feat(openchallenges): filter challenges by input data types (EDAM Con…

…cept IDs) (#2647)

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

@@ -43,7 +43,6 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/Eda
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamConceptSearchQueryDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamConceptSortDto.java
 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

apps/openchallenges/challenge-service/requests.http

@@ -44,9 +44,9 @@ GET {{basePath}}/challenges?searchTerms=mortality%20dream
 
 GET {{basePath}}/challenges?minStartDate=2017-01-01&maxStartDate=2017-12-31
 
-### List the challenges that include the input data type 'genomic'.
+### Get the challenges whose input data types include the EDAM concept ID 2 or 18
 
-GET {{basePath}}/challenges?inputDataTypes=genomic
+GET {{basePath}}/challenges?inputDataTypes=2,18
 
 ### List the challenges by category: featured
 

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeApiDelegate.java

@@ -36,7 +36,7 @@ default ResponseEntity<ChallengeDto> getChallenge(Long challengeId) {
               for (MediaType mediaType : MediaType.parseMediaTypes(request.getHeader("Accept"))) {
                 if (mediaType.isCompatibleWith(MediaType.valueOf("application/json"))) {
                   String exampleString =
-                      "{ \"avatarUrl\" : \"https://openchallenges.io\", \"endDate\" : \"2017-07-21T00:00:00.000+00:00\", \"description\" : \"This is an example description of the challenge.\", \"platform\" : { \"name\" : \"name\", \"id\" : 1, \"slug\" : \"example-challenge-platform\" }, \"starredCount\" : 100, \"createdAt\" : \"2022-07-04T22:19:11Z\", \"incentives\" : [ \"publication\", \"publication\" ], \"submissionTypes\" : [ \"container_image\", \"container_image\" ], \"websiteUrl\" : \"https://openchallenges.io\", \"name\" : \"name\", \"id\" : 1, \"categories\" : [ \"featured\", \"featured\" ], \"headline\" : \"Example challenge headline\", \"operation\" : { \"classId\" : \"http://edamontology.org/operation_0230\", \"preferredLabel\" : \"Sequence generation\" }, \"slug\" : \"awesome-challenge\", \"startDate\" : \"2017-07-21T00:00:00.000+00:00\", \"doi\" : \"https://doi.org/123/abc\", \"status\" : \"active\", \"inputDataTypes\" : [ { \"classId\" : \"http://edamontology.org/data_0850\", \"preferredLabel\" : \"Sequence set\" }, { \"classId\" : \"http://edamontology.org/data_0850\", \"preferredLabel\" : \"Sequence set\" } ], \"updatedAt\" : \"2022-07-04T22:19:11Z\" }";
+                      "{ \"avatarUrl\" : \"https://openchallenges.io\", \"endDate\" : \"2017-07-21T00:00:00.000+00:00\", \"description\" : \"This is an example description of the challenge.\", \"platform\" : { \"name\" : \"name\", \"id\" : 1, \"slug\" : \"example-challenge-platform\" }, \"starredCount\" : 100, \"createdAt\" : \"2022-07-04T22:19:11Z\", \"incentives\" : [ \"publication\", \"publication\" ], \"submissionTypes\" : [ \"container_image\", \"container_image\" ], \"websiteUrl\" : \"https://openchallenges.io\", \"name\" : \"name\", \"id\" : 1, \"categories\" : [ \"featured\", \"featured\" ], \"headline\" : \"Example challenge headline\", \"operation\" : { \"classId\" : \"http://edamontology.org/operation_0230\", \"preferredLabel\" : \"Sequence generation\" }, \"slug\" : \"awesome-challenge\", \"startDate\" : \"2017-07-21T00:00:00.000+00:00\", \"doi\" : \"https://doi.org/123/abc\", \"status\" : \"active\", \"inputDataTypes\" : [ { \"classId\" : \"http://edamontology.org/data_0850\", \"preferredLabel\" : \"Sequence set\", \"id\" : 1 }, { \"classId\" : \"http://edamontology.org/data_0850\", \"preferredLabel\" : \"Sequence set\", \"id\" : 1 } ], \"updatedAt\" : \"2022-07-04T22:19:11Z\" }";
                   ApiUtil.setExampleResponse(request, "application/json", exampleString);
                   break;
                 }

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

@@ -61,7 +61,7 @@ public class ChallengeDto {
 
   @JsonProperty("inputDataTypes")
   @Valid
-  private List<EdamDataDto> inputDataTypes = null;
+  private List<EdamConceptDto> inputDataTypes = null;
 
   @JsonProperty("categories")
   @Valid
@@ -380,12 +380,12 @@ public void setSubmissionTypes(List<ChallengeSubmissionTypeDto> submissionTypes)
     this.submissionTypes = submissionTypes;
   }
 
-  public ChallengeDto inputDataTypes(List<EdamDataDto> inputDataTypes) {
+  public ChallengeDto inputDataTypes(List<EdamConceptDto> inputDataTypes) {
     this.inputDataTypes = inputDataTypes;
     return this;
   }
 
-  public ChallengeDto addInputDataTypesItem(EdamDataDto inputDataTypesItem) {
+  public ChallengeDto addInputDataTypesItem(EdamConceptDto inputDataTypesItem) {
     if (this.inputDataTypes == null) {
       this.inputDataTypes = new ArrayList<>();
     }
@@ -400,11 +400,11 @@ public ChallengeDto addInputDataTypesItem(EdamDataDto inputDataTypesItem) {
    */
   @Valid
   @Schema(name = "inputDataTypes", required = false)
-  public List<EdamDataDto> getInputDataTypes() {
+  public List<EdamConceptDto> getInputDataTypes() {
     return inputDataTypes;
   }
 
-  public void setInputDataTypes(List<EdamDataDto> inputDataTypes) {
+  public void setInputDataTypes(List<EdamConceptDto> inputDataTypes) {
     this.inputDataTypes = inputDataTypes;
   }
 

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

@@ -63,6 +63,10 @@ public class ChallengeSearchQueryDto {
   @Valid
   private List<ChallengeSubmissionTypeDto> submissionTypes = null;
 
+  @JsonProperty("inputDataTypes")
+  @Valid
+  private List<Long> inputDataTypes = null;
+
   @JsonProperty("categories")
   @Valid
   private List<ChallengeCategoryDto> categories = null;
@@ -379,6 +383,36 @@ public void setSubmissionTypes(List<ChallengeSubmissionTypeDto> submissionTypes)
     this.submissionTypes = submissionTypes;
   }
 
+  public ChallengeSearchQueryDto inputDataTypes(List<Long> inputDataTypes) {
+    this.inputDataTypes = inputDataTypes;
+    return this;
+  }
+
+  public ChallengeSearchQueryDto addInputDataTypesItem(Long inputDataTypesItem) {
+    if (this.inputDataTypes == null) {
+      this.inputDataTypes = new ArrayList<>();
+    }
+    this.inputDataTypes.add(inputDataTypesItem);
+    return this;
+  }
+
+  /**
+   * An array of EDAM concept ID used to filter the results.
+   *
+   * @return inputDataTypes
+   */
+  @Schema(
+      name = "inputDataTypes",
+      description = "An array of EDAM concept ID used to filter the results.",
+      required = false)
+  public List<Long> getInputDataTypes() {
+    return inputDataTypes;
+  }
+
+  public void setInputDataTypes(List<Long> inputDataTypes) {
+    this.inputDataTypes = inputDataTypes;
+  }
+
   public ChallengeSearchQueryDto categories(List<ChallengeCategoryDto> categories) {
     this.categories = categories;
     return this;
@@ -454,6 +488,7 @@ public boolean equals(Object o) {
         && Objects.equals(this.organizations, challengeSearchQuery.organizations)
         && Objects.equals(this.status, challengeSearchQuery.status)
         && Objects.equals(this.submissionTypes, challengeSearchQuery.submissionTypes)
+        && Objects.equals(this.inputDataTypes, challengeSearchQuery.inputDataTypes)
         && Objects.equals(this.categories, challengeSearchQuery.categories)
         && Objects.equals(this.searchTerms, challengeSearchQuery.searchTerms);
   }
@@ -473,6 +508,7 @@ public int hashCode() {
         organizations,
         status,
         submissionTypes,
+        inputDataTypes,
         categories,
         searchTerms);
   }
@@ -493,6 +529,7 @@ public String toString() {
     sb.append("    organizations: ").append(toIndentedString(organizations)).append("\n");
     sb.append("    status: ").append(toIndentedString(status)).append("\n");
     sb.append("    submissionTypes: ").append(toIndentedString(submissionTypes)).append("\n");
+    sb.append("    inputDataTypes: ").append(toIndentedString(inputDataTypes)).append("\n");
     sb.append("    categories: ").append(toIndentedString(categories)).append("\n");
     sb.append("    searchTerms: ").append(toIndentedString(searchTerms)).append("\n");
     sb.append("}");

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

@@ -101,9 +101,9 @@ public class ChallengeEntity {
       inverseJoinColumns = @JoinColumn(name = "edam_concept_id"))
   @IndexedEmbedded(
       name = "input_data_types",
-      includePaths = {"class_id", "preferred_label"})
+      includePaths = {"id", "class_id", "preferred_label"})
   @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
-  private List<EdamDataEntity> inputDataTypes;
+  private List<EdamConceptEntity> inputDataTypes;
 
   @OneToMany(mappedBy = "challenge", fetch = FetchType.LAZY)
   @IndexedEmbedded(includePaths = {"name"})

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

@@ -34,7 +34,7 @@ public class ChallengeInputDataTypeEntity {
 
   @ManyToOne(fetch = FetchType.LAZY)
   @JoinColumn(name = "edam_concept_id", nullable = false)
-  private EdamDataEntity edamData;
+  private EdamConceptEntity edamConcept;
 
   @Column(name = "created_at")
   private OffsetDateTime createdAt;

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

@@ -30,6 +30,7 @@ public class EdamConceptEntity {
   @Id
   @GeneratedValue(strategy = GenerationType.IDENTITY)
   @Column(nullable = false, updatable = false)
+  @GenericField(name = "id")
   private Long id;
 
   @Column(name = "class_id", nullable = false)

apps/openchallenges/challenge-service/src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/mapper/ChallengeMapper.java

@@ -17,7 +17,7 @@ public class ChallengeMapper extends BaseMapper<ChallengeEntity, ChallengeDto> {
 
   private SimpleChallengePlatformMapper platformMapper = new SimpleChallengePlatformMapper();
   private EdamOperationMapper edamOperationMapper = new EdamOperationMapper();
-  private EdamDataMapper edamDataMapper = new EdamDataMapper();
+  private EdamConceptMapper edamConceptMapper = new EdamConceptMapper();
 
   @Override
   public ChallengeEntity convertToEntity(ChallengeDto dto, Object... args) {
@@ -31,10 +31,10 @@ public ChallengeEntity convertToEntity(ChallengeDto dto, Object... args) {
   @Override
   public ChallengeDto convertToDto(ChallengeEntity entity, Object... args) {
     ChallengeDto dto = new ChallengeDto();
-    LOG.info("challenge dto initial: {}", dto);
+    LOG.trace("challenge dto initial: {}", dto);
     if (entity != null) {
       BeanUtils.copyProperties(entity, dto, "stars", "inputDataTypes", "platform", "operation");
-      LOG.info("challenge dto before set: {}", dto);
+      LOG.trace("challenge dto before set: {}", dto);
       dto.setStatus(ChallengeStatusDto.fromValue(entity.getStatus()));
       dto.setPlatform(platformMapper.convertToDto(entity.getPlatform()));
       if (entity.getOperation() != null) {
@@ -52,9 +52,9 @@ public ChallengeDto convertToDto(ChallengeEntity entity, Object... args) {
           entity.getCategories().stream()
               .map(o -> ChallengeCategoryDto.fromValue(o.getName()))
               .toList());
-      dto.inputDataTypes(edamDataMapper.convertToDtoList(entity.getInputDataTypes()));
+      dto.inputDataTypes(edamConceptMapper.convertToDtoList(entity.getInputDataTypes()));
       dto.starredCount(entity.getStars().size());
-      LOG.info("challenge dto: {}", dto);
+      LOG.trace("challenge dto: {}", dto);
     }
     return dto;
   }

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

@@ -64,6 +64,9 @@ private SearchResult<ChallengeEntity> getSearchResult(
     if (query.getSubmissionTypes() != null && !query.getSubmissionTypes().isEmpty()) {
       predicates.add(getChallengeSubmissionTypesPredicate(pf, query));
     }
+    if (query.getInputDataTypes() != null && !query.getInputDataTypes().isEmpty()) {
+      predicates.add(getInputDataTypesPredicate(pf, query));
+    }
     if (query.getIncentives() != null && !query.getIncentives().isEmpty()) {
       predicates.add(getChallengeIncentivesPredicate(pf, query));
     }
@@ -167,6 +170,17 @@ private SearchPredicate getChallengeSubmissionTypesPredicate(
         .toPredicate();
   }
 
+  private SearchPredicate getInputDataTypesPredicate(
+      SearchPredicateFactory pf, ChallengeSearchQueryDto query) {
+    return pf.bool(
+            b -> {
+              for (Long edamConceptId : query.getInputDataTypes()) {
+                b.should(pf.match().field("input_data_types.id").matching(edamConceptId));
+              }
+            })
+        .toPredicate();
+  }
+
   /**
    * Matches the challenges whose at least one of their contributors is in the list of
    * contributors/organizations specified.