[BI-1720] - Export Multiple Environment Datasets as Zip

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

@@ -30,8 +30,7 @@
 import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;
 import javax.inject.Inject;
 import javax.validation.Valid;
-import java.util.List;
-import java.util.UUID;
+import java.util.*;
 
 @Slf4j
 @Controller
@@ -92,17 +91,22 @@ public HttpResponse<Response<BrAPITrial>> getExperimentById(
 
     @Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/export{?queryParams*}")
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
-    @Produces(value={"text/csv", "application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"})
+    @Produces(value={"text/csv", "application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "application/octet-stream"})
     public HttpResponse<StreamedFile> datasetExport(
             @PathVariable("programId") UUID programId, @PathVariable("experimentId") UUID experimentId,
             @QueryValue @Valid ExperimentExportQuery queryParams) {
         String downloadErrorMessage = "An error occurred while generating the download file. Contact the development team at bidevteam@cornell.edu.";
         try {
             Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program does not exist"));
-            DownloadFile datasetFile = experimentService.exportObservations(program, experimentId, queryParams);
+
+            // if a list of environmentIds are sent, return multiple files (zipped),
+            // else if a single environmentId is sent, return single file (CSV/Excel),
+            // else (if no environmentIds are sent), return a single file (CSV/Excel) including all Environments.
+            DownloadFile downloadFile = experimentService.exportObservations(program, experimentId, queryParams);
+
             HttpResponse<StreamedFile> response = HttpResponse
-                    .ok(datasetFile.getStreamedFile())
-                    .header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + datasetFile.getFileName());
+                    .ok(downloadFile.getStreamedFile())
+                    .header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + downloadFile.getFileName());
             return response;
         } catch (Exception e) {
             log.info(e.getMessage(), e);

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 +1,83 @@
+/*
+ * 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.MediaType;
+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.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.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>>>> getStudies(
+            @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/model/request/query/ExperimentExportQuery.java

@@ -2,15 +2,9 @@
 
 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.breedinginsight.brapps.importer.model.exports.FileType;
-import org.jooq.tools.StringUtils;
 
 import javax.validation.constraints.NotNull;
-import java.util.ArrayList;
-import java.util.List;
 
 @Getter
 @Introspected

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

@@ -5,7 +5,6 @@
 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.breedinginsight.brapps.importer.services.ExternalReferenceSource;
 import org.jooq.tools.StringUtils;
 
 import java.util.ArrayList;
@@ -39,7 +38,7 @@ public SearchRequest constructSearchRequest() {
         if (!StringUtils.isBlank(getSize())) {
             filters.add(constructFilterRequest("size", getSize()));
         }
-        if (getExternalReferenceSource() != null) {
+        if (!StringUtils.isBlank(getExternalReferenceSource())) {
             filters.add(constructFilterRequest("externalReferenceSource", getExternalReferenceSource()));
         }
         if (!StringUtils.isBlank(getExternalReferenceId())) {

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

@@ -0,0 +1,61 @@
+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;
+    private String externalReferenceSource;
+    private String externalReferenceId;
+
+    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()));
+        }
+        if (!StringUtils.isBlank(getExternalReferenceSource())) {
+            filters.add(constructFilterRequest("externalReferenceSource", getExternalReferenceSource()));
+        }
+        if (!StringUtils.isBlank(getExternalReferenceId())) {
+            filters.add(constructFilterRequest("externalReferenceId", getExternalReferenceId()));
+        }
+        return new SearchRequest(filters);
+    }
+}

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

@@ -0,0 +1,50 @@
+/*
+ * 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.brapps.importer.daos.BrAPIStudyDAO;
+
+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);
+        }
+    }
+
+}