[BI-1366] Subscribe Ontology

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

@@ -4,12 +4,9 @@
 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.breedinginsight.api.auth.ProgramSecured;
 import org.breedinginsight.api.auth.ProgramSecuredRole;
-import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
 import org.breedinginsight.api.auth.SecurityService;
 import org.breedinginsight.api.model.v1.request.SharedOntologyProgramRequest;
 import org.breedinginsight.api.model.v1.response.DataResponse;
@@ -19,8 +16,8 @@
 import org.breedinginsight.api.model.v1.response.metadata.Status;
 import org.breedinginsight.api.model.v1.response.metadata.StatusCode;
 import org.breedinginsight.api.v1.controller.metadata.AddMetadata;
-import org.breedinginsight.model.SharedProgram;
-import org.breedinginsight.model.Trait;
+import org.breedinginsight.model.SharedOntology;
+import org.breedinginsight.model.SubscribedOntology;
 import org.breedinginsight.services.OntologyService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.services.exceptions.UnprocessableEntityException;
@@ -67,15 +64,20 @@ public OntologyController(SecurityService securityService, OntologyService ontol
     @Produces(MediaType.APPLICATION_JSON)
     @AddMetadata
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
-    public HttpResponse<Response<DataResponse<SharedProgram>>> getAvailablePrograms(
+    public HttpResponse<Response<DataResponse<SharedOntology>>> getAvailablePrograms(
             @PathVariable UUID programId, @QueryValue(defaultValue = "false") Boolean shared) {
-        List<SharedProgram> sharedPrograms = ontologyService.getSharedOntology(programId, shared);
-        List<org.breedinginsight.api.model.v1.response.metadata.Status> metadataStatus = new ArrayList<>();
-        metadataStatus.add(new Status(StatusCode.INFO, "Successful Query"));
-        Pagination pagination = new Pagination(sharedPrograms.size(), 1, 1, 0);
-        Metadata metadata = new Metadata(pagination, metadataStatus);
-        Response<DataResponse<SharedProgram>> response = new Response(metadata, new DataResponse<>(sharedPrograms));
-        return HttpResponse.ok(response);
+        try {
+            List<SharedOntology> sharedOntologies = ontologyService.getSharedOntology(programId, shared);
+            List<Status> metadataStatus = new ArrayList<>();
+            metadataStatus.add(new Status(StatusCode.INFO, "Successful Query"));
+            Pagination pagination = new Pagination(sharedOntologies.size(), 1, 1, 0);
+            Metadata metadata = new Metadata(pagination, metadataStatus);
+            Response<DataResponse<SharedOntology>> response = new Response(metadata, new DataResponse<>(sharedOntologies));
+            return HttpResponse.ok(response);
+        } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
+        }
     }
 
     /**
@@ -94,22 +96,26 @@ public HttpResponse<Response<DataResponse<SharedProgram>>> getAvailablePrograms(
     @Post("/programs/{programId}/ontology/shared/programs")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
-    public HttpResponse<Response<DataResponse<SharedProgram>>> shareOntology(
+    public HttpResponse<Response<DataResponse<SharedOntology>>> shareOntology(
             @PathVariable UUID programId, @Body List<SharedOntologyProgramRequest> request) {
         try {
-            List<SharedProgram> sharedPrograms = ontologyService.shareOntology(programId, securityService.getUser(), request);
-            List<org.breedinginsight.api.model.v1.response.metadata.Status> metadataStatus = new ArrayList<>();
+            List<SharedOntology> sharedOntologies = ontologyService.shareOntology(programId, securityService.getUser(), request);
+            List<Status> metadataStatus = new ArrayList<>();
             metadataStatus.add(new Status(StatusCode.INFO, "Successful Creation"));
-            Pagination pagination = new Pagination(sharedPrograms.size(), 1, 1, 0);
+            Pagination pagination = new Pagination(sharedOntologies.size(), 1, 1, 0);
             Metadata metadata = new Metadata(pagination, metadataStatus);
-            Response<DataResponse<SharedProgram>> response = new Response(metadata, new DataResponse<>(sharedPrograms));
+            Response<DataResponse<SharedOntology>> response = new Response(metadata, new DataResponse<>(sharedOntologies));
             return HttpResponse.ok(response);
         } catch (ValidatorException e) {
             log.error("Validation errors", e);
             HttpResponse response = HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY).body(e.getErrors());
             return response;
         } catch (UnprocessableEntityException e) {
+            log.error(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
         }
     }
 
@@ -124,14 +130,99 @@ public HttpResponse<Response<DataResponse<SharedProgram>>> shareOntology(
     @Delete("/programs/{programId}/ontology/shared/programs/{sharedProgramId}")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
-    public HttpResponse<Response<DataResponse<Trait>>> revokeOntology(
+    public HttpResponse revokeOntology(
             @PathVariable UUID programId, @PathVariable UUID sharedProgramId) {
         try {
             ontologyService.revokeOntology(programId, sharedProgramId);
             return HttpResponse.ok();
         } catch (UnprocessableEntityException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
+        }
+    }
+
+    /**
+     * Scoped under the program that is subscribing. Accept a shared ontology.
+     *
+     * @param programId -- Program that is subscribing to an ontology
+     * @param sharingProgramId -- Program that has shared its ontology.
+     * @return
+     */
+    @Put("/programs/{programId}/ontology/subscribe/{sharingProgramId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @AddMetadata
+    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    public HttpResponse<Response<SubscribedOntology>> subscribeOntology(
+            @PathVariable UUID programId, @PathVariable UUID sharingProgramId) {
+        try {
+            SubscribedOntology shareRequest = ontologyService.subscribeOntology(programId, sharingProgramId);
+            Response<SubscribedOntology> response = new Response(shareRequest);
+            return HttpResponse.ok(response);
+        } catch (UnprocessableEntityException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
+        }
+    }
+
+    /**
+     * Scoped under the program that is subscribing. Unsubscribe from a shared ontology.
+     *
+     * @param programId -- Program that is unsubscribing from an ontology
+     * @param sharingProgramId -- Program that has shared its ontology.
+     * @return
+     */
+    @Delete("/programs/{programId}/ontology/subscribe/{sharingProgramId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    public HttpResponse unsubscribeOntology(
+            @PathVariable UUID programId, @PathVariable UUID sharingProgramId) {
+        try {
+            ontologyService.unsubscribeOntology(programId, sharingProgramId);
+            return HttpResponse.ok();
+        } catch (UnprocessableEntityException e) {
+            log.error(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
         } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
+        }
+    }
+
+    /**
+     * Retrieves subscription options for programs that have shared their ontology with the requesting program.
+     * Will indicate whether the program has subscribed to a given ontology or not.
+     *
+     * @param programId -- Program request information
+     * @return
+     * {
+     *     programId,   -- Program that owns the ontology the request program is subscribed 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.
+     * }
+     */
+    @Get("/programs/{programId}/ontology/subscribe")
+    @Produces(MediaType.APPLICATION_JSON)
+    @AddMetadata
+    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    public HttpResponse<Response<DataResponse<SubscribedOntology>>> getSubscribedOntology(
+            @PathVariable UUID programId) {
+        try {
+            List<SubscribedOntology> shareRequests = ontologyService.getSubscribeOntologyOptions(programId);
+            List<Status> metadataStatus = new ArrayList<>();
+            metadataStatus.add(new Status(StatusCode.INFO, "Successful Creation"));
+            Pagination pagination = new Pagination(shareRequests.size(), 1, 1, 0);
+            Metadata metadata = new Metadata(pagination, metadataStatus);
+            Response<DataResponse<SubscribedOntology>> response = new Response(metadata, new DataResponse<>(shareRequests));
+            return HttpResponse.ok(response);
+        }  catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
         }
     }

src/main/java/org/breedinginsight/daos/ObservationDAO.java

@@ -33,6 +33,7 @@
 import javax.inject.Inject;
 import java.util.List;
 import java.util.Optional;
+import java.util.UUID;
 
 import static org.brapi.v2.model.BrAPIWSMIMEDataTypes.APPLICATION_JSON;
 
@@ -77,6 +78,25 @@ public List<BrAPIObservation> getObservationsByVariableDbIds(List<String> observ
 
     }
 
+    public List<BrAPIObservation> getObservationsByVariableAndBrAPIProgram(String brapiProgramId, List<String> observationVariableDbIds) {
+
+        try {
+            BrAPIObservationSearchRequest request = new BrAPIObservationSearchRequest()
+                    .observationVariableDbIds(observationVariableDbIds)
+                    .programDbIds(List.of(brapiProgramId));
+
+            ObservationsApi api = brAPIProvider.getObservationsAPI(BrAPIClientType.PHENO);
+            return BrAPIDAOUtil.search(
+                    api::searchObservationsPost,
+                    this::searchObservationsSearchResultsDbIdGet,
+                    request
+            );
+        } catch (ApiException e) {
+            throw new InternalServerException("Observations brapi search error", e);
+        }
+
+    }
+
     private ApiResponse<Pair<Optional<BrAPIObservationListResponse>, Optional<BrAPIAcceptedSearchResponse>>>
     searchObservationsSearchResultsDbIdGet(String searchResultsDbId, Integer page, Integer pageSize) throws ApiException {
         ObservationsApi api = brAPIProvider.getObservationsAPI(BrAPIClientType.PHENO);

src/main/java/org/breedinginsight/daos/ProgramOntologyDAO.java

@@ -62,11 +62,25 @@ public void revokeSharedOntology(ProgramSharedOntologyEntity sharedOntology) {
         programSharedOntologyDao.delete(sharedOntology);
     }
 
-    public boolean programSubscribedSharedOntology(UUID programId) {
-        List<ProgramSharedOntologyEntity> shareRecords = programSharedOntologyDao.fetchBySharedProgramId(programId);
-        return !shareRecords.stream()
+    public Optional<ProgramSharedOntologyEntity> getSubscribedSharedOntology(UUID programId) {
+        List<ProgramSharedOntologyEntity> shareRecords = programSharedOntologyDao.fetchBySharedProgramId(programId).stream()
                 .filter(shareRecord -> shareRecord.getActive())
-                .collect(Collectors.toList())
-                .isEmpty();
+                .collect(Collectors.toList());
+
+        return shareRecords.size() > 0 ? Optional.of(shareRecords.get(0)) : Optional.empty();
+    }
+
+    public void acceptSharedOntology(ProgramSharedOntologyEntity sharedOntology) {
+        sharedOntology.setActive(true);
+        programSharedOntologyDao.update(sharedOntology);
+    }
+
+    public void denySharedOntology(ProgramSharedOntologyEntity sharedOntology) {
+        sharedOntology.setActive(false);
+        programSharedOntologyDao.update(sharedOntology);
+    }
+
+    public List<ProgramSharedOntologyEntity> getSubscriptionOptions(UUID programId) {
+        return programSharedOntologyDao.fetchBySharedProgramId(programId);
     }
 }

src/main/java/org/breedinginsight/daos/TraitDAO.java

@@ -218,7 +218,28 @@ public List<BrAPIObservation> getObservationsForTraits(List<UUID> traitIds) {
         return observationDao.getObservationsByVariableDbIds(brapiVariableIds);
     }
 
+    public List<BrAPIObservation> getObservationsForTraitsByBrAPIProgram(String brapiProgramId, List<UUID> traitIds) {
+
+        List<String> ids = traitIds.stream()
+                .map(trait -> trait.toString())
+                .collect(Collectors.toList());
+
+        List<BrAPIObservationVariable> variables = searchVariables(ids);
+
+        // TODO: make sure have all expected external references
+        if (variables.size() != ids.size()) {
+            throw new InternalServerException("Observation variables search results mismatch");
+        }
+
+        List<String> brapiVariableIds = variables.stream()
+                .map(variable -> variable.getObservationVariableDbId()).collect(Collectors.toList());
+
+        return observationDao.getObservationsByVariableAndBrAPIProgram(brapiProgramId, brapiVariableIds);
+    }
+
     public List<BrAPIObservationVariable> searchVariables(List<String> variableIds) {
+
+        if (variableIds == null || variableIds.size() == 0) return new ArrayList<>();
         try {
             BrAPIObservationVariableSearchRequest request = new BrAPIObservationVariableSearchRequest()
                     .externalReferenceIDs(variableIds);
@@ -573,5 +594,4 @@ private void saturateTrait(Trait trait, BrAPIObservationVariable brApiVariable)
         Scale scale = trait.getScale();
         scale.setBrAPIProperties(brApiVariable.getScale());
     }
-
 }

src/main/java/org/breedinginsight/model/SharedProgram.java → src/main/java/org/breedinginsight/model/SharedOntology.java

@@ -9,7 +9,7 @@
 @Builder
 @AllArgsConstructor
 @NoArgsConstructor
-public class SharedProgram {
+public class SharedOntology {
     private UUID programId;
     private String programName;
     private Boolean shared;

src/main/java/org/breedinginsight/model/SubscribedOntology.java

@@ -0,0 +1,17 @@
+package org.breedinginsight.model;
+
+import lombok.*;
+
+import java.util.UUID;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@AllArgsConstructor
+@Builder
+public class SubscribedOntology {
+    private UUID programId;
+    private String programName;
+    private Boolean subscribed;
+    private Boolean editable;
+}