[BI-1294] Implement Caching Layer for Experiments

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPITrialDAO.java

@@ -1,187 +1,31 @@
-/*
- * 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.brapps.importer.daos;
 
-import io.micronaut.context.annotation.Property;
 import org.brapi.client.v2.model.exceptions.ApiException;
-import org.brapi.client.v2.modules.core.TrialsApi;
 import org.brapi.v2.model.core.BrAPITrial;
-import org.brapi.v2.model.core.request.BrAPITrialSearchRequest;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
-import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
-import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.model.Program;
-import org.breedinginsight.services.ProgramService;
-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;
+import java.util.Collection;
+import java.util.List;
+import java.util.Optional;
+import java.util.UUID;
 
-@Singleton
-public class BrAPITrialDAO {
-    @Property(name = "brapi.server.reference-source")
-    private String BRAPI_REFERENCE_SOURCE;
+public interface BrAPITrialDAO {
+    List<BrAPITrial> getTrialsByName(List<String> trialNames, Program program) throws ApiException;
 
-    private final ProgramDAO programDAO;
-    private final ImportDAO importDAO;
-    private final BrAPIDAOUtil brAPIDAOUtil;
-    private final ProgramService programService;
-    private final BrAPIEndpointProvider brAPIEndpointProvider;
+    List<BrAPITrial> createBrAPITrials(List<BrAPITrial> brAPITrialList, UUID programId, ImportUpload upload)
+            throws ApiException;
 
-    private final String referenceSource;
+    BrAPITrial updateBrAPITrial(String trialDbId, BrAPITrial trial, UUID programId) throws ApiException;
 
-    @Inject
-    public BrAPITrialDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brAPIDAOUtil, ProgramService programService, @Property(name = "brapi.server.reference-source") String referenceSource, BrAPIEndpointProvider brAPIEndpointProvider) {
-        this.programDAO = programDAO;
-        this.importDAO = importDAO;
-        this.brAPIDAOUtil = brAPIDAOUtil;
-        this.programService = programService;
-        this.referenceSource = referenceSource;
-        this.brAPIEndpointProvider = brAPIEndpointProvider;
-    }
+    List<BrAPITrial> getTrials(UUID programId) throws ApiException;
 
-    public List<BrAPITrial> getTrialsByName(List<String> trialNames, Program program) throws ApiException {
-        if(trialNames.isEmpty()) {
-            return Collections.emptyList();
-        }
+    Optional<BrAPITrial> getTrialById(UUID programId, UUID trialId) throws ApiException, DoesNotExistException;
 
-        BrAPITrialSearchRequest trialSearch = new BrAPITrialSearchRequest();
-        trialSearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
-        trialSearch.trialNames(trialNames);
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);
-        return brAPIDAOUtil.search(
-                api::searchTrialsPost,
-                api::searchTrialsSearchResultsDbIdGet,
-                trialSearch
-        );
-    }
+    Optional<BrAPITrial> getTrialByDbId(String trialDbId, Program program) throws ApiException;
 
-    private List<BrAPITrial> getTrialsByExRef(String referenceSource, String referenceId, Program program) throws ApiException {
-        BrAPITrialSearchRequest trialSearch = new BrAPITrialSearchRequest();
-        trialSearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
-        trialSearch.externalReferenceSources(List.of(referenceSource));
-        trialSearch.externalReferenceIDs(List.of(referenceId));
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);
-        return brAPIDAOUtil.search(
-                api::searchTrialsPost,
-                api::searchTrialsSearchResultsDbIdGet,
-                trialSearch
-        );
-    }
-
-    public List<BrAPITrial> createBrAPITrials(List<BrAPITrial> brAPITrialList, UUID programId, ImportUpload upload) throws ApiException {
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), TrialsApi.class);
-        return brAPIDAOUtil.post(brAPITrialList, upload, api::trialsPost, importDAO::update);
-    }
-    public BrAPITrial updateBrAPITrial(String trialDbId, BrAPITrial trial, UUID programId) throws ApiException {
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), TrialsApi.class);
-        return brAPIDAOUtil.put(trialDbId, trial, api::trialsTrialDbIdPut);
-    }
-    /**
-     * Fetch formatted trials/experiments for this program
-     * @param programId
-     * @return List<formatted BrAPITrial>
-     * @throws ApiException
-     */
-    public List<BrAPITrial> getTrials(UUID programId) throws ApiException, DoesNotExistException {
-        BrAPITrialSearchRequest trialSearch = new BrAPITrialSearchRequest();
-        //TODO check external references filter works once implemented in BI-1552
-        trialSearch.externalReferenceSources(List.of(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS)));
-        trialSearch.externalReferenceIDs(List.of(programId.toString()));
-
-        Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
-        trialSearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
-
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);
-        return processExperimentsForDisplay(brAPIDAOUtil.search(
-                api::searchTrialsPost,
-                api::searchTrialsSearchResultsDbIdGet,
-                trialSearch), program.getKey(), programId, true);
-    }
-
-    //Removes program key from trial name and adds dataset information
-    private List<BrAPITrial> processExperimentsForDisplay(List<BrAPITrial> trials, String programKey, UUID programId, boolean metadata) throws ApiException {
-        List<BrAPITrial> displayExperiments = new ArrayList<>();
-        for (BrAPITrial trial: trials) {
-            trial.setTrialName(Utilities.removeProgramKey(trial.getTrialName(), programKey, ""));
-            List<String> datasets = new ArrayList<>();
-
-            if (metadata) {
-                //todo presumably BI-1193 replace dummy value with list of datasets once datasets implemented
-                datasets.add("Observation Dataset");
-                trial.putAdditionalInfoItem("datasets", datasets);
-            }
-
-            displayExperiments.add(trial);
-        }
-        return displayExperiments;
-    }
-
-    public Optional<BrAPITrial> getTrialById(UUID programId, UUID trialDbId) throws ApiException, DoesNotExistException {
-        Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
-        String refSoure = Utilities.generateReferenceSource(BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.TRIALS);
-        List<BrAPITrial> trials = getTrialsByExRef(refSoure, trialDbId.toString(), program);
-
-        return Utilities.getSingleOptional(trials);
-    }
-
-    public Optional<BrAPITrial> getTrialByDbId(String trialDbId, Program program) throws ApiException {
-        List<BrAPITrial> trials = getTrialsByDbIds(List.of(trialDbId), program);
-        return Utilities.getSingleOptional(trials);
-    }
-    public List<BrAPITrial> getTrialsByDbIds(Collection<String> trialDbIds, Program program) throws ApiException {
-        if(trialDbIds.isEmpty()) {
-            return Collections.emptyList();
-        }
-
-        BrAPITrialSearchRequest trialSearch = new BrAPITrialSearchRequest();
-        trialSearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
-        trialSearch.trialDbIds(new ArrayList<>(trialDbIds));
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);
-        return brAPIDAOUtil.search(
-                api::searchTrialsPost,
-                api::searchTrialsSearchResultsDbIdGet,
-                trialSearch
-        );
-    }
-
-    public List<BrAPITrial> getTrialsByExperimentIds(Collection<UUID> experimentIds, Program program) throws ApiException {
-        if(experimentIds.isEmpty()) {
-            return Collections.emptyList();
-        }
-
-        BrAPITrialSearchRequest trialSearch = new BrAPITrialSearchRequest();
-        trialSearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
-        //trialSearch.trialDbIds(experimentIds.stream().map(id -> id.toString()).collect(Collectors.toList()));
-        trialSearch.externalReferenceSources(List.of(referenceSource + "/" + ExternalReferenceSource.TRIALS.getName()));
-        trialSearch.externalReferenceIDs(experimentIds.stream().map(id -> id.toString()).collect(Collectors.toList()));
-        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);
-        return brAPIDAOUtil.search(
-                api::searchTrialsPost,
-                api::searchTrialsSearchResultsDbIdGet,
-                trialSearch
-        );
-    }
+    List<BrAPITrial> getTrialsByDbIds(Collection<String> trialDbIds, Program program) throws ApiException;
 
+    List<BrAPITrial> getTrialsByExperimentIds(Collection<UUID> experimentIds, Program program) throws ApiException;
 }
-
-