { + "AMP": true, + "HOMDEL": true + }, + "mutationEventTypes": { + "any": true + }, + "structuralVariants": null, + "includeDriver": true, + "includeVUS": true, + "includeUnknownOncogenicity": true, + "includeUnknownTier": true, + "includeGermline": true, + "includeSomatic": true, + "includeUnknownStatus": true, + "tiersBooleanMap": {} + } + }, + "url": "/api/column-store/sample-lists-counts/fetch?", + "label": "CaseList", + "studies": [ + "genie_public" + ], + "filterUrl": "/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}" + }, + { + "hash": 2068869541, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + "attributes": [ + { 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+ "includeUnknownStatus": true, + "tiersBooleanMap": {} + } + } + }, + "url": "/api/column-store/clinical-data-counts/fetch?", + "label": "ClinicalDataCounts", + "studies": [ + "genie_public" + ], + "filterUrl": "/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}" + }, + { + "hash": 2119685176, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + "clinicalDataFilters": [ + { + "attributeId": "AGE_AT_SEQ_REPORT", + "values": [ + { + "end": 25 + } + ] + } + ], + "studyIds": [ + "genie_public" + ], + "alterationFilter": { + "copyNumberAlterationEventTypes": { + "AMP": true, + "HOMDEL": true + }, + "mutationEventTypes": { + "any": true + }, + "structuralVariants": null, + "includeDriver": true, + "includeVUS": true, + "includeUnknownOncogenicity": true, + "includeUnknownTier": true, + "includeGermline": true, + "includeSomatic": true, + "includeUnknownStatus": true, + "tiersBooleanMap": {} + } + }, + "url": "/api/column-store/mutated-genes/fetch?", + "label": "MutatedGenes", + "studies": [ + "genie_public" + ], + "filterUrl": 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"includeSomatic": true, + "includeUnknownStatus": true, + "tiersBooleanMap": {} + } + }, + "url": "/api/column-store/filtered-samples/fetch?", + "label": "FilteredSamples", + "studies": [ + "genie_public" + ], + "filterUrl": "/study/summary?id=genie_public#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE_AT_SEQ_REPORT\",\"values\":[{\"end\":25}]}],\"studyIds\":[\"genie_public\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}" + }, + { + "hash": -258471519, + "filterString": "Age at Which Sequencing was Reported:≤ 25", + "data": { + "clinicalDataFilters": [ + { + "attributeId": "AGE_AT_SEQ_REPORT", + "values": [ + { + "end": 25 + } + ] + } + ], + "studyIds": [ + 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+ ] + } +] \ No newline at end of file diff --git a/test/api-e2e/watch.js b/test/api-e2e/watch.js new file mode 100644 index 00000000000..1f5bac806cc --- /dev/null +++ b/test/api-e2e/watch.js @@ -0,0 +1,47 @@ +const fs = require('fs/promises'); +const watch = require('fs').watch; +const path = require('path'); + +let apiTestRoot; + +if (!process.env.BACKEND_ROOT) { + console.log("YOU MUST EXPORT BACKEND_ROOT ENV VARIABLE"); + process.exit(1); +} else { + apiTestRoot = `${process.env.BACKEND_ROOT}/test/api-e2e`; +} + +async function mergeFiles(){ + + const files = (await fs.readdir(`${apiTestRoot}/specs`)).map(fileName => { + return path.join(`${apiTestRoot}/specs`, fileName); + }); + + const jsons = files.map(path => { + return fs.readFile(path).then(data => { + try { + const json = JSON.parse(data); + return { file: path, suites: json }; + } catch (ex) { + console.log('invalid apiTest json spec'); + return []; + } + }); + }); + + Promise.all(jsons) + .then(d => { + fs.writeFile(`${process.cwd()}/api-e2e/json/merged-tests.json`, JSON.stringify(d)); + }) + .then(r => console.log('merged-tests.json written')); + +} + +watch(`${apiTestRoot}/specs`, async function(event, filename) { + if (event === 'change') { + mergeFiles() + } +}); + + +mergeFiles(); \ No newline at end of file