BI-1921 - Support Field Book Study Import from DeltaBreed

src/main/java/org/breedinginsight/brapi/v2/ExperimentController.java → src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java

@@ -1,4 +1,4 @@
-package org.breedinginsight.brapi.v2;
+package org.breedinginsight.api.v1.controller;
 
 import io.micronaut.http.HttpHeaders;
 import io.micronaut.http.HttpResponse;
@@ -9,28 +9,22 @@
 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.BrAPITrial;
 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.ExperimentExportQuery;
-import org.breedinginsight.brapi.v2.model.request.query.ExperimentQuery;
 import org.breedinginsight.brapi.v2.services.BrAPITrialService;
 import org.breedinginsight.model.Dataset;
 import org.breedinginsight.model.DownloadFile;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
-import org.breedinginsight.utilities.response.ResponseUtils;
 import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;
+
 import javax.inject.Inject;
 import javax.validation.Valid;
-import java.util.*;
+import java.util.Optional;
+import java.util.UUID;
 
 @Slf4j
 @Controller
@@ -47,48 +41,6 @@ public ExperimentController(BrAPITrialService experimentService, ExperimentQuery
         this.programService = programService;
     }
 
-    @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/trials{?queryParams*}")
-    @Produces(MediaType.APPLICATION_JSON)
-    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
-    public HttpResponse<Response<DataResponse<List<BrAPITrial>>>> getExperiments(
-            @PathVariable("programId") UUID programId,
-            @QueryValue @QueryValid(using = ExperimentQueryMapper.class) @Valid ExperimentQuery queryParams) {
-        try {
-            log.debug("fetching trials for program: " + programId);
-
-            List<BrAPITrial> experiments = experimentService.getExperiments(programId);
-            SearchRequest searchRequest = queryParams.constructSearchRequest();
-            return ResponseUtils.getBrapiQueryResponse(experiments, experimentQueryMapper, queryParams, searchRequest);
-        } catch (ApiException e) {
-            log.info(e.getMessage(), e);
-            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving experiments");
-        } catch (DoesNotExistException e) {
-            log.info(e.getMessage(), e);
-            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
-        }
-    }
-
-    @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/trials/{trialId}")
-    @Produces(MediaType.APPLICATION_JSON)
-    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
-    public HttpResponse<Response<BrAPITrial>> getExperimentById(
-            @PathVariable("programId") UUID programId,
-            @PathVariable("trialId") UUID trialId,
-            @QueryValue(defaultValue = "false") Boolean stats){
-        try {
-            String logMsg = "fetching trial id:" +  trialId +" for program: " + programId;
-            if(stats){
-                logMsg += " with stats";
-            }
-            log.debug(logMsg);
-            Response<BrAPITrial> response = new Response<>(experimentService.getTrialDataByUUID(programId, trialId, stats));
-            return HttpResponse.ok(response);
-        } catch (DoesNotExistException e) {
-            log.info(e.getMessage(), e);
-            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
-        }
-    }
-
     @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", "application/octet-stream"})

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

@@ -52,7 +52,7 @@ public TokenController(SecurityService securityService, TokenService tokenServic
 
     @Get("/api-token{?returnUrl}")
     @Secured(SecurityRule.IS_AUTHENTICATED)
-    public HttpResponse apiToken(@QueryValue @Nullable String returnUrl) {
+    public HttpResponse<?> apiToken(@QueryValue @Nullable String returnUrl) {
 
         AuthenticatedUser actingUser = securityService.getUser();
         Optional<ApiToken> token = tokenService.generateApiToken(actingUser);
@@ -61,12 +61,12 @@ public HttpResponse apiToken(@QueryValue @Nullable String returnUrl) {
             ApiToken apiToken = token.get();
 
             if(returnUrl != null) {
-                if(StringUtils.trim(returnUrl).isEmpty()) {
+                if(StringUtils.trim(returnUrl).isEmpty() || "undefined".equalsIgnoreCase(returnUrl)) {
                     return HttpResponse.badRequest("returnUrl cannot be blank");
                 }
                 URI location = UriBuilder.of(returnUrl)
                                          .queryParam("status", 200)
-                                         .queryParam("token", apiToken.getAccessToken())
+                                         .queryParam("access_token", apiToken.getAccessToken())
                                          .build();
 
                 return HttpResponse.seeOther(location)

src/main/java/org/breedinginsight/api/v1/controller/auth/OIDCDiscoveryController.java

@@ -0,0 +1,69 @@
+/*
+ * 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.api.v1.controller.auth;
+
+import io.micronaut.context.annotation.Property;
+import io.micronaut.http.HttpResponse;
+import io.micronaut.http.MediaType;
+import io.micronaut.http.annotation.Controller;
+import io.micronaut.http.annotation.Get;
+import io.micronaut.http.annotation.Produces;
+import io.micronaut.security.annotation.Secured;
+import io.micronaut.security.rules.SecurityRule;
+import org.breedinginsight.dao.db.tables.pojos.ProgramEntity;
+import org.breedinginsight.daos.ProgramDAO;
+
+import javax.inject.Inject;
+import java.util.UUID;
+
+@Controller
+@Secured(SecurityRule.IS_ANONYMOUS)
+public class OIDCDiscoveryController {
+
+    private static final String OIDC_CONFIG = "    {\n" +
+                                              "      \"issuer\": \"%s\",\n" +
+                                              "      \"authorization_endpoint\": \"%s/programs/%s/brapi/authorize\",\n" +
+                                              "      \"jwks_uri\": \"\",\n" +
+                                              "      \"token_endpoint\": \"\",\n" +
+                                              "      \"grant_types_supported\": [\"implicit\"],\n" +
+                                              "      \"response_types_supported\": [\"token\"],\n" +
+                                              "      \"subject_types_supported\": [\"public\"],\n" +
+                                              "      \"id_token_signing_alg_values_supported\": []\n" +
+                                              "    }\n";
+
+    private final String webUrl;
+    private final ProgramDAO programDAO;
+
+    @Inject
+    public OIDCDiscoveryController(@Property(name="web.base-url") String webUrl, ProgramDAO programDAO) {
+        this.webUrl = webUrl;
+        this.programDAO = programDAO;
+    }
+
+
+    @Get("/${micronaut.bi.api.version}/programs/{programId}/.well-known/openid-configuration")
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse getOpenIdConfig(UUID programId) {
+        ProgramEntity programEntity = programDAO.fetchOneById(programId);
+        if(programEntity != null) {
+            return HttpResponse.ok(String.format(OIDC_CONFIG, webUrl, webUrl, programId));
+        }
+
+        return HttpResponse.notFound("unknown program");
+    }
+}

src/main/java/org/breedinginsight/brapi/v2/GermplasmController.java → src/main/java/org/breedinginsight/brapi/v2/BrAPIGermplasmController.java

@@ -51,7 +51,7 @@
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
 @Secured(SecurityRule.IS_AUTHENTICATED)
-public class GermplasmController {
+public class BrAPIGermplasmController {
 
     private final BrAPIGermplasmService germplasmService;
     private final GermplasmQueryMapper germplasmQueryMapper;
@@ -64,7 +64,7 @@ public class GermplasmController {
 
 
     @Inject
-    public GermplasmController(BrAPIGermplasmService germplasmService, GermplasmQueryMapper germplasmQueryMapper, ProgramDAO programDAO, BrAPIGermplasmDAO germplasmDAO, GenotypeService genoService, BrAPIEndpointProvider brAPIEndpointProvider) {
+    public BrAPIGermplasmController(BrAPIGermplasmService germplasmService, GermplasmQueryMapper germplasmQueryMapper, ProgramDAO programDAO, BrAPIGermplasmDAO germplasmDAO, GenotypeService genoService, BrAPIEndpointProvider brAPIEndpointProvider) {
         this.germplasmService = germplasmService;
         this.germplasmQueryMapper = germplasmQueryMapper;
         this.programDAO = programDAO;

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

@@ -0,0 +1,90 @@
+/*
+ * 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.annotation.*;
+import io.micronaut.security.annotation.Secured;
+import io.micronaut.security.rules.SecurityRule;
+import lombok.extern.slf4j.Slf4j;
+import org.brapi.v2.model.pheno.BrAPIImage;
+import org.breedinginsight.api.auth.ProgramSecured;
+import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
+import org.breedinginsight.brapi.v1.controller.BrapiVersion;
+
+import java.util.List;
+import java.util.UUID;
+
+@Slf4j
+@Controller("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2)
+@Secured(SecurityRule.IS_AUTHENTICATED)
+public class BrAPIImagesController {
+    /*
+    TODO
+    - POST images
+    - PUT imagesImageDbIdImagecontent
+    - PUT imagesImageDbIdPut
+     */
+    @Get("/images")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse imagesGet(@PathVariable("programId") UUID programId,
+                                  @QueryValue("imageDbId") String imageDbId,
+                                  @QueryValue("imageName") String imageName,
+                                  @QueryValue("observationUnitDbId") String observationUnitDbId,
+                                  @QueryValue("observationDbId") String observationDbId,
+                                  @QueryValue("descriptiveOntologyTerm") String descriptiveOntologyTerm,
+                                  @QueryValue("commonCropName") String commonCropName,
+                                  @QueryValue("programDbId") String programDbId,
+                                  @QueryValue("externalReferenceID") String externalReferenceID,
+                                  @QueryValue("externalReferenceId") String externalReferenceId,
+                                  @QueryValue("externalReferenceSource") String externalReferenceSource,
+                                  @QueryValue("page") Integer page,
+                                  @QueryValue("pageSize") Integer pageSize) {
+        return HttpResponse.notFound();
+    }
+
+    @Get("/images/{imageDbId}")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse imagesImageDbIdGet(@PathVariable("programId") UUID programId,
+                                           @PathVariable("imageDbId") String imageDbId) {
+        return HttpResponse.notFound();
+    }
+
+    @Put("/images/{imageDbId}/imagecontent")
+    @Consumes({"image/_*"})
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse imagesImageDbIdImagecontentPut(@PathVariable("programId") UUID programId,
+                                                       @PathVariable("imageDbId") String imageDbId,
+                                                       @Body Object body) {
+        return HttpResponse.notFound();
+    }
+
+    @Put("/images/{imageDbId}")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse imagesImageDbIdPut(@PathVariable("programId") UUID programId,
+                                           @PathVariable("imageDbId") String imageDbId,
+                                           @Body BrAPIImage body) {
+        return HttpResponse.notFound();
+    }
+
+    @Post("/images")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse imagesPost(@PathVariable("programId") UUID programId, @Body List<BrAPIImage> body) {
+        return HttpResponse.notFound();
+    }
+}

src/main/java/org/breedinginsight/brapi/v2/ListController.java → src/main/java/org/breedinginsight/brapi/v2/BrAPIListController.java

@@ -50,15 +50,15 @@
 @Slf4j
 @Controller
 @Secured(SecurityRule.IS_AUTHENTICATED)
-public class ListController {
+public class BrAPIListController {
 
     private final ProgramService programService;
     private final BrAPIListService listService;
     private final ListQueryMapper listQueryMapper;
 
     @Inject
-    public ListController(ProgramService programService, BrAPIListService listService,
-                          ListQueryMapper listQueryMapper) {
+    public BrAPIListController(ProgramService programService, BrAPIListService listService,
+                               ListQueryMapper listQueryMapper) {
         this.programService = programService;
         this.listService = listService;
         this.listQueryMapper = listQueryMapper;