feat(openchallenges): create endpoint to search EDAM concepts

apps/openchallenges/api-gateway/src/main/java/org/sagebionetworks/openchallenges/api/gateway/config/SecurityConfig.java

@@ -19,6 +19,7 @@ SecurityWebFilterChain securityWebFilterChain(ServerHttpSecurity http) {
         .permitAll().pathMatchers("/api/v1/challengeInputDataTypes/**")
         .permitAll().pathMatchers("/api/v1/challengePlatforms/**")
         .permitAll().pathMatchers("/api/v1/challenges/**")
+        .permitAll().pathMatchers("/api/v1/edamConcepts/**")
         .permitAll().pathMatchers("/api/v1/images/**")
         .permitAll().pathMatchers("/api/v1/organizations/**")
         .permitAll()

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

@@ -13,6 +13,9 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/Challenge
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengePlatformApi.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengePlatformApiController.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengePlatformApiDelegate.java
+src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/EdamConceptApi.java
+src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/EdamConceptApiController.java
+src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/EdamConceptApiDelegate.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/configuration/EnumConverterConfiguration.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/configuration/HomeController.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/configuration/SpringDocConfiguration.java
@@ -35,6 +38,9 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/Cha
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeSubmissionTypeDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengesPageDto.java
 src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengesPerYearDto.java
+src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamConceptDto.java
+src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamConceptSearchQueryDto.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/PageMetadataDto.java

apps/openchallenges/challenge-service/build.gradle

@@ -100,13 +100,43 @@ jacocoTestReport {
   reports {
     xml.required = true
   }
+
+    afterEvaluate {
+    // A single star (*) selects files AND subdirectories.
+    // Exclude Java classes from the JaCoCo report. These files must be excluded from SonarCloud
+    // report separatedly (see SonarCloud config)
+    def autoGeneratedFiles = [
+      '**/api/*.*',
+      '**/configuration/EnumConverterConfiguration*.*',
+      '**/configuration/HomeController*.*',
+      '**/configuration/SpringDocConfiguration*.*',
+      '**/model/dto/**',
+      '**/RFC3339DateFormat.*'
+    ]
+    classDirectories.setFrom(files(classDirectories.files.collect {
+        fileTree(dir: it, exclude: autoGeneratedFiles
+        )
+    }))
+  }
 }
 
 sonar {
+    // A single star (*) only selects files, not subdirectories.
+  def autoGeneratedFiles = [
+    '**/api/*',
+    '**/configuration/EnumConverterConfiguration*.*',
+    '**/configuration/HomeController*.*',
+    '**/configuration/SpringDocConfiguration*.*',
+    '**/model/dto/**',
+    '**/RFC3339DateFormat.*'
+  ]
   properties {
     property("sonar.host.url", "https://sonarcloud.io")
     property("sonar.organization", "sage-bionetworks")
     property("sonar.projectKey", "${project.name}")
+    // We still scan the auto-generated files to be aware of the bugs and code smells they include.
+    // property("sonar.exclusions", autoGeneratedFiles.join(","))
+    property("sonar.coverage.exclusions", autoGeneratedFiles.join(","))
     // Include the pull request number (ignored if not set)
     property("sonar.pullrequest.key", System.getenv('SONAR_PULL_REQUEST_NUMBER'))
   }

apps/openchallenges/challenge-service/requests.http

@@ -134,4 +134,12 @@ GET {{basePath}}/challenges/1/contributions
 
 ### Get the number of challenges tracked per year.
 
-GET {{basePath}}/challengeAnalytics/challengesPerYear
+GET {{basePath}}/challengeAnalytics/challengesPerYear
+
+### List the EDAM concepts
+
+GET {{basePath}}/edamConcepts
+
+### List the EDAM concepts that match the space-separated search terms "sequence".
+
+GET {{basePath}}/edamConcepts?searchTerms=sequence

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

@@ -0,0 +1,90 @@
+/**
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech) (6.2.1).
+ * https://openapi-generator.tech Do not edit the class manually.
+ */
+package org.sagebionetworks.openchallenges.challenge.service.api;
+
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.Parameter;
+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 io.swagger.v3.oas.annotations.tags.Tag;
+import javax.annotation.Generated;
+import javax.validation.Valid;
+import javax.validation.constraints.*;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.BasicErrorDto;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptSearchQueryDto;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptsPageDto;
+import org.springframework.http.ResponseEntity;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.*;
+
+@Generated(value = "org.openapitools.codegen.languages.SpringCodegen")
+@Validated
+@Tag(name = "EdamConcept", description = "Operations about EDAM concepts.")
+public interface EdamConceptApi {
+
+  default EdamConceptApiDelegate getDelegate() {
+    return new EdamConceptApiDelegate() {};
+  }
+
+  /**
+   * GET /edamConcepts : List EDAM concepts List EDAM concepts
+   *
+   * @param edamConceptSearchQuery The search query used to find EDAM concepts. (optional)
+   * @return Success (status code 200) or Invalid request (status code 400) or The request cannot be
+   *     fulfilled due to an unexpected server error (status code 500)
+   */
+  @Operation(
+      operationId = "listEdamConcepts",
+      summary = "List EDAM concepts",
+      tags = {"EdamConcept"},
+      responses = {
+        @ApiResponse(
+            responseCode = "200",
+            description = "Success",
+            content = {
+              @Content(
+                  mediaType = "application/json",
+                  schema = @Schema(implementation = EdamConceptsPageDto.class)),
+              @Content(
+                  mediaType = "application/problem+json",
+                  schema = @Schema(implementation = EdamConceptsPageDto.class))
+            }),
+        @ApiResponse(
+            responseCode = "400",
+            description = "Invalid request",
+            content = {
+              @Content(
+                  mediaType = "application/json",
+                  schema = @Schema(implementation = BasicErrorDto.class)),
+              @Content(
+                  mediaType = "application/problem+json",
+                  schema = @Schema(implementation = BasicErrorDto.class))
+            }),
+        @ApiResponse(
+            responseCode = "500",
+            description = "The request cannot be fulfilled due to an unexpected server error",
+            content = {
+              @Content(
+                  mediaType = "application/json",
+                  schema = @Schema(implementation = BasicErrorDto.class)),
+              @Content(
+                  mediaType = "application/problem+json",
+                  schema = @Schema(implementation = BasicErrorDto.class))
+            })
+      })
+  @RequestMapping(
+      method = RequestMethod.GET,
+      value = "/edamConcepts",
+      produces = {"application/json", "application/problem+json"})
+  default ResponseEntity<EdamConceptsPageDto> listEdamConcepts(
+      @Parameter(
+              name = "edamConceptSearchQuery",
+              description = "The search query used to find EDAM concepts.")
+          @Valid
+          EdamConceptSearchQueryDto edamConceptSearchQuery) {
+    return getDelegate().listEdamConcepts(edamConceptSearchQuery);
+  }
+}

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

@@ -0,0 +1,25 @@
+package org.sagebionetworks.openchallenges.challenge.service.api;
+
+import java.util.Optional;
+import javax.annotation.Generated;
+import javax.validation.constraints.*;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestMapping;
+
+@Generated(value = "org.openapitools.codegen.languages.SpringCodegen")
+@Controller
+@RequestMapping("${openapi.openChallengesChallengeREST.base-path:/v1}")
+public class EdamConceptApiController implements EdamConceptApi {
+
+  private final EdamConceptApiDelegate delegate;
+
+  public EdamConceptApiController(@Autowired(required = false) EdamConceptApiDelegate delegate) {
+    this.delegate = Optional.ofNullable(delegate).orElse(new EdamConceptApiDelegate() {});
+  }
+
+  @Override
+  public EdamConceptApiDelegate getDelegate() {
+    return delegate;
+  }
+}

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

@@ -0,0 +1,52 @@
+package org.sagebionetworks.openchallenges.challenge.service.api;
+
+import java.util.Optional;
+import javax.annotation.Generated;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptSearchQueryDto;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptsPageDto;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.context.request.NativeWebRequest;
+
+/**
+ * A delegate to be called by the {@link EdamConceptApiController}}. Implement this interface with a
+ * {@link org.springframework.stereotype.Service} annotated class.
+ */
+@Generated(value = "org.openapitools.codegen.languages.SpringCodegen")
+public interface EdamConceptApiDelegate {
+
+  default Optional<NativeWebRequest> getRequest() {
+    return Optional.empty();
+  }
+
+  /**
+   * GET /edamConcepts : List EDAM concepts List EDAM concepts
+   *
+   * @param edamConceptSearchQuery The search query used to find EDAM concepts. (optional)
+   * @return Success (status code 200) or Invalid request (status code 400) or The request cannot be
+   *     fulfilled due to an unexpected server error (status code 500)
+   * @see EdamConceptApi#listEdamConcepts
+   */
+  default ResponseEntity<EdamConceptsPageDto> listEdamConcepts(
+      EdamConceptSearchQueryDto edamConceptSearchQuery) {
+    getRequest()
+        .ifPresent(
+            request -> {
+              for (MediaType mediaType : MediaType.parseMediaTypes(request.getHeader("Accept"))) {
+                if (mediaType.isCompatibleWith(MediaType.valueOf("application/json"))) {
+                  String exampleString = "null";
+                  ApiUtil.setExampleResponse(request, "application/json", exampleString);
+                  break;
+                }
+                if (mediaType.isCompatibleWith(MediaType.valueOf("application/problem+json"))) {
+                  String exampleString =
+                      "Custom MIME type example not yet supported: application/problem+json";
+                  ApiUtil.setExampleResponse(request, "application/problem+json", exampleString);
+                  break;
+                }
+              }
+            });
+    return new ResponseEntity<>(HttpStatus.NOT_IMPLEMENTED);
+  }
+}

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

@@ -0,0 +1,22 @@
+package org.sagebionetworks.openchallenges.challenge.service.api;
+
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptSearchQueryDto;
+import org.sagebionetworks.openchallenges.challenge.service.model.dto.EdamConceptsPageDto;
+import org.sagebionetworks.openchallenges.challenge.service.service.EdamConceptService;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Component;
+
+@Component
+public class EdamConceptApiDelegateImpl implements EdamConceptApiDelegate {
+
+  private final EdamConceptService edamConceptService;
+
+  public EdamConceptApiDelegateImpl(EdamConceptService edamConceptService) {
+    this.edamConceptService = edamConceptService;
+  }
+
+  @Override
+  public ResponseEntity<EdamConceptsPageDto> listEdamConcepts(EdamConceptSearchQueryDto query) {
+    return ResponseEntity.ok(edamConceptService.listEdamConcepts(query));
+  }
+}