BI-2100 - BrAPI Hackathon Integration of Helium with DeltaBreed

src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java

@@ -0,0 +1,137 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.brapi.v2;
+
+import io.micronaut.http.HttpResponse;
+import io.micronaut.http.HttpStatus;
+import io.micronaut.http.annotation.*;
+import io.micronaut.security.annotation.Secured;
+import io.micronaut.security.rules.SecurityRule;
+import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.model.exceptions.ApiException;
+import org.brapi.v2.model.BrAPIIndexPagination;
+import org.brapi.v2.model.BrAPIMetadata;
+import org.brapi.v2.model.germ.BrAPIPedigreeNode;
+import org.brapi.v2.model.germ.response.BrAPIPedigreeListResponse;
+import org.brapi.v2.model.germ.response.BrAPIPedigreeListResponseResult;
+import org.breedinginsight.api.auth.ProgramSecured;
+import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
+import org.breedinginsight.brapi.v1.controller.BrapiVersion;
+import org.breedinginsight.brapi.v2.dao.BrAPIPedigreeDAO;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.services.ProgramService;
+import org.breedinginsight.utilities.Utilities;
+
+import javax.annotation.Nullable;
+import javax.inject.Inject;
+import java.util.*;
+
+@Slf4j
+@Controller("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2)
+@Secured(SecurityRule.IS_AUTHENTICATED)
+public class BrAPIPedigreeController {
+    private final BrAPIPedigreeDAO pedigreeDAO;
+
+    private final ProgramService programService;
+
+    @Inject
+    public BrAPIPedigreeController(BrAPIPedigreeDAO pedigreeDAO,
+                                   ProgramService programService) {
+        this.pedigreeDAO = pedigreeDAO;
+        this.programService = programService;
+    }
+
+    @Get("/pedigree")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse<BrAPIPedigreeListResponse> pedigreeGet(@PathVariable("programId") UUID programId,
+                                                               @Nullable @QueryValue("accessionNumber") String accessionNumber,
+                                                               @Nullable @QueryValue("collection") String collection,
+                                                               @Nullable @QueryValue("familyCode") String familyCode,
+                                                               @Nullable @QueryValue("binomialName") String binomialName,
+                                                               @Nullable @QueryValue("genus") Boolean genus,
+                                                               @Nullable @QueryValue("species") String species,
+                                                               @Nullable @QueryValue("synonym") String synonym,
+                                                               @Nullable @QueryValue("includeParents") Boolean includeParents,
+                                                               @Nullable @QueryValue("includeSiblings") Boolean includeSiblings,
+                                                               @Nullable @QueryValue("includeProgeny") Boolean includeProgeny,
+                                                               @Nullable @QueryValue("includeFullTree") Boolean includeFullTree,
+                                                               @Nullable @QueryValue("pedigreeDepth") Integer pedigreeDepth,
+                                                               @Nullable @QueryValue("progenyDepth") Integer progenyDepth,
+                                                               @Nullable @QueryValue("commonCropName") String commonCropName,
+                                                               @Nullable @QueryValue("programDbId") String programDbId,
+                                                               @Nullable @QueryValue("trialDbId") String trialDbId,
+                                                               @Nullable @QueryValue("studyDbId") String studyDbId,
+                                                               @Nullable @QueryValue("germplasmDbId") String germplasmDbId,
+                                                               @Nullable @QueryValue("germplasmName") String germplasmName,
+                                                               @Nullable @QueryValue("germplasmPUI") String germplasmPUI,
+                                                               @Nullable @QueryValue("externalReferenceId") String externalReferenceId,
+                                                               @Nullable @QueryValue("externalReferenceSource") String externalReferenceSource,
+                                                               @Nullable @QueryValue("page") Integer page,
+                                                               @Nullable @QueryValue("pageSize") Integer pageSize) {
+
+        log.debug("pedigreeGet: fetching pedigree by filters");
+
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.warn("Program id: " + programId + " not found");
+            return HttpResponse.notFound();
+        }
+
+        try {
+            List<BrAPIPedigreeNode> pedigree = pedigreeDAO.getPedigree(
+                    program.get(),
+                    Optional.ofNullable(includeParents),
+                    Optional.ofNullable(includeSiblings),
+                    Optional.ofNullable(includeProgeny),
+                    Optional.ofNullable(includeFullTree),
+                    Optional.ofNullable(pedigreeDepth),
+                    Optional.ofNullable(progenyDepth),
+                    Optional.ofNullable(germplasmName));
+
+            return HttpResponse.ok(
+                    new BrAPIPedigreeListResponse()
+                            .metadata(new BrAPIMetadata().pagination(new BrAPIIndexPagination().currentPage(0)
+                                    .totalPages(1)
+                                    .pageSize(pedigree.size())
+                                    .totalCount(pedigree.size())))
+                            .result(new BrAPIPedigreeListResponseResult().data(pedigree))
+            );
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "error fetching pedigree");
+        }
+    }
+
+    @Post("/pedigree")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse<?> pedigreePost(@PathVariable("programId") UUID programId, @Body List<BrAPIPedigreeNode> body) {
+        //DO NOT IMPLEMENT - Users are only able to create pedigree via the DeltaBreed UI
+        return HttpResponse.notFound();
+    }
+
+    @Put("/pedigree")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse<?> pedigreePut(@PathVariable("programId") UUID programId, @Body Map<String, BrAPIPedigreeNode> body) {
+        //DO NOT IMPLEMENT - Users aren't yet able to update observation units
+        return HttpResponse.notFound();
+    }
+
+    // TODO: search and retrieve endpoints
+    // already have some work done, search call in BrAPIPedigreeDAO
+
+}

src/main/java/org/breedinginsight/brapi/v2/BrAPIV2Controller.java

@@ -43,6 +43,7 @@
 import java.io.IOException;
 import java.util.List;
 import java.util.UUID;
+import java.util.concurrent.TimeUnit;
 import java.util.stream.Collectors;
 
 @Slf4j
@@ -147,7 +148,7 @@ public BrAPIServerInfoResponse programServerinfo(@PathVariable("programId") UUID
                 .build();
 
                 for(BrAPIService service : programServices) {
-                    service.setService(programBrAPIBase + service.getService());
+                    service.setService(service.getService());
                 }
 
                 BrAPIServerInfo programServerInfo = new BrAPIServerInfo();
@@ -230,7 +231,10 @@ private HttpResponse<String> executeRequest(String path, UUID programId, HttpReq
     }
 
     private HttpResponse<String> makeCall(Request brapiRequest) {
-        OkHttpClient client = new OkHttpClient();
+        // TODO: use config parameter for timeout
+        OkHttpClient client = new OkHttpClient.Builder()
+                .readTimeout(5, TimeUnit.MINUTES)
+                .build();
         try (Response brapiResponse = client.newCall(brapiRequest).execute()) {
             if(brapiResponse.isSuccessful()) {
                 try(ResponseBody body = brapiResponse.body()) {