[BI-1363] Share Ontology

src/main/java/org/breedinginsight/api/model/v1/request/SharedOntologyProgramRequest.java

@@ -0,0 +1,20 @@
+package org.breedinginsight.api.model.v1.request;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+import java.util.UUID;
+
+@Getter
+@Setter
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+@Introspected
+public class SharedOntologyProgramRequest {
+    @NotBlank
+    private UUID programId;
+    private String programName;
+}

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

@@ -0,0 +1,138 @@
+package org.breedinginsight.api.v1.controller;
+
+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.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;
+import org.breedinginsight.api.model.v1.response.Response;
+import org.breedinginsight.api.model.v1.response.metadata.Metadata;
+import org.breedinginsight.api.model.v1.response.metadata.Pagination;
+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.services.OntologyService;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.services.exceptions.UnprocessableEntityException;
+import org.breedinginsight.services.exceptions.ValidatorException;
+
+import javax.inject.Inject;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+@Slf4j
+@Controller("/${micronaut.bi.api.version}")
+public class OntologyController {
+
+    private SecurityService securityService;
+    private OntologyService ontologyService;
+
+    @Inject
+    public OntologyController(SecurityService securityService, OntologyService ontologyService) {
+        this.securityService = securityService;
+        this.ontologyService = ontologyService;
+    }
+
+    /**
+     * Returns all available programs available to share programs ontology with. Includes programs
+     * currently being shared with and their editable (unshareable) status.
+     *
+     * @param programId
+     * @param shared
+     * @return
+     * {
+     *     data: [
+     *      {
+     *          programName: string, -- Program name
+     *          programId: UUID, -- Program ID
+     *          shared: boolean,
+     *          accepted: boolean || null, -- null if shared = false
+     *          editable: boolean || null   -- null if shared = false
+     *      }
+     *     ]
+     * }
+     */
+    @Get("/programs/{programId}/ontology/shared/programs{?shared}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @AddMetadata
+    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    public HttpResponse<Response<DataResponse<SharedProgram>>> 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);
+    }
+
+    /**
+     * Accepts a list of programs to shared the ontology with.
+     * @param programId
+     * @return List of programs successfully shared to with acceptable status
+     * {
+     *     data: [
+     *      {
+     *          programName: string, -- Program name
+     *          programId: UUID, -- Required. Program ID
+     *      }
+     *     ]
+     * }
+     */
+    @Post("/programs/{programId}/ontology/shared/programs")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    public HttpResponse<Response<DataResponse<SharedProgram>>> 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<>();
+            metadataStatus.add(new Status(StatusCode.INFO, "Successful Creation"));
+            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);
+        } catch (ValidatorException e) {
+            log.error("Validation errors", e);
+            HttpResponse response = HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY).body(e.getErrors());
+            return response;
+        } catch (UnprocessableEntityException e) {
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        }
+    }
+
+    /**
+     * Revokes access to shared ontology from a program. If program is not currently shared with
+     * will return 404.
+     *
+     * @param programId
+     * @param sharedProgramId
+     * @return
+     */
+    @Delete("/programs/{programId}/ontology/shared/programs/{sharedProgramId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    public HttpResponse<Response<DataResponse<Trait>>> revokeOntology(
+            @PathVariable UUID programId, @PathVariable UUID sharedProgramId) {
+        try {
+            ontologyService.revokeOntology(programId, sharedProgramId);
+            return HttpResponse.ok();
+        } catch (UnprocessableEntityException e) {
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        } catch (DoesNotExistException e) {
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
+        }
+    }
+}

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

@@ -36,9 +36,7 @@
 import org.breedinginsight.dao.db.tables.BiUserTable;
 import org.breedinginsight.dao.db.tables.daos.ProgramDao;
 import org.breedinginsight.dao.db.tables.pojos.ProgramEntity;
-import org.breedinginsight.model.Program;
-import org.breedinginsight.model.ProgramBrAPIEndpoints;
-import org.breedinginsight.model.Species;
+import org.breedinginsight.model.*;
 import org.breedinginsight.model.User;
 import org.breedinginsight.services.brapi.BrAPIClientProvider;
 import org.breedinginsight.services.brapi.BrAPIClientType;
@@ -76,7 +74,7 @@ public class ProgramDAO extends ProgramDao {
     private String referenceSource;
     private Duration requestTimeout;
 
-    private final static String SYSTEM_DEFAULT = "System Default";
+    private final static String SYSTEM_DEFAULT = BrAPIConstants.SYSTEM_DEFAULT.getValue();
 
     @Inject
     public ProgramDAO(Configuration config, DSLContext dsl, BrAPIProvider brAPIProvider, BrAPIClientProvider brAPIClientProvider,
@@ -364,6 +362,5 @@ private Duration getRequestTimeout() {
 
         return Duration.of(5, ChronoUnit.MINUTES);
     }
-
 }
 

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

@@ -18,18 +18,55 @@
 package org.breedinginsight.daos;
 
 import org.breedinginsight.dao.db.tables.daos.ProgramOntologyDao;
+import org.breedinginsight.dao.db.tables.daos.ProgramSharedOntologyDao;
+import org.breedinginsight.dao.db.tables.pojos.ProgramSharedOntologyEntity;
 import org.jooq.Configuration;
 import org.jooq.DSLContext;
 
 import javax.inject.Inject;
+import javax.inject.Singleton;
+import java.util.List;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.stream.Collectors;
 
+@Singleton
 public class ProgramOntologyDAO extends ProgramOntologyDao {
 
     private DSLContext dsl;
+    private ProgramSharedOntologyDao programSharedOntologyDao;
 
     @Inject
-    public ProgramOntologyDAO(Configuration config, DSLContext dsl) {
+    public ProgramOntologyDAO(Configuration config, DSLContext dsl, ProgramSharedOntologyDao programSharedOntologyDao) {
         super(config);
         this.dsl = dsl;
+        this.programSharedOntologyDao = programSharedOntologyDao;
+    }
+
+    public void createSharedOntologies(List<ProgramSharedOntologyEntity> shareRecords) {
+        programSharedOntologyDao.insert(shareRecords);
+    }
+
+    public List<ProgramSharedOntologyEntity> getSharedOntologies(UUID programId) {
+        return programSharedOntologyDao.fetchByProgramId(programId);
+    }
+
+    public Optional<ProgramSharedOntologyEntity> getSharedOntologyById(UUID programId, UUID sharedProgramId) {
+        List<ProgramSharedOntologyEntity> sharedOntologies = getSharedOntologies(programId).stream()
+                .filter(programSharedOntologyEntity -> programSharedOntologyEntity.getSharedProgramId().equals(sharedProgramId))
+                .collect(Collectors.toList());
+        return sharedOntologies.size() > 0 ? Optional.of(sharedOntologies.get(0)) : Optional.empty();
+    }
+
+    public void revokeSharedOntology(ProgramSharedOntologyEntity sharedOntology) {
+        programSharedOntologyDao.delete(sharedOntology);
+    }
+
+    public boolean programSubscribedSharedOntology(UUID programId) {
+        List<ProgramSharedOntologyEntity> shareRecords = programSharedOntologyDao.fetchBySharedProgramId(programId);
+        return !shareRecords.stream()
+                .filter(shareRecord -> shareRecord.getActive())
+                .collect(Collectors.toList())
+                .isEmpty();
     }
 }

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

@@ -0,0 +1,18 @@
+package org.breedinginsight.model;
+
+import com.fasterxml.jackson.annotation.JsonValue;
+
+public enum BrAPIConstants {
+    SYSTEM_DEFAULT("System Default");
+
+    private String value;
+
+    BrAPIConstants(String value) {
+        this.value = value;
+    }
+
+    @JsonValue
+    public String getValue() {
+        return value;
+    }
+}

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

@@ -24,6 +24,7 @@
 import lombok.experimental.SuperBuilder;
 import org.brapi.v2.model.core.BrAPIProgram;
 import org.brapi.v2.model.pheno.BrAPIObservationVariable;
+import org.breedinginsight.dao.db.tables.ProgramTable;
 import org.breedinginsight.dao.db.tables.pojos.ProgramEntity;
 import org.breedinginsight.dao.db.tables.pojos.SpeciesEntity;
 import org.jooq.Record;
@@ -65,22 +66,26 @@ public Program(ProgramEntity programEntity){
     }
 
     public static Program parseSQLRecord(Record record){
+        return parseSQLRecord(record, PROGRAM);
+    }
+
+    public static Program parseSQLRecord(Record record, ProgramTable programTable) {
 
         // Generate our program record
         Program program = Program.builder()
-                .id(record.getValue(PROGRAM.ID))
-                .name(record.getValue(PROGRAM.NAME))
-                .abbreviation(record.getValue(PROGRAM.ABBREVIATION))
-                .objective(record.getValue(PROGRAM.OBJECTIVE))
-                .documentationUrl(record.getValue(PROGRAM.DOCUMENTATION_URL))
-                .brapiUrl(record.getValue(PROGRAM.BRAPI_URL))
-                .key(record.getValue(PROGRAM.KEY))
-                .createdAt(record.getValue(PROGRAM.CREATED_AT))
-                .updatedAt(record.getValue(PROGRAM.UPDATED_AT))
-                .createdBy(record.getValue(PROGRAM.CREATED_BY))
-                .updatedBy(record.getValue(PROGRAM.UPDATED_BY))
-                .active(record.getValue(PROGRAM.ACTIVE))
-                .germplasmSequence(record.getValue(PROGRAM.GERMPLASM_SEQUENCE))
+                .id(record.getValue(programTable.ID))
+                .name(record.getValue(programTable.NAME))
+                .abbreviation(record.getValue(programTable.ABBREVIATION))
+                .objective(record.getValue(programTable.OBJECTIVE))
+                .documentationUrl(record.getValue(programTable.DOCUMENTATION_URL))
+                .brapiUrl(record.getValue(programTable.BRAPI_URL))
+                .key(record.getValue(programTable.KEY))
+                .createdAt(record.getValue(programTable.CREATED_AT))
+                .updatedAt(record.getValue(programTable.UPDATED_AT))
+                .createdBy(record.getValue(programTable.CREATED_BY))
+                .updatedBy(record.getValue(programTable.UPDATED_BY))
+                .active(record.getValue(programTable.ACTIVE))
+                .germplasmSequence(record.getValue(programTable.GERMPLASM_SEQUENCE))
                 .build();
 
         return program;

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

@@ -0,0 +1,18 @@
+package org.breedinginsight.model;
+
+import lombok.*;
+
+import java.util.UUID;
+
+@Getter
+@Setter
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class SharedProgram {
+    private UUID programId;
+    private String programName;
+    private Boolean shared;
+    private Boolean accepted;
+    private Boolean editable;
+}