BI-2376 - Create Delete Endpoint for Deltabreed Experiment Controller

src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java

@@ -298,4 +298,43 @@ public HttpResponse deleteExperimentalCollaborator(
         }
 
     }
+
+    /**
+     * Deletes an experiment.
+     * @param programId The UUID of the program
+     * @param experimentId The UUID of the experiment
+     * @param hard Specifies hard or soft delete
+     * @return A Http Response
+     */
+    @Delete("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}{?hard}")
+    @ProgramSecured(roles = {ProgramSecuredRole.PROGRAM_ADMIN, ProgramSecuredRole.SYSTEM_ADMIN})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse deleteExperiment(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @QueryValue(defaultValue = "false") Boolean hard
+    ) throws ApiException {
+        try {
+            Optional<Program> program = programService.getById(programId);
+            if(program.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+            int observationCount = experimentService.deleteExperiment(program.get(), experimentId, hard);
+            if (observationCount > 0 && hard) {
+                // 409 Conflict. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/409
+                return HttpResponse.status(HttpStatus.CONFLICT);
+            }
+            // 204 No Content indicates successful delete. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/204
+            return HttpResponse.noContent();
+        } catch (ApiException e) {
+            log.error("Error deleting experiment.\n\tprogramId: " + programId +  "\n\texperimentId: " + experimentId + "\n\thard: " + hard);
+            if (e.getCode() == 404) {
+                return HttpResponse.notFound();
+            } else {
+                return HttpResponse.serverError();
+            }
+        }
+    }
+
+
 }

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

@@ -0,0 +1,15 @@
+package org.breedinginsight.brapi.v2.dao;
+
+import org.breedinginsight.daos.cache.ProgramCache;
+
+import java.util.UUID;
+
+public abstract class BrAPICachedDAO<T> {
+
+    protected ProgramCache<T> programCache;
+
+    public void repopulateCache(UUID programId) {
+        this.programCache.invalidate(programId);
+        this.programCache.populate(programId);
+    }
+}

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

@@ -18,11 +18,8 @@
 package org.breedinginsight.brapi.v2.dao;
 
 import io.micronaut.http.HttpResponse;
-import io.micronaut.http.HttpStatus;
-import io.micronaut.http.exceptions.HttpStatusException;
 import lombok.extern.slf4j.Slf4j;
 import okhttp3.HttpUrl;
-import okhttp3.OkHttpClient;
 import okhttp3.Request;
 import org.brapi.client.v2.ApiResponse;
 import org.brapi.client.v2.model.exceptions.ApiException;
@@ -38,27 +35,19 @@
 import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 import org.brapi.v2.model.core.response.BrAPIListsListResponseResult;
 import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
-import org.breedinginsight.api.model.v1.response.DataResponse;
-import org.breedinginsight.api.model.v1.response.Response;
-import org.breedinginsight.brapi.v1.controller.BrapiVersion;
 import org.breedinginsight.brapps.importer.daos.ImportDAO;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.daos.ProgramDAO;
-import org.breedinginsight.model.ProgramBrAPIEndpoints;
-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.validation.constraints.NotNull;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
-import java.util.concurrent.TimeUnit;
 
 @Slf4j
 public class BrAPIListDAO {
@@ -79,7 +68,7 @@ public BrAPIListDAO(ProgramDAO programDAO,
         this.brAPIEndpointProvider = brAPIEndpointProvider;
     }
 
-    public List<BrAPIListSummary> getListByName(List<String> listNames, UUID programId) throws ApiException {
+    public List<BrAPIListSummary> getListsByName(List<String> listNames, UUID programId) throws ApiException {
         if(listNames.isEmpty()) {
             return Collections.emptyList();
         }
@@ -100,7 +89,7 @@ public BrAPIListsSingleResponse getListById(String listId, UUID programId) throw
         return response.getBody();
     }
 
-    public List<BrAPIListSummary> getListBySearch(@NotNull BrAPIListSearchRequest searchRequest, UUID programId) throws ApiException {
+    public List<BrAPIListSummary> getListsBySearch(@NotNull BrAPIListSearchRequest searchRequest, UUID programId) throws ApiException {
         ListsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ListsApi.class);
         List<BrAPIListSummary> programLists = brAPIDAOUtil.search(api::searchListsPost, api::searchListsSearchResultsDbIdGet, searchRequest);
         if (searchRequest.getExternalReferenceSources() != null && searchRequest.getExternalReferenceIDs() != null) {
@@ -112,7 +101,7 @@ public List<BrAPIListSummary> getListBySearch(@NotNull BrAPIListSearchRequest se
 
     }
 
-    public List<BrAPIListSummary> getListByTypeAndExternalRef(@NotNull BrAPIListTypes listType, UUID programId, String externalReferenceSource, UUID externalReferenceId) throws ApiException {
+    public List<BrAPIListSummary> getListsByTypeAndExternalRef(@NotNull BrAPIListTypes listType, UUID programId, String externalReferenceSource, UUID externalReferenceId) throws ApiException {
         BrAPIListSearchRequest searchRequest = new BrAPIListSearchRequest()
                 .externalReferenceIDs(List.of(externalReferenceId.toString()))
                 .externalReferenceSources(List.of(externalReferenceSource))

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

@@ -36,7 +36,6 @@
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 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;
@@ -54,7 +53,7 @@
 
 @Singleton
 @Slf4j
-public class BrAPIObservationDAO {
+public class BrAPIObservationDAO extends BrAPICachedDAO<BrAPIObservation> {
 
     private ProgramDAO programDAO;
     private ImportDAO importDAO;
@@ -63,7 +62,6 @@ public class BrAPIObservationDAO {
     private final BrAPIEndpointProvider brAPIEndpointProvider;
     private final String referenceSource;
     private boolean runScheduledTasks;
-    private final ProgramCache<BrAPIObservation> programObservationCache;
 
     @Inject
     public BrAPIObservationDAO(ProgramDAO programDAO,
@@ -81,7 +79,7 @@ public BrAPIObservationDAO(ProgramDAO programDAO,
         this.brAPIEndpointProvider = brAPIEndpointProvider;
         this.referenceSource = referenceSource;
         this.runScheduledTasks = runScheduledTasks;
-        this.programObservationCache = programCacheProvider.getProgramCache(this::fetchProgramObservations, BrAPIObservation.class);
+        this.programCache = programCacheProvider.getProgramCache(this::fetchProgramObservations, BrAPIObservation.class);
     }
 
     @Scheduled(initialDelay = "3s")
@@ -93,7 +91,7 @@ public void setup() {
         log.debug("populating observation cache");
         List<Program> programs = programDAO.getActive();
         if (programs != null) {
-            programObservationCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
+            programCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
         }
     }
 
@@ -163,7 +161,7 @@ private void processObservations(String programKey, List<BrAPIObservation> obser
      * Get all observations for a program from the cache.
      */
     private Map<String, BrAPIObservation> getProgramObservations(UUID programId) throws ApiException {
-        return programObservationCache.get(programId);
+        return programCache.get(programId);
     }
 
     // Note: not using cache, because unique studyName (with "[ProgramKey-ExtraInfo]") is not stored directly on Observation.
@@ -259,7 +257,7 @@ public List<BrAPIObservation> createBrAPIObservations(List<BrAPIObservation> brA
                     List<BrAPIObservation> postResponse = brAPIDAOUtil.post(brAPIObservationList, upload, api::observationsPost, importDAO::update);
                     return processObservationsForCache(postResponse, program.getKey());
                 };
-                return programObservationCache.post(programId, postFunction);
+                return programCache.post(programId, postFunction);
             }
             return new ArrayList<>();
         } catch (Exception e) {
@@ -287,7 +285,7 @@ public BrAPIObservation updateBrAPIObservation(String dbId, BrAPIObservation obs
                     }
                     return processObservationsForCache(List.of(updatedObservation), program.getKey());
             };
-            return programObservationCache.post(programId, postFunction).get(0);
+            return programCache.post(programId, postFunction).get(0);
         } catch (ApiException e) {
             log.error(Utilities.generateApiExceptionLogMessage(e));
             throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
@@ -343,7 +341,7 @@ public List<BrAPIObservation> updateBrAPIObservation(Map<String, BrAPIObservatio
                 }
             }
             Map<String, BrAPIObservation> processedObservations = processObservationsForCache(updatedObservations, program.getKey());
-            return programObservationCache.postThese(programId,processedObservations);
+            return programCache.postThese(programId,processedObservations);
         } catch (ApiException e) {
             log.error("Error updating observation: " + Utilities.generateApiExceptionLogMessage(e), e);
             throw e;

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

@@ -41,7 +41,6 @@
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 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.ProgramService;
@@ -61,7 +60,7 @@
 
 @Slf4j
 @Singleton
-public class BrAPIObservationUnitDAO {
+public class BrAPIObservationUnitDAO extends BrAPICachedDAO<BrAPIObservationUnit> {
     private final ProgramDAO programDAO;
     private final ImportDAO importDAO;
     private final BrAPIDAOUtil brAPIDAOUtil;
@@ -75,8 +74,6 @@ public class BrAPIObservationUnitDAO {
     private final Gson gson = new JSON().getGson();
     private final Type treatmentlistType = new TypeToken<ArrayList<BrAPIObservationTreatment>>(){}.getType();
 
-    private final ProgramCache<BrAPIObservationUnit> programObservationUnitCache;
-
     @Inject
     public BrAPIObservationUnitDAO(ProgramDAO programDAO,
                                    ImportDAO importDAO,
@@ -95,7 +92,7 @@ public BrAPIObservationUnitDAO(ProgramDAO programDAO,
         this.runScheduledTasks = runScheduledTasks;
         this.programService = programService;
         this.germplasmService = germplasmService;
-        this.programObservationUnitCache = programCacheProvider.getProgramCache(this::fetchProgramObservationUnits, BrAPIObservationUnit.class);
+        this.programCache = programCacheProvider.getProgramCache(this::fetchProgramObservationUnits, BrAPIObservationUnit.class);
     }
 
     @Scheduled(initialDelay = "3s")
@@ -107,7 +104,7 @@ public void setup() {
         log.debug("populating observation unit cache");
         List<Program> programs = programDAO.getActive();
         if(programs != null) {
-            programObservationUnitCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
+            programCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
         }
     }
 
@@ -157,7 +154,7 @@ private Map<String, BrAPIObservationUnit> processObservationUnitsForCache(List<B
      * Get all observation units for a program from the cache.
      */
     private Map<String, BrAPIObservationUnit> getProgramObservationUnits(UUID programId) throws ApiException {
-        return programObservationUnitCache.get(programId);
+        return programCache.get(programId);
     }
 
     public List<BrAPIObservationUnit> getObservationUnitByName(List<String> observationUnitNames, Program program) throws ApiException {
@@ -183,7 +180,7 @@ public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservat
                     List<BrAPIObservationUnit> ous = brAPIDAOUtil.post(brAPIObservationUnitList, upload, api::observationunitsPost, importDAO::update);
                     return processObservationUnitsForCache(ous, program, false);
                 };
-                return programObservationUnitCache.post(programId, postFunction);
+                return programCache.post(programId, postFunction);
             }
             return new ArrayList<>();
         } catch (Exception e) {
@@ -205,7 +202,7 @@ public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservat
                     List<BrAPIObservationUnit> ous = brAPIDAOUtil.post(brAPIObservationUnitList, api::observationunitsPost);
                     return processObservationUnitsForCache(ous, program, false);
                 };
-                return programObservationUnitCache.post(programId, postFunction);
+                return programCache.post(programId, postFunction);
             }
             return new ArrayList<>();
         } catch (Exception e) {

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

@@ -30,7 +30,6 @@
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 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;
@@ -46,7 +45,7 @@
 
 @Slf4j
 @Singleton
-public class BrAPIStudyDAO {
+public class BrAPIStudyDAO extends BrAPICachedDAO<BrAPIStudy> {
     @Property(name = "brapi.server.reference-source")
     private String referenceSource;
     @Property(name = "micronaut.bi.api.run-scheduled-tasks")
@@ -56,16 +55,14 @@ public class BrAPIStudyDAO {
     private ImportDAO importDAO;
     private final BrAPIDAOUtil brAPIDAOUtil;
     private final BrAPIEndpointProvider brAPIEndpointProvider;
-    private final ProgramCache<BrAPIStudy> programStudyCache;
-
 
     @Inject
     public BrAPIStudyDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brAPIDAOUtil, BrAPIEndpointProvider brAPIEndpointProvider, ProgramCacheProvider programCacheProvider) {
         this.programDAO = programDAO;
         this.importDAO = importDAO;
         this.brAPIDAOUtil = brAPIDAOUtil;
         this.brAPIEndpointProvider = brAPIEndpointProvider;
-        this.programStudyCache = programCacheProvider.getProgramCache(this::fetchProgramStudy, BrAPIStudy.class);
+        this.programCache = programCacheProvider.getProgramCache(this::fetchProgramStudy, BrAPIStudy.class);
     }
 
     @Scheduled(initialDelay = "2s")
@@ -77,7 +74,7 @@ public void setup() {
         log.debug("populating study cache");
         List<Program> programs = programDAO.getActive();
         if(programs != null) {
-            programStudyCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
+            programCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
         }
     }
 
@@ -115,7 +112,7 @@ private Map<String, BrAPIStudy> fetchProgramStudy(UUID programId) throws ApiExce
      * @throws ApiException
      */
     public List<BrAPIStudy> getStudies(UUID programId) throws ApiException {
-        return new ArrayList<>(programStudyCache.get(programId).values());
+        return new ArrayList<>(programCache.get(programId).values());
     }
 
     public Optional<BrAPIStudy> getStudyByName(String studyName, Program program) throws ApiException {
@@ -153,7 +150,7 @@ public List<BrAPIStudy> getStudiesByExperimentID(@NotNull UUID experimentId, Pro
     }
 
     public List<BrAPIStudy> getStudiesByEnvironmentIds(@NotNull Collection<UUID> environmentIds, Program program) throws ApiException {
-        return programStudyCache.get(program.getId())
+        return programCache.get(program.getId())
                                 .entrySet()
                                 .stream()
                                 .filter(entry -> environmentIds.contains(UUID.fromString(entry.getKey())))
@@ -193,7 +190,7 @@ public List<BrAPIStudy> createBrAPIStudies(List<BrAPIStudy> brAPIStudyList, UUID
                             .post(brAPIStudyList, upload, api::studiesPost, importDAO::update);
                     return environmentById(postedStudies);
                 };
-                createdStudies.addAll(programStudyCache.post(programId, postCallback));
+                createdStudies.addAll(programCache.post(programId, postCallback));
             }
 
             return createdStudies;

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

@@ -45,4 +45,8 @@ List<BrAPITrial> createBrAPITrials(List<BrAPITrial> brAPITrialList, UUID program
     List<BrAPITrial> getTrialsByDbIds(Collection<String> trialDbIds, Program program) throws ApiException;
 
     List<BrAPITrial> getTrialsByExperimentIds(Collection<UUID> experimentIds, Program program) throws ApiException;
+
+    void deleteBrAPITrial(Program program, BrAPITrial trial, boolean hard) throws ApiException;
+
+    void repopulateCache(UUID programId);
 }

src/main/java/org/breedinginsight/brapi/v2/dao/impl/BrAPITrialDAOImpl.java

@@ -21,6 +21,8 @@
 import io.micronaut.http.server.exceptions.InternalServerException;
 import io.micronaut.scheduling.annotation.Scheduled;
 import lombok.extern.slf4j.Slf4j;
+import okhttp3.HttpUrl;
+import okhttp3.Request;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.client.v2.modules.core.TrialsApi;
 import org.brapi.v2.model.BrAPIExternalReference;
@@ -277,4 +279,25 @@ public List<BrAPITrial> getTrialsByExperimentIds(Collection<UUID> experimentIds,
                 trialSearch
         ), program.getKey());
     }
+
+    @Override
+    public void deleteBrAPITrial(Program program, BrAPITrial trial, boolean hard) throws ApiException {
+        // TODO: Switch to using the TrialsApi from the BrAPI client library once the delete endpoints are merged into it.
+        var programBrAPIBaseUrl = brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId());
+        var requestUrl = HttpUrl.parse(programBrAPIBaseUrl + "/trials/" + trial.getTrialDbId()).newBuilder();
+        requestUrl.addQueryParameter("hardDelete", Boolean.toString(hard));
+        HttpUrl url = requestUrl.build();
+        var brapiRequest = new Request.Builder().url(url)
+                .method("DELETE", null)
+                .addHeader("Content-Type", "application/json")
+                .build();
+
+        brAPIDAOUtil.makeCall(brapiRequest);
+    }
+
+    @Override
+    public void repopulateCache(UUID programId) {
+        this.programExperimentCache.invalidate(programId);
+        this.programExperimentCache.populate(programId);
+    }
 }