BrAPI Study - strip program key

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

@@ -72,6 +72,7 @@ public GermplasmController(BrAPIGermplasmService germplasmService, GermplasmQuer
         this.brAPIEndpointProvider = brAPIEndpointProvider;
     }
 
+    // TODO: expand to fully support BrAPI request body.
     @Post("/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/search/germplasm{?queryParams*}")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})

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

@@ -0,0 +1,68 @@
+package org.breedinginsight.brapi.v2;
+
+import io.micronaut.http.HttpResponse;
+import io.micronaut.http.HttpStatus;
+import io.micronaut.http.MediaType;
+import io.micronaut.http.annotation.*;
+import io.micronaut.http.server.exceptions.InternalServerException;
+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.core.BrAPIStudy;
+import org.breedinginsight.api.auth.ProgramSecured;
+import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
+import org.breedinginsight.api.model.v1.request.query.SearchRequest;
+import org.breedinginsight.api.model.v1.response.DataResponse;
+import org.breedinginsight.api.model.v1.response.Response;
+import org.breedinginsight.api.model.v1.validators.QueryValid;
+import org.breedinginsight.brapi.v1.controller.BrapiVersion;
+import org.breedinginsight.brapi.v2.model.request.query.StudyQuery;
+import org.breedinginsight.brapi.v2.services.BrAPIStudyService;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.utilities.response.ResponseUtils;
+import org.breedinginsight.utilities.response.mappers.StudyQueryMapper;
+
+import javax.inject.Inject;
+import javax.validation.Valid;
+import java.util.List;
+import java.util.UUID;
+
+@Slf4j
+@Controller("/${micronaut.bi.api.version}")
+@Secured(SecurityRule.IS_AUTHENTICATED)
+public class StudyController {
+
+    private final BrAPIStudyService studyService;
+    private final StudyQueryMapper studyQueryMapper;
+
+
+    @Inject
+    public StudyController(BrAPIStudyService studyService, StudyQueryMapper studyQueryMapper) {
+        this.studyService = studyService;
+        this.studyQueryMapper = studyQueryMapper;
+    }
+
+    @Get("/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/studies{?queryParams*}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse<Response<DataResponse<List<BrAPIStudy>>>> getStudy(
+            @PathVariable("programId") UUID programId,
+            @QueryValue @QueryValid(using = StudyQueryMapper.class) @Valid StudyQuery queryParams) {
+        try {
+            log.debug("fetching studies for program: " + programId);
+
+            List<BrAPIStudy> studies = studyService.getStudies(programId);
+            queryParams.setSortField(studyQueryMapper.getDefaultSortField());
+            queryParams.setSortOrder(studyQueryMapper.getDefaultSortOrder());
+            SearchRequest searchRequest = queryParams.constructSearchRequest();
+            return ResponseUtils.getBrapiQueryResponse(studies, studyQueryMapper, queryParams, searchRequest);
+        } catch (ApiException e) {
+            log.info(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving study");
+        } catch (IllegalArgumentException e) {
+            log.info(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, "Error parsing requested date format");
+        }
+    }
+}

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIStudyDAO.java

@@ -0,0 +1,198 @@
+/*
+ * 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.dao;
+
+import com.google.gson.JsonObject;
+import io.micronaut.context.annotation.Context;
+import io.micronaut.context.annotation.Property;
+import io.micronaut.http.server.exceptions.InternalServerException;
+import io.micronaut.scheduling.annotation.Scheduled;
+import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.model.exceptions.ApiException;
+import org.brapi.client.v2.modules.core.StudiesApi;
+import org.brapi.v2.model.BrAPIExternalReference;
+import org.brapi.v2.model.core.BrAPIStudy;
+import org.brapi.v2.model.core.request.BrAPIStudySearchRequest;
+import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
+import org.breedinginsight.daos.ProgramDAO;
+import org.breedinginsight.daos.cache.ProgramCache;
+import org.breedinginsight.daos.cache.ProgramCacheProvider;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.utilities.BrAPIDAOUtil;
+import org.breedinginsight.utilities.Utilities;
+
+import javax.inject.Inject;
+import javax.inject.Singleton;
+import java.util.*;
+import java.util.stream.Collectors;
+
+@Slf4j
+@Singleton
+@Context
+public class BrAPIStudyDAO {
+
+    private final ProgramDAO programDAO;
+    private final BrAPIDAOUtil brAPIDAOUtil;
+
+    @Property(name = "brapi.server.reference-source")
+    private String referenceSource;
+
+    @Property(name = "micronaut.bi.api.run-scheduled-tasks")
+    private boolean runScheduledTasks;
+
+    private final ProgramCache<BrAPIStudy> programStudyCache;
+
+    private final BrAPIEndpointProvider brAPIEndpointProvider;
+
+    @Inject
+    public BrAPIStudyDAO(ProgramDAO programDAO, BrAPIDAOUtil brAPIDAOUtil, ProgramCacheProvider programCacheProvider, BrAPIEndpointProvider brAPIEndpointProvider) {
+        this.programDAO = programDAO;
+        this.brAPIDAOUtil = brAPIDAOUtil;
+        this.programStudyCache = programCacheProvider.getProgramCache(this::fetchProgramStudy, BrAPIStudy.class);
+        this.brAPIEndpointProvider = brAPIEndpointProvider;
+    }
+
+    @Scheduled(initialDelay = "2s")
+    public void setup() {
+        if(!runScheduledTasks) {
+            return;
+        }
+        // Populate study cache for all programs on startup
+        log.debug("populating study cache");
+        List<Program> programs = programDAO.getActive();
+        if(programs != null) {
+            programStudyCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
+        }
+    }
+
+    /**
+     * Fetch the study for this program, and process it to remove storage specific values
+     * @param programId
+     * @return this program's study
+     * @throws ApiException
+     */
+    public List<BrAPIStudy> getStudies(UUID programId) throws ApiException {
+        return new ArrayList<>(programStudyCache.get(programId).values());
+    }
+
+    /**
+     * Fetch formatted study for this program
+     * @param programId
+     * @return Map<Key = string representing study UUID, value = formatted BrAPIStudy>
+     * @throws ApiException
+     */
+    private Map<String, BrAPIStudy> fetchProgramStudy(UUID programId) throws ApiException {
+        StudiesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), StudiesApi.class);
+        // Get the program key
+        List<Program> programs = programDAO.get(programId);
+        if (programs.size() != 1) {
+            throw new InternalServerException("Program was not found for given key");
+        }
+        Program program = programs.get(0);
+
+        // Set query params and make call
+        BrAPIStudySearchRequest studySearch = new BrAPIStudySearchRequest();
+        studySearch.externalReferenceIDs(List.of(programId.toString()));
+        studySearch.externalReferenceSources(List.of(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS)));
+        return processStudyForDisplay(brAPIDAOUtil.search(
+                api::searchStudiesPost,
+                api::searchStudiesSearchResultsDbIdGet,
+                studySearch
+        ), program.getKey());
+    }
+
+    /**
+     * Process study into a format for display
+     * @param programStudy
+     * @return Map<Key = string representing study UUID, value = formatted BrAPIStudy>
+     * @throws ApiException
+     */
+    private Map<String,BrAPIStudy> processStudyForDisplay(List<BrAPIStudy> programStudy, String programKey) {
+        // Process the study
+        Map<String, BrAPIStudy> programStudyMap = new HashMap<>();
+        log.trace("processing germ for display: " + programStudy);
+        Map<String, BrAPIStudy> programStudyByFullName = new HashMap<>();
+        for (BrAPIStudy study: programStudy) {
+            programStudyByFullName.put(study.getStudyName(), study);
+            // Remove program key from studyName, trialName and locationName.
+            if (study.getStudyName() != null) {
+                // Study name is appended with program key and experiment sequence number, need to remove.
+                study.setStudyName(Utilities.removeProgramKeyAndUnknownAdditionalData(study.getStudyName(), programKey));
+            }
+            if (study.getTrialName() != null) {
+                study.setTrialName(Utilities.removeProgramKey(study.getTrialName(), programKey));
+            }
+            if (study.getLocationName() != null) {
+                study.setLocationName(Utilities.removeProgramKey(study.getLocationName(), programKey));
+            }
+        }
+
+        String refSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES);
+        // Add to map.
+        for (BrAPIStudy study: programStudy) {
+            JsonObject additionalInfo = study.getAdditionalInfo();
+            if(additionalInfo == null) {
+                additionalInfo = new JsonObject();
+                study.setAdditionalInfo(additionalInfo);
+            }
+
+            BrAPIExternalReference extRef = study.getExternalReferences().stream()
+                    .filter(reference -> reference.getReferenceSource().equals(refSource))
+                    .findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
+            String studyId = extRef.getReferenceID();
+            programStudyMap.put(studyId, study);
+        }
+
+        return programStudyMap;
+    }
+
+    public BrAPIStudy getStudyByUUID(String studyId, UUID programId) throws ApiException, DoesNotExistException {
+        Map<String, BrAPIStudy> cache = programStudyCache.get(programId);
+        BrAPIStudy study = null;
+        if (cache != null) {
+            study = cache.get(studyId);
+        }
+        if (study == null) {
+            throw new DoesNotExistException("UUID for this study does not exist");
+        }
+        return study;
+    }
+
+    public Optional<BrAPIStudy> getStudyByDBID(String studyDbId, UUID programId) throws ApiException {
+        Map<String, BrAPIStudy> cache = programStudyCache.get(programId);
+        //key is UUID, want to filter by DBID
+        BrAPIStudy study = null;
+        if (cache != null) {
+            study = cache.values().stream().filter(x -> x.getStudyDbId().equals(studyDbId)).collect(Collectors.toList()).get(0);
+        }
+        return Optional.ofNullable(study);
+    }
+
+    public List<BrAPIStudy> getStudiesByDBID(Collection<String> studyDbIds, UUID programId) throws ApiException {
+        Map<String, BrAPIStudy> cache = programStudyCache.get(programId);
+        //key is UUID, want to filter by DBID
+        List<BrAPIStudy> studies = new ArrayList<>();
+        if (cache != null) {
+            studies = cache.values().stream().filter(x -> studyDbIds.contains(x.getStudyDbId())).collect(Collectors.toList());
+        }
+        return studies;
+    }
+
+}

src/main/java/org/breedinginsight/brapi/v2/model/request/query/StudyQuery.java

@@ -0,0 +1,53 @@
+package org.breedinginsight.brapi.v2.model.request.query;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+import org.breedinginsight.api.model.v1.request.query.FilterRequest;
+import org.breedinginsight.api.model.v1.request.query.SearchRequest;
+import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
+import org.jooq.tools.StringUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Getter
+@Introspected
+public class StudyQuery extends BrapiQuery {
+    private String studyType;
+    private String locationDbId;
+    private String studyCode;
+    private String studyPUI;
+    private String commonCropName;
+    private String trialDbId;
+    private String studyDbId;
+    private String studyName;
+
+    public SearchRequest constructSearchRequest() {
+        List<FilterRequest> filters = new ArrayList<>();
+        if (!StringUtils.isBlank(getStudyType())) {
+            filters.add(constructFilterRequest("studyType", getStudyType()));
+        }
+        if (!StringUtils.isBlank(getLocationDbId())) {
+            filters.add(constructFilterRequest("locationDbId", getLocationDbId()));
+        }
+        if (!StringUtils.isBlank(getStudyCode())) {
+            filters.add(constructFilterRequest("studyCode", getStudyCode()));
+        }
+        if (!StringUtils.isBlank(getStudyPUI())) {
+            filters.add(constructFilterRequest("studyPUI", getStudyPUI()));
+        }
+        if (!StringUtils.isBlank(getCommonCropName())) {
+            filters.add(constructFilterRequest("commonCropName", getCommonCropName()));
+        }
+        if (!StringUtils.isBlank(getTrialDbId())) {
+            filters.add(constructFilterRequest("trialDbId", getTrialDbId()));
+        }
+        if (!StringUtils.isBlank(getStudyDbId())) {
+            filters.add(constructFilterRequest("studyDbId", getStudyDbId()));
+        }
+        if (!StringUtils.isBlank(getStudyName())) {
+            filters.add(constructFilterRequest("studyName", getStudyName()));
+        }
+        return new SearchRequest(filters);
+    }
+}

src/main/java/org/breedinginsight/brapi/v2/services/BrAPIStudyService.java

@@ -0,0 +1,59 @@
+/*
+ * 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.services;
+
+import io.micronaut.http.server.exceptions.InternalServerException;
+import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.model.exceptions.ApiException;
+import org.brapi.v2.model.core.BrAPIStudy;
+import org.breedinginsight.brapi.v2.dao.BrAPIStudyDAO;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
+
+import javax.inject.Inject;
+import javax.inject.Singleton;
+import java.util.List;
+import java.util.UUID;
+
+@Slf4j
+@Singleton
+public class BrAPIStudyService {
+
+    private final BrAPIStudyDAO studyDAO;
+
+    @Inject
+    public BrAPIStudyService(BrAPIStudyDAO studyDAO) {
+        this.studyDAO = studyDAO;
+    }
+
+    public List<BrAPIStudy> getStudies(UUID programId) throws ApiException {
+        try {
+            return studyDAO.getStudies(programId);
+        } catch (ApiException e) {
+            throw new InternalServerException(e.getMessage(), e);
+        }
+    }
+
+    public BrAPIStudy getStudyByUUID(UUID programId, String studyId) throws DoesNotExistException {
+        try {
+            return studyDAO.getStudyByUUID(studyId, programId);
+        } catch (ApiException e) {
+            throw new InternalServerException(e.getMessage(), e);
+        }
+    }
+
+}