[BI-1364] View a shared ontology that a program is subscribed to

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

@@ -201,7 +201,7 @@ public HttpResponse unsubscribeOntology(
      * @param programId -- Program request information
      * @return
      * {
-     *     programId,   -- Program that owns the ontology the request program is subscribed to.
+     *     programId,   -- Program that owns the ontology the request program may subscribe to.
      *     programName,
      *     subscribed,  -- boolean. Whether the requesting program is subscribed to this ontology or not.
      *     editable     -- boolean || null. Indicates whether this program can unsubscribe from this ontology or not. Null if not subscribed to this ontology.

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

@@ -38,7 +38,9 @@
 import org.breedinginsight.model.Editable;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.Trait;
+import org.breedinginsight.services.OntologyService;
 import org.breedinginsight.services.TraitService;
+import org.breedinginsight.services.exceptions.BadRequestException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.services.exceptions.ValidatorException;
 import org.breedinginsight.utilities.response.ResponseUtils;
@@ -50,6 +52,7 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
+import java.util.concurrent.atomic.AtomicReference;
 
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
@@ -58,13 +61,15 @@ public class TraitController {
     private TraitService traitService;
     private SecurityService securityService;
     private TraitQueryMapper traitQueryMapper;
+    private OntologyService ontologyService;
 
     @Inject
     public TraitController(TraitService traitService, SecurityService securityService,
-                           TraitQueryMapper traitQueryMapper){
+                           TraitQueryMapper traitQueryMapper, OntologyService ontologyService){
         this.traitService = traitService;
         this.securityService = securityService;
         this.traitQueryMapper = traitQueryMapper;
+        this.ontologyService = ontologyService;
     }
 
     @Get("/programs/{programId}/traits{?traitsQuery*}")
@@ -75,7 +80,7 @@ public HttpResponse<Response<DataResponse<Trait>>> getTraits(
             @QueryValue @QueryValid(using = TraitQueryMapper.class) @Valid TraitsQuery traitsQuery) {
 
         try {
-            List<Trait> traits = traitService.getByProgramId(programId, traitsQuery.getFull());
+            List<Trait> traits = ontologyService.getTraitsByProgramId(programId, traitsQuery.getFull());
             return ResponseUtils.getQueryResponse(traits, traitQueryMapper, traitsQuery);
         } catch (DoesNotExistException e) {
             return HttpResponse.notFound();
@@ -91,7 +96,7 @@ public HttpResponse<Response<DataResponse<Program>>> postTraitsSearch(
             @Body @SearchValid(using = TraitQueryMapper.class) SearchRequest searchRequest) {
 
         try {
-            List<Trait> traits = traitService.getByProgramId(programId, true);
+            List<Trait> traits = ontologyService.getTraitsByProgramId(programId, true);
             return ResponseUtils.getQueryResponse(traits, traitQueryMapper, searchRequest, queryParams);
         } catch (DoesNotExistException e) {
             return HttpResponse.notFound();
@@ -137,7 +142,7 @@ public HttpResponse<Response<Editable>> getTraitEditable(@PathVariable UUID prog
     public HttpResponse<Response<DataResponse<Trait>>> createTraits(@PathVariable UUID programId, @Body @Valid List<Trait> traits) {
         AuthenticatedUser actingUser = securityService.getUser();
         try {
-            List<Trait> createdTraits = traitService.createTraits(programId, traits, actingUser, true);
+            List<Trait> createdTraits = ontologyService.createTraits(programId, traits, actingUser, true);
             List<Status> metadataStatus = new ArrayList<>();
             // Users query successfully
             metadataStatus.add(new Status(StatusCode.INFO, "Successful Creation"));
@@ -146,6 +151,9 @@ public HttpResponse<Response<DataResponse<Trait>>> createTraits(@PathVariable UU
             Metadata metadata = new Metadata(pagination, metadataStatus);
             Response<DataResponse<Trait>> response = new Response<>(metadata, new DataResponse<>(createdTraits));
             return HttpResponse.ok(response);
+        } catch (BadRequestException e){
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.BAD_REQUEST, e.getMessage());
         } catch (DoesNotExistException e){
             log.info(e.getMessage());
             return HttpResponse.notFound();
@@ -162,7 +170,7 @@ public HttpResponse<Response<DataResponse<Trait>>> createTraits(@PathVariable UU
     public HttpResponse<Response<DataResponse<Trait>>> updateTraits(@PathVariable UUID programId, @Body @Valid List<Trait> traits) {
         AuthenticatedUser actingUser = securityService.getUser();
         try {
-            List<Trait> updatedTraits = traitService.updateTraits(programId, traits, actingUser);
+            List<Trait> updatedTraits = ontologyService.updateTraits(programId, traits, actingUser);
             List<Status> metadataStatus = new ArrayList<>();
             // Users query successfully
             metadataStatus.add(new Status(StatusCode.INFO, "Successful Creation"));
@@ -171,6 +179,9 @@ public HttpResponse<Response<DataResponse<Trait>>> updateTraits(@PathVariable UU
             Metadata metadata = new Metadata(pagination, metadataStatus);
             Response<DataResponse<Trait>> response = new Response<>(metadata, new DataResponse<>(updatedTraits));
             return HttpResponse.ok(response);
+        } catch (BadRequestException e) {
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.BAD_REQUEST, e.getMessage());
         } catch (DoesNotExistException e) {
             log.info(e.getMessage());
             return HttpResponse.notFound();

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

@@ -31,6 +31,7 @@
 import org.breedinginsight.api.v1.controller.metadata.AddMetadata;
 import org.breedinginsight.model.ProgramUpload;
 import org.breedinginsight.model.Trait;
+import org.breedinginsight.services.OntologyService;
 import org.breedinginsight.services.TraitUploadService;
 import org.breedinginsight.services.exceptions.*;
 import org.breedinginsight.utilities.response.ResponseUtils;
@@ -47,12 +48,14 @@ public class TraitUploadController {
     private TraitUploadService traitUploadService;
     private SecurityService securityService;
     private TraitQueryMapper traitQueryMapper;
+    private OntologyService ontologyService;
 
     public TraitUploadController(TraitUploadService traitUploadService, SecurityService securityService,
-                                 TraitQueryMapper traitQueryMapper) {
+                                 TraitQueryMapper traitQueryMapper, OntologyService ontologyService) {
         this.traitUploadService = traitUploadService;
         this.securityService = securityService;
         this.traitQueryMapper = traitQueryMapper;
+        this.ontologyService = ontologyService;
     }
 
     // only allowing one trait upload to exist (per user per program) so put is more appropriate than post
@@ -67,9 +70,12 @@ public HttpResponse<Response<ProgramUpload>> putTraitUpload(@PathVariable UUID p
 
         try {
             AuthenticatedUser actingUser = securityService.getUser();
-            ProgramUpload programUpload = traitUploadService.updateTraitUpload(programId, file, actingUser);
+            ProgramUpload programUpload = ontologyService.updateTraitUpload(programId, file, actingUser);
             Response<ProgramUpload> response = new Response(programUpload);
             return HttpResponse.ok(response);
+        } catch (BadRequestException e) {
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.BAD_REQUEST, e.getMessage());
         } catch (DoesNotExistException e) {
             log.info(e.getMessage());
             return HttpResponse.notFound();
@@ -146,11 +152,14 @@ public HttpResponse confirmTraitUpload(@PathVariable UUID programId,
                                            @PathVariable UUID traitUploadId) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
-            traitUploadService.confirmUpload(programId, traitUploadId, actingUser);
+            ontologyService.confirmUpload(programId, traitUploadId, actingUser);
             return HttpResponse.ok();
         } catch (DoesNotExistException e) {
             log.info(e.getMessage());
             return HttpResponse.notFound();
+        } catch (BadRequestException e) {
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.BAD_REQUEST, e.getMessage());
         } catch (ValidatorException e) {
             log.info(e.getErrors().toString());
             HttpResponse response = HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY).body(e.getErrors());

src/main/java/org/breedinginsight/services/OntologyService.java

@@ -1,6 +1,8 @@
 package org.breedinginsight.services;
 
 import io.micronaut.http.HttpStatus;
+import io.micronaut.http.exceptions.HttpStatusException;
+import io.micronaut.http.multipart.CompletedFileUpload;
 import io.micronaut.http.server.exceptions.InternalServerException;
 import org.brapi.v2.model.core.BrAPIProgram;
 import org.breedinginsight.api.auth.AuthenticatedUser;
@@ -11,13 +13,8 @@
 import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.daos.ProgramOntologyDAO;
 import org.breedinginsight.daos.TraitDAO;
-import org.breedinginsight.model.Program;
-import org.breedinginsight.model.SharedOntology;
-import org.breedinginsight.model.SubscribedOntology;
-import org.breedinginsight.model.Trait;
-import org.breedinginsight.services.exceptions.DoesNotExistException;
-import org.breedinginsight.services.exceptions.UnprocessableEntityException;
-import org.breedinginsight.services.exceptions.ValidatorException;
+import org.breedinginsight.model.*;
+import org.breedinginsight.services.exceptions.*;
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
@@ -32,13 +29,15 @@ public class OntologyService {
     private ProgramOntologyDAO programOntologyDAO;
     private TraitDAO traitDAO;
     private TraitService traitService;
+    private TraitUploadService traitUploadService;
 
     @Inject
-    public OntologyService(ProgramDAO programDAO, ProgramOntologyDAO programOntologyDAO, TraitDAO traitDAO, TraitService traitService) {
+    public OntologyService(ProgramDAO programDAO, ProgramOntologyDAO programOntologyDAO, TraitDAO traitDAO, TraitService traitService, TraitUploadService traitUploadService) {
         this.programDAO = programDAO;
         this.programOntologyDAO = programOntologyDAO;
         this.traitDAO = traitDAO;
         this.traitService = traitService;
+        this.traitUploadService = traitUploadService;
     }
 
     /**
@@ -302,6 +301,67 @@ public void unsubscribeOntology(UUID programId, UUID sharingProgramId) throws Do
         programOntologyDAO.denySharedOntology(sharedOntology);
     }
 
+    public List<Trait> getTraitsByProgramId(UUID programId, boolean getFullTrait) throws DoesNotExistException {
+        return traitService.getByProgramId(getSubscribedOntologyProgramId(programId), getFullTrait);
+    }
+
+    public List<Trait> updateTraits(UUID programId, List<Trait> traits, AuthenticatedUser actingUser)
+            throws DoesNotExistException, HttpStatusException, ValidatorException, BadRequestException {
+        UUID lookupId = getSubscribedOntologyProgramId(programId);
+        if(lookupId != programId) {
+            throw new BadRequestException("Subscribed ontology terms cannot be updated");
+        }
+
+        return traitService.updateTraits(lookupId, traits, actingUser);
+    }
+
+    public List<Trait> createTraits(UUID programId, List<Trait> traits, AuthenticatedUser actingUser, Boolean throwDuplicateErrors)
+            throws DoesNotExistException, ValidatorException, BadRequestException {
+        UUID lookupId = getSubscribedOntologyProgramId(programId);
+        if(lookupId != programId) {
+            throw new BadRequestException("Subscribed ontology terms cannot be created");
+        }
+
+        return traitService.createTraits(lookupId, traits, actingUser, throwDuplicateErrors);
+    }
+
+    public ProgramUpload updateTraitUpload(UUID programId, CompletedFileUpload file, AuthenticatedUser actingUser)
+            throws DoesNotExistException, UnsupportedTypeException, ValidatorException, AuthorizationException, HttpStatusException, BadRequestException {
+        UUID lookupId = getSubscribedOntologyProgramId(programId);
+        if(lookupId != programId) {
+            throw new BadRequestException("Subscribed ontology terms cannot be imported");
+        }
+
+        return traitUploadService.updateTraitUpload(lookupId, file, actingUser);
+    }
+
+    public void confirmUpload(UUID programId, UUID traitUploadId, AuthenticatedUser actingUser)
+            throws DoesNotExistException, ValidatorException, BadRequestException {
+        UUID lookupId = getSubscribedOntologyProgramId(programId);
+        if(lookupId != programId) {
+            throw new BadRequestException("Subscribed ontology terms cannot be imported");
+        }
+
+        traitUploadService.confirmUpload(lookupId, traitUploadId, actingUser);
+    }
+
+    public UUID getSubscribedOntologyProgramId(UUID programId) throws DoesNotExistException {
+        // get shared ontology programs
+        List<SubscribedOntology> subscriptionOptions = getSubscribeOntologyOptions(programId);
+
+        // check if we are subscribed to one of the programs
+        SubscribedOntology subscribedOntology = null;
+        for (SubscribedOntology sharingProgram : subscriptionOptions) {
+            if (sharingProgram.getSubscribed()) {
+                subscribedOntology = sharingProgram;
+            }
+        }
+
+        UUID lookupId = subscribedOntology == null ? programId : subscribedOntology.getProgramId();
+
+        return lookupId;
+    }
+
     public List<SubscribedOntology> getSubscribeOntologyOptions(UUID programId) throws DoesNotExistException {
 
         Program program = getProgram(programId);

src/main/java/org/breedinginsight/services/exceptions/BadRequestException.java

@@ -0,0 +1,25 @@
+/*
+ * 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.services.exceptions;
+
+public class BadRequestException extends Exception {
+
+    public BadRequestException(String message) {
+        super(message);
+    }
+}