Merging release v0.9

.env.template

@@ -54,4 +54,7 @@ AWS_REGION=<aws region>
 AWS_ACCESS_KEY_ID=<access key>
 AWS_SECRET_KEY=<secret>
 AWS_GENO_BUCKET=<s3 bucket for genotypic data uploads>
-AWS_S3_ENDPOINT=<s3 endpoint, default https://s3.us-east-1.amazonaws.com>
+AWS_S3_ENDPOINT=<s3 endpoint, default https://s3.us-east-1.amazonaws.com>
+
+BRAPI_VENDOR_SUBMISSION_ENABLED=false #can a submission be sent to a vendor via BrAPI
+BRAPI_VENDOR_CHECK_FREQUENCY=1d #how often to check for vendor updates for sample submissions

docker-compose.yml

@@ -85,6 +85,7 @@ services:
       backend:
         aliases:
           - dbserver
+    shm_size: 2g
   brapi-server:
     image: breedinginsight/brapi-java-server:develop
     container_name: brapi-server
@@ -100,7 +101,7 @@ services:
       - ${BRAPI_SERVER_PORT}:8080
     volumes:
       - ./src/main/resources/brapi/properties/application.properties:/home/brapi/properties/application.properties
-      - ./src/main/resources/brapi/sql/:/home/brapi/sql/
+      - ./src/main/resources/brapi/sql:/home/brapi/db/sql
     networks:
       backend:
         aliases:
@@ -144,7 +145,7 @@ services:
         source: gigwa_data
         target: /usr/local/tomcat/config
   mongo:
-    image: mongo:4.2.21
+    image: mongo:4.2.24
     container_name: ${GIGWA_CONTAINER_NAME:-gigwa}_db
     restart: always
     command: --profile 0 --slowms 60000 --storageEngine wiredTiger --wiredTigerCollectionBlockCompressor=zstd --directoryperdb --quiet
@@ -163,7 +164,7 @@ services:
           - gigwa_db
   localstack:
     container_name: "localstack"
-    image: localstack/localstack
+    image: localstack/localstack:3.0.2
     restart: always
     ports:
       - "4566:4566"
@@ -172,7 +173,7 @@ services:
         aliases:
           - localstack
     environment:
-      - HOSTNAME_EXTERNAL=localstack
+      - LOCALSTACK_HOST=localstack
 
 networks:
   backend:

localstack/startup_info.json

@@ -0,0 +1 @@
+[{"timestamp": "2022-11-17T17:01:36.401503", "localstack_version": "1.2.0", "localstack_ext_version": "1.2.0", "pro_activated": false}]

pom.xml

@@ -23,7 +23,7 @@
     <version>1.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
-    <name>Breeding Insight API</name>
+    <name>DeltaBreed API</name>
     <description></description>
     <url>https://breedinginsight.org</url>
 
@@ -57,6 +57,10 @@
             <name>David Phillips</name>
             <email>[email protected]</email>
         </developer>
+        <developer>
+            <name>Matthew Mandych</name>
+            <email>[email protected]</email>
+        </developer>
     </developers>
 
     <properties>
@@ -72,7 +76,7 @@
         <jvm.options>-Xmx1024m -XX:MaxPermSize=256m --enable-preview</jvm.options>
 
         <jooq.version>3.16.3</jooq.version>
-        <postgres.version>42.3.2</postgres.version>
+        <postgres.version>42.3.8</postgres.version>
         <logback.version>1.2.10</logback.version>
         <lombok.version>1.18.22</lombok.version>
         <gson.version>2.8.9</gson.version>
@@ -149,6 +153,13 @@
                 <enabled>false</enabled>
             </releases>
         </repository>
+        <repository>
+            <id>ossrh</id>
+            <url>https://s01.oss.sonatype.org/content/repositories/snapshots/</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+        </repository>
     </repositories>
 
     <dependencyManagement>

settings.xml

@@ -49,13 +49,6 @@
                     <releases><enabled>true</enabled></releases>
                     <snapshots><enabled>true</enabled></snapshots>
                 </repository>
-                <repository>
-                    <id>github-brapi</id>
-                    <name>GitHub Breeding Insight Apache Maven Packages</name>
-                    <url>https://maven.pkg.github.com/Breeding-Insight/brapi</url>
-                    <releases><enabled>true</enabled></releases>
-                    <snapshots><enabled>true</enabled></snapshots>
-                </repository>
                 <repository>
                     <id>github-fannypack</id>
                     <name>FannyPack github repository</name>
@@ -73,11 +66,6 @@
             <username>${GITHUB_ACTOR}</username>
             <password>${GITHUB_TOKEN}</password>
         </server>
-        <server>
-            <id>github-brapi</id>
-            <username>${GITHUB_ACTOR}</username>
-            <password>${GITHUB_TOKEN}</password>
-        </server>
         <server>
             <id>github-fannypack</id>
             <username>${GITHUB_ACTOR}</username>

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

@@ -7,7 +7,6 @@
 import io.micronaut.security.annotation.Secured;
 import io.micronaut.security.rules.SecurityRule;
 import lombok.extern.slf4j.Slf4j;
-import org.apache.commons.lang3.StringUtils;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.api.auth.*;
 import org.breedinginsight.api.model.v1.response.DataResponse;
@@ -17,18 +16,14 @@
 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.dao.db.tables.pojos.BreedingMethodEntity;
 import org.breedinginsight.dao.db.tables.pojos.ProgramBreedingMethodEntity;
-import org.breedinginsight.daos.BreedingMethodDAO;
 import org.breedinginsight.services.BreedingMethodService;
 import org.breedinginsight.services.exceptions.BadRequestException;
 
 import javax.inject.Inject;
-import javax.validation.Valid;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
-import java.util.stream.Collectors;
 
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
@@ -64,7 +59,7 @@ public HttpResponse<Response<DataResponse<ProgramBreedingMethodEntity>>> getSyst
     @Post("programs/{programId}/breeding-methods")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
-    public HttpResponse<Response<ProgramBreedingMethodEntity>> createProgramBreedingMethod(@PathVariable UUID programId, @Body ProgramBreedingMethodEntity breedingMethod) throws BadRequestException, ApiException {
+    public HttpResponse<?> createProgramBreedingMethod(@PathVariable UUID programId, @Body ProgramBreedingMethodEntity breedingMethod) throws ApiException{
         log.debug("Saving new program breeding method");
 
         try {
@@ -79,6 +74,8 @@ public HttpResponse<Response<ProgramBreedingMethodEntity>> createProgramBreeding
             response.metadata = metadata;
 
             return HttpResponse.ok(response);
+        } catch (BadRequestException ex) {
+            return HttpResponse.badRequest(ex.getMessage());
         } catch (Exception e) {
             log.error("Error creating program breeding method", e);
             throw e;
@@ -110,7 +107,7 @@ public HttpResponse<Response<DataResponse<ProgramBreedingMethodEntity>>> getProg
     @Put("programs/{programId}/breeding-methods/{breedingMethodId}")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
-    public HttpResponse<Response<ProgramBreedingMethodEntity>> updateProgramBreedingMethod(@PathVariable UUID programId, @PathVariable UUID breedingMethodId, @Body ProgramBreedingMethodEntity breedingMethod) throws BadRequestException, ApiException {
+    public HttpResponse<?> updateProgramBreedingMethod(@PathVariable UUID programId, @PathVariable UUID breedingMethodId, @Body ProgramBreedingMethodEntity breedingMethod) throws ApiException {
         log.debug("Saving new program breeding method");
 
         try {
@@ -128,6 +125,8 @@ public HttpResponse<Response<ProgramBreedingMethodEntity>> updateProgramBreeding
             response.metadata = metadata;
 
             return HttpResponse.ok(response);
+        } catch (BadRequestException ex) {
+            return HttpResponse.badRequest(ex.getMessage());
         } catch (Exception e) {
             log.error("Error updating program breeding method", e);
             throw e;

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"})
@@ -97,19 +49,21 @@ public HttpResponse<StreamedFile> datasetExport(
             @QueryValue @Valid ExperimentExportQuery queryParams) {
         String downloadErrorMessage = "An error occurred while generating the download file. Contact the development team at [email protected].";
         try {
-            Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program does not exist"));
+            Optional<Program> program = programService.getById(programId);
+            if(program.isEmpty()) {
+                return HttpResponse.notFound();
+            }
 
             // 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);
+            DownloadFile downloadFile = experimentService.exportObservations(program.get(), experimentId, queryParams);
 
-            HttpResponse<StreamedFile> response = HttpResponse
+            return HttpResponse
                     .ok(downloadFile.getStreamedFile())
                     .header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + downloadFile.getFileName());
-            return response;
         } catch (Exception e) {
-            log.info(e.getMessage(), e);
+            log.info(downloadErrorMessage, e);
             HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, downloadErrorMessage).contentType(MediaType.TEXT_PLAIN).body(downloadErrorMessage);
             return response;
         }

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

@@ -4,6 +4,8 @@
 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;
@@ -81,7 +83,7 @@ public HttpResponse<Response<DataResponse<SharedOntology>>> getAvailablePrograms
     }
 
     /**
-     * Accepts a list of programs to shared the ontology with.
+     * Accepts a list of programs to share the ontology with.
      * @param programId
      * @return List of programs successfully shared to with acceptable status
      * {
@@ -210,7 +212,7 @@ public HttpResponse unsubscribeOntology(
     @Get("/programs/{programId}/ontology/subscribe")
     @Produces(MediaType.APPLICATION_JSON)
     @AddMetadata
-    @ProgramSecured(roles = {ProgramSecuredRole.BREEDER})
+    @Secured(SecurityRule.IS_AUTHENTICATED)
     public HttpResponse<Response<DataResponse<SubscribedOntology>>> getSubscribedOntology(
             @PathVariable UUID programId) {
         try {

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)