#162 add study id for runs

src/main/java/org/icgc_argo/workflow/search/graphql/fetchers/EntityDataFetchers.java

@@ -62,8 +62,9 @@ public AsyncDataFetcher getDataFetcher() {
                   }
                   if (ANALYSIS_ENTITY.equals(values.get("__typename"))) {
                     final Object analysisId = values.get("analysisId");
-                    if (analysisId instanceof String) {
-                      return Mono.just(new Analysis((String) analysisId));
+                    final Object studyId = values.get("studyId");
+                    if (analysisId instanceof String && studyId instanceof String) {
+                      return Mono.just(new Analysis((String) analysisId, (String) studyId));
                     }
                   }
                   if (WORKFLOW_ENTITY.equals(values.get("__typename"))) {

src/main/java/org/icgc_argo/workflow/search/graphql/fetchers/RunDataFetchers.java

@@ -21,6 +21,7 @@
 import static com.google.common.base.Strings.isNullOrEmpty;
 import static java.util.stream.Collectors.toUnmodifiableList;
 import static org.icgc_argo.workflow.search.model.SearchFields.ANALYSIS_ID;
+import static org.icgc_argo.workflow.search.model.SearchFields.STUDY_ID;
 import static org.icgc_argo.workflow.search.util.Converter.asImmutableMap;
 import static org.icgc_argo.workflow.search.util.JacksonUtils.convertValue;
 
@@ -108,17 +109,21 @@ public AsyncDataFetcher<List<GqlRun>> getNestedRunInAnalysisDataFetcher() {
     return environment -> {
       val analysis = (Analysis) environment.getSource();
       val analysisId = analysis.getAnalysisId();
+      val studyId = analysis.getStudyId();
 
       ImmutableMap<String, Object> filter = asImmutableMap(environment.getArgument("filter"));
       val filerAnalysisId = filter.getOrDefault(ANALYSIS_ID, analysisId);
+      val filterStudyId = filter.getOrDefault(STUDY_ID, studyId);
 
       // short circuit here since can't find runs for invalid analysisId
-      if (isNullOrEmpty(analysisId) || !analysisId.equals(filerAnalysisId)) {
+      if ((isNullOrEmpty(analysisId) || !analysisId.equals(filerAnalysisId))
+          && (isNullOrEmpty(studyId) || !analysisId.equals(filterStudyId))) {
         return Mono.empty();
       }
 
       Map<String, Object> mergedFilter = new HashMap<>(filter);
       mergedFilter.put(ANALYSIS_ID, analysisId);
+      mergedFilter.put(STUDY_ID, studyId);
 
       // Need to cast to get appropriate jackson annotation (camelCase property naming)
       return runService.getRuns(mergedFilter, null);

src/main/java/org/icgc_argo/workflow/search/model/SearchFields.java

@@ -40,4 +40,5 @@ public class SearchFields {
   public static final String ANALYSIS_ID = "analysisId";
   public static final String CPUS = "cpus";
   public static final String MEMORY = "memory";
+  public static final String STUDY_ID = "studyId";
 }

src/main/java/org/icgc_argo/workflow/search/model/graphql/Analysis.java

@@ -37,6 +37,8 @@ public class Analysis {
 
   private String analysisId;
 
+  private String studyId;
+
   @SneakyThrows
   public static Analysis parse(@NonNull Map<String, Object> sourceMap) {
     return MAPPER.convertValue(sourceMap, Analysis.class);

src/main/java/org/icgc_argo/workflow/search/repository/RunRepository.java

@@ -59,6 +59,13 @@ public class RunRepository {
           "parameters.analysis_id",
           "parameters.normal_aln_analysis_id",
           "parameters.tumour_aln_analysis_id");
+
+  private static final List<String> STUDY_SEARCH_FIELDS =
+      List.of(
+          "parameters.study_id",
+          "parameters.normal_aln_study_id",
+          "parameters.tumour_aln_study_id");
+
   private static final Map<String, Function<String, AbstractQueryBuilder<?>>> QUERY_RESOLVER =
       argumentPathMap();
 
@@ -182,6 +189,13 @@ private static Map<String, Function<String, AbstractQueryBuilder<?>>> argumentPa
               q.minimumShouldMatch("100%");
               return q;
             })
+        .put(
+            STUDY_ID,
+            value -> {
+              val q = new MultiMatchQueryBuilder(value, STUDY_SEARCH_FIELDS.toArray(String[]::new));
+              q.minimumShouldMatch("100%");
+              return q;
+            })
         .put(REPOSITORY, RunRepository::repositoryQueryFunc)
         .build();
   }

src/main/resources/schema.graphqls

@@ -17,6 +17,8 @@ type Run @key(fields: "runId") {
     commandLine: String
     engineParameters: EngineParameters
     tasks(taskId: String, state: String, tag: String): [Task]
+    producedAnalyses(filter: RunsFilter): [Analysis] @fetch(from: "producedAnalyses")
+    inputAnalyses(filter: RunsFilter): [Analysis] @requires(fields: "parameters") @fetch(from: "inputAnalyses")
 }
 
 type EngineParameters {
@@ -75,6 +77,7 @@ input RunsFilter {
     state: String
     repository: String
     analysisId: String
+    studyId: String
 }
 
 input TasksFilter {
@@ -94,6 +97,7 @@ directive @fetch(from : String!) on FIELD_DEFINITION
 
 type Analysis @key(fields: "analysisId") @extends {
     analysisId: ID! @external
+    studyId: String! @external
     inputForRuns(filter: RunsFilter): [Run]
 }