feat(openchallenges): filter EDAM concepts by sections (Sage-Bionetwo…

…rks#2640)

apps/openchallenges/challenge-service/.openapi-generator/FILES

@@ -43,6 +43,7 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/Eda
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamConceptsPageDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamDataDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamOperationDto.java
+src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamSectionDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/PageMetadataDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/SimpleChallengePlatformDto.java
 src/main/resources/openapi.yaml

apps/openchallenges/challenge-service/requests.http

@@ -142,4 +142,8 @@ GET {{basePath}}/edamConcepts
 
 ### List the EDAM concepts that match the space-separated search terms "sequence".
 
-GET {{basePath}}/edamConcepts?searchTerms=sequence
+GET {{basePath}}/edamConcepts?searchTerms=sequence
+
+### List the EDAM concepts that belong to the "data" or "format" section.
+
+GET {{basePath}}/edamConcepts?sections=data,format

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/configuration/EnumConverterConfiguration.java

@@ -9,6 +9,7 @@
 import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeSortDto;
 import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeStatusDto;
 import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeSubmissionTypeDto;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamSectionDto;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.core.convert.converter.Converter;
@@ -105,4 +106,14 @@ public ChallengeSubmissionTypeDto convert(String source) {
       }
     };
   }
+
+  @Bean
+  Converter<String, EdamSectionDto> edamSectionConverter() {
+    return new Converter<String, EdamSectionDto>() {
+      @Override
+      public EdamSectionDto convert(String source) {
+        return EdamSectionDto.fromValue(source);
+      }
+    };
+  }
 }

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamConceptSearchQueryDto.java

@@ -4,8 +4,11 @@
 import com.fasterxml.jackson.annotation.JsonTypeName;
 import io.swagger.v3.oas.annotations.media.Schema;
 import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Objects;
 import javax.annotation.Generated;
+import javax.validation.Valid;
 import javax.validation.constraints.*;
 
 /** An EDAM concept search query. */
@@ -24,6 +27,10 @@ public class EdamConceptSearchQueryDto {
   @JsonProperty("searchTerms")
   private String searchTerms;
 
+  @JsonProperty("sections")
+  @Valid
+  private List<EdamSectionDto> sections = null;
+
   public EdamConceptSearchQueryDto pageNumber(Integer pageNumber) {
     this.pageNumber = pageNumber;
     return this;
@@ -90,6 +97,37 @@ public void setSearchTerms(String searchTerms) {
     this.searchTerms = searchTerms;
   }
 
+  public EdamConceptSearchQueryDto sections(List<EdamSectionDto> sections) {
+    this.sections = sections;
+    return this;
+  }
+
+  public EdamConceptSearchQueryDto addSectionsItem(EdamSectionDto sectionsItem) {
+    if (this.sections == null) {
+      this.sections = new ArrayList<>();
+    }
+    this.sections.add(sectionsItem);
+    return this;
+  }
+
+  /**
+   * An array of EDAM sections (sub-ontologies) used to filter the results.
+   *
+   * @return sections
+   */
+  @Valid
+  @Schema(
+      name = "sections",
+      description = "An array of EDAM sections (sub-ontologies) used to filter the results.",
+      required = false)
+  public List<EdamSectionDto> getSections() {
+    return sections;
+  }
+
+  public void setSections(List<EdamSectionDto> sections) {
+    this.sections = sections;
+  }
+
   @Override
   public boolean equals(Object o) {
     if (this == o) {
@@ -101,12 +139,13 @@ public boolean equals(Object o) {
     EdamConceptSearchQueryDto edamConceptSearchQuery = (EdamConceptSearchQueryDto) o;
     return Objects.equals(this.pageNumber, edamConceptSearchQuery.pageNumber)
         && Objects.equals(this.pageSize, edamConceptSearchQuery.pageSize)
-        && Objects.equals(this.searchTerms, edamConceptSearchQuery.searchTerms);
+        && Objects.equals(this.searchTerms, edamConceptSearchQuery.searchTerms)
+        && Objects.equals(this.sections, edamConceptSearchQuery.sections);
   }
 
   @Override
   public int hashCode() {
-    return Objects.hash(pageNumber, pageSize, searchTerms);
+    return Objects.hash(pageNumber, pageSize, searchTerms, sections);
   }
 
   @Override
@@ -116,6 +155,7 @@ public String toString() {
     sb.append("    pageNumber: ").append(toIndentedString(pageNumber)).append("\n");
     sb.append("    pageSize: ").append(toIndentedString(pageSize)).append("\n");
     sb.append("    searchTerms: ").append(toIndentedString(searchTerms)).append("\n");
+    sb.append("    sections: ").append(toIndentedString(sections)).append("\n");
     sb.append("}");
     return sb.toString();
   }

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamSectionDto.java

@@ -0,0 +1,47 @@
+package org.sagebionetworks.openchallenges.challenge.service.model.dto;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+import java.util.*;
+import javax.annotation.Generated;
+import javax.validation.constraints.*;
+
+/** The EDAM section (sub-ontology). */
+@Generated(value = "org.openapitools.codegen.languages.SpringCodegen")
+public enum EdamSectionDto {
+  DATA("data"),
+
+  FORMAT("format"),
+
+  IDENTIFIER("identifier"),
+
+  OPERATION("operation"),
+
+  TOPIC("topic");
+
+  private String value;
+
+  EdamSectionDto(String value) {
+    this.value = value;
+  }
+
+  @JsonValue
+  public String getValue() {
+    return value;
+  }
+
+  @Override
+  public String toString() {
+    return String.valueOf(value);
+  }
+
+  @JsonCreator
+  public static EdamSectionDto fromValue(String value) {
+    for (EdamSectionDto b : EdamSectionDto.values()) {
+      if (b.value.equals(value)) {
+        return b;
+      }
+    }
+    throw new IllegalArgumentException("Unexpected value '" + value + "'");
+  }
+}

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/entity/EdamConceptEntity.java

@@ -10,8 +10,11 @@
 import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;
+import org.hibernate.search.mapper.pojo.bridge.mapping.annotation.ValueBridgeRef;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
+import org.sagebionetworks.openchallenges.challenge.service.model.search.EdamSectionValueBridge;
 
 @Entity
 @Table(name = "edam_concept")
@@ -29,6 +32,9 @@ public class EdamConceptEntity {
 
   @Column(name = "class_id", nullable = false)
   @FullTextField(name = "class_id")
+  @KeywordField(
+      name = "section",
+      valueBridge = @ValueBridgeRef(type = EdamSectionValueBridge.class))
   private String classId;
 
   @Column(name = "preferred_label", nullable = false)

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/repository/CustomEdamConceptRepositoryImpl.java

@@ -11,6 +11,7 @@
 import org.hibernate.search.mapper.orm.Search;
 import org.hibernate.search.mapper.orm.session.SearchSession;
 import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptSearchQueryDto;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamSectionDto;
 import org.sagebionetworks.openchallenges.challenge.service.model.entity.EdamConceptEntity;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
@@ -38,6 +39,9 @@ private SearchResult<EdamConceptEntity> getSearchResult(
     if (query.getSearchTerms() != null && !query.getSearchTerms().isBlank()) {
       predicates.add(getSearchTermsPredicate(pf, query, fields));
     }
+    if (query.getSections() != null && !query.getSections().isEmpty()) {
+      predicates.add(getEdamSectionsPredicate(pf, query));
+    }
 
     SearchPredicate topLevelPredicate = buildTopLevelPredicate(pf, predicates);
 
@@ -64,6 +68,24 @@ private SearchPredicate getSearchTermsPredicate(
         .toPredicate();
   }
 
+  /**
+   * Searches the EDAM concepts whose section is in the list of sections specified.
+   *
+   * @param pf
+   * @param query
+   * @return
+   */
+  private SearchPredicate getEdamSectionsPredicate(
+      SearchPredicateFactory pf, EdamConceptSearchQueryDto query) {
+    return pf.bool(
+            b -> {
+              for (EdamSectionDto section : query.getSections()) {
+                b.should(pf.match().field("section").matching(section.toString()));
+              }
+            })
+        .toPredicate();
+  }
+
   /**
    * Combines the search predicates.
    *

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/search/EdamSectionValueBridge.java

@@ -0,0 +1,22 @@
+package org.sagebionetworks.openchallenges.challenge.service.model.search;
+
+import org.hibernate.search.mapper.pojo.bridge.ValueBridge;
+import org.hibernate.search.mapper.pojo.bridge.runtime.ValueBridgeToIndexedValueContext;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamSectionDto;
+
+public class EdamSectionValueBridge implements ValueBridge<String, String> {
+
+  @Override
+  public String toIndexedValue(String value, ValueBridgeToIndexedValueContext context) {
+    for (EdamSectionDto section : EdamSectionDto.values()) {
+      // The first condition is used to map EDAM concept class IDs to concept sections when new
+      // concept are created (e.g. during mass indexing). This value bridge is also called when
+      // sending search queries to Elasticsearch, which is why the second condition is required to
+      // map the user input to an existing EDAM concept.
+      if (value.contains("/" + section.getValue() + "_") || section.getValue().equals(value)) {
+        return section.getValue();
+      }
+    }
+    return null;
+  }
+}

apps/openchallenges/challenge-service/src/main/resources/logback.xml

@@ -5,5 +5,8 @@
 
   <include resource="logback-common.xml" />
 
+  <logger name="org.hibernate" level="info" />
+  <logger name="org.hibernate.search.query" level="info" />
+
   <!-- <logger name="org.apache.kafka" level="debug" /> -->
 </configuration>

apps/openchallenges/challenge-service/src/main/resources/openapi.yaml

@@ -1024,6 +1024,16 @@ components:
       type: object
       x-java-class-annotations:
       - '@lombok.Builder'
+    EdamSection:
+      description: The EDAM section (sub-ontology).
+      enum:
+      - data
+      - format
+      - identifier
+      - operation
+      - topic
+      example: data
+      type: string
     EdamConceptSearchQuery:
       description: An EDAM concept search query.
       properties:
@@ -1043,6 +1053,12 @@ components:
           description: A string of search terms used to filter the results.
           example: sequence image
           type: string
+        sections:
+          description: An array of EDAM sections (sub-ontologies) used to filter the
+            results.
+          items:
+            $ref: '#/components/schemas/EdamSection'
+          type: array
       type: object
     EdamConceptId:
       description: The unique identifier of the EDAM concept.

libs/openchallenges/api-client-angular/src/lib/.openapi-generator/FILES

@@ -42,6 +42,7 @@ model/edamConceptsPage.ts
 model/edamConceptsPageAllOf.ts
 model/edamData.ts
 model/edamOperation.ts
+model/edamSection.ts
 model/image.ts
 model/imageAspectRatio.ts
 model/imageHeight.ts

libs/openchallenges/api-client-angular/src/lib/model/edamConceptSearchQuery.ts

@@ -9,6 +9,7 @@
  * https://openapi-generator.tech
  * Do not edit the class manually.
  */
+import { EdamSection } from './edamSection';
 
 
 /**
@@ -27,5 +28,9 @@ export interface EdamConceptSearchQuery {
      * A string of search terms used to filter the results.
      */
     searchTerms?: string;
+    /**
+     * An array of EDAM sections (sub-ontologies) used to filter the results.
+     */
+    sections?: Array<EdamSection>;
 }
 

libs/openchallenges/api-client-angular/src/lib/model/edamSection.ts

@@ -0,0 +1,26 @@
+/**
+ * OpenChallenges REST API
+ * No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
+ *
+ * The version of the OpenAPI document: 1.0.0
+ * 
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+
+
+/**
+ * The EDAM section (sub-ontology).
+ */
+export type EdamSection = 'data' | 'format' | 'identifier' | 'operation' | 'topic';
+
+export const EdamSection = {
+    Data: 'data' as EdamSection,
+    Format: 'format' as EdamSection,
+    Identifier: 'identifier' as EdamSection,
+    Operation: 'operation' as EdamSection,
+    Topic: 'topic' as EdamSection
+};
+

libs/openchallenges/api-client-angular/src/lib/model/models.ts

@@ -26,6 +26,7 @@ export * from './edamConceptsPage';
 export * from './edamConceptsPageAllOf';
 export * from './edamData';
 export * from './edamOperation';
+export * from './edamSection';
 export * from './image';
 export * from './imageAspectRatio';
 export * from './imageHeight';

libs/openchallenges/api-description/build/challenge.openapi.yaml

@@ -721,6 +721,16 @@ components:
             - challengePlatforms
       x-java-class-annotations:
         - '@lombok.Builder'
+    EdamSection:
+      description: The EDAM section (sub-ontology).
+      type: string
+      enum:
+        - data
+        - format
+        - identifier
+        - operation
+        - topic
+      example: data
     EdamConceptSearchQuery:
       type: object
       description: An EDAM concept search query.
@@ -741,6 +751,11 @@ components:
           description: A string of search terms used to filter the results.
           type: string
           example: sequence image
+        sections:
+          description: An array of EDAM sections (sub-ontologies) used to filter the results.
+          type: array
+          items:
+            $ref: '#/components/schemas/EdamSection'
     EdamConceptId:
       description: The unique identifier of the EDAM concept.
       type: integer