BI-1910 - Allow Breeder to Upload a Genotype Sample File

.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

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>
@@ -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/geno/SampleSubmissionController.java

@@ -0,0 +1,284 @@
+/*
+ * 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.geno;
+
+import com.google.gson.Gson;
+import com.google.gson.JsonObject;
+import io.micronaut.context.annotation.Property;
+import io.micronaut.http.*;
+import io.micronaut.http.annotation.*;
+import io.micronaut.http.server.types.files.StreamedFile;
+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.geno.BrAPIVendorOrderSubmission;
+import org.breedinginsight.api.auth.*;
+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.model.*;
+import org.breedinginsight.services.ProgramService;
+import org.breedinginsight.services.SampleSubmissionService;
+import org.breedinginsight.services.UserService;
+import org.breedinginsight.utilities.Utilities;
+
+import javax.annotation.Nullable;
+import javax.inject.Inject;
+import javax.validation.constraints.NotBlank;
+import java.io.IOException;
+import java.util.List;
+import java.util.Optional;
+import java.util.UUID;
+
+@Slf4j
+@Controller("/${micronaut.bi.api.version}")
+@Secured(SecurityRule.IS_AUTHENTICATED)
+public class SampleSubmissionController {
+
+    private final boolean brapiSubmissionEnabled;
+    private final SampleSubmissionService sampleSubmissionService;
+    private final ProgramService programService;
+    private final SecurityService securityService;
+    private final UserService userService;
+
+    private final Gson gson;
+
+    @Inject
+    public SampleSubmissionController(@Property(name = "brapi.vendor-submission-enabled") boolean brapiSubmissionEnabled, SampleSubmissionService sampleSubmissionService, ProgramService programService, SecurityService securityService, UserService userService) {
+        this.brapiSubmissionEnabled = brapiSubmissionEnabled;
+        this.sampleSubmissionService = sampleSubmissionService;
+        this.programService = programService;
+        this.securityService = securityService;
+        this.userService = userService;
+        this.gson = new Gson();
+    }
+
+    @Get("programs/{programId}/submissions")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = ProgramSecuredRoleGroup.ALL)
+    public HttpResponse<Response<DataResponse<SampleSubmission>>> getProgramSampleSubmissions(@PathVariable UUID programId) {
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.info(String.format("programId not found: %s", programId.toString()));
+            return HttpResponse.notFound();
+        }
+
+        List<SampleSubmission> submissions = sampleSubmissionService.getProgramSubmissions(program.get());
+        Metadata metadata = new Metadata(new Pagination(submissions.size(), submissions.size(), 1, 0),
+                List.of(new Status(StatusCode.INFO, "Successful Query")));
+        Response<DataResponse<SampleSubmission>> response = new Response<>(metadata, new DataResponse<>(submissions));
+        return HttpResponse.ok(response);
+    }
+
+    @Get("programs/{programId}/submissions/{submissionId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = ProgramSecuredRoleGroup.ALL)
+    public HttpResponse<Response<SampleSubmission>> getSubmissionById(@PathVariable UUID programId, @PathVariable UUID submissionId, @QueryValue(value = "details", defaultValue = "false") @Nullable Boolean fetchDetails) {
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.info(String.format("programId not found: %s", programId.toString()));
+            return HttpResponse.notFound();
+        }
+
+        try {
+            Optional<SampleSubmission> submission = sampleSubmissionService.getSampleSubmission(program.get(), submissionId, fetchDetails);
+
+            if(submission.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+
+            Metadata metadata = new Metadata(new Pagination(1, 1, 1, 0),
+                    List.of(new Status(StatusCode.INFO, "Successful Query")));
+            Response<SampleSubmission> response = new Response<>(metadata, submission.get());
+            return HttpResponse.ok(response);
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        }
+    }
+
+    @Put("programs/{programId}/submissions/{submissionId}/status")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN})
+    public HttpResponse<Response<SampleSubmission>> updateSubmissionStatus(@PathVariable UUID programId, @PathVariable UUID submissionId, @Body String body) {
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.info(String.format("programId not found: %s", programId.toString()));
+            return HttpResponse.notFound();
+        }
+
+        AuthenticatedUser actingUser = securityService.getUser();
+        Optional<User> user = userService.getById(actingUser.getId());
+        if (user.isEmpty()) {
+            return HttpResponse.unauthorized();
+        }
+
+        SampleSubmission.Status status = SampleSubmission.Status.fromValue(gson.fromJson(body, JsonObject.class).get("status").getAsString());
+        if(status == null) {
+            HttpResponse response = HttpResponse.badRequest("Unrecognized status");
+            return response;
+        }
+
+        try {
+            Optional<SampleSubmission> submission = sampleSubmissionService.updateSubmissionStatus(program.get(), submissionId, status, user.get());
+
+            if(submission.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+
+            Metadata metadata = new Metadata(new Pagination(1, 1, 1, 0),
+                    List.of(new Status(StatusCode.INFO, "Successful Update")));
+            Response<SampleSubmission> response = new Response<>(metadata, submission.get());
+            return HttpResponse.ok(response);
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        }
+    }
+
+
+    @Get("/programs/{programId}/submissions/{submissionId}/dart")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    @Produces(value={"text/csv", "application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "application/octet-stream"})
+    public HttpResponse<StreamedFile> generateDArTFile(@PathVariable UUID programId, @PathVariable UUID submissionId) {
+        try {
+            Optional<Program> program = programService.getById(programId);
+            if(program.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+            Optional<DownloadFile> downloadFile = sampleSubmissionService.generateDArTFile(program.get(), submissionId);
+            if(downloadFile.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+            HttpResponse<StreamedFile> response = HttpResponse
+                    .ok(downloadFile.get().getStreamedFile())
+                    .header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + downloadFile.get().getFileName());
+            return response;
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        } catch (IOException e) {
+            log.error("Error generating DArT file", e);
+            HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error generating DArT file").contentType(MediaType.TEXT_PLAIN).body("Error generating DArT file");
+            return response;
+        }
+    }
+
+    @Get("/programs/{programId}/submissions/{submissionId}/lookup")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    @Produces(value={"text/csv", "application/vnd.ms-excel", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "application/octet-stream"})
+    public HttpResponse<StreamedFile> generateLookupFile(@PathVariable UUID programId, @PathVariable UUID submissionId) {
+        try {
+            Optional<Program> program = programService.getById(programId);
+            if(program.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+            Optional<DownloadFile> downloadFile = sampleSubmissionService.generateLookupFile(program.get(), submissionId);
+            if(downloadFile.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+            HttpResponse<StreamedFile> response = HttpResponse
+                    .ok(downloadFile.get().getStreamedFile())
+                    .header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + downloadFile.get().getFileName());
+            return response;
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        } catch (IOException e) {
+            log.error("Error generating lookup file", e);
+            HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error generating lookup file").contentType(MediaType.TEXT_PLAIN).body("Error generating lookup file");
+            return response;
+        }
+    }
+
+    @Post("programs/{programId}/submissions/{submissionId}/submit")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN})
+    public HttpResponse<Response<BrAPIVendorOrderSubmission>> submitOrder(@PathVariable UUID programId, @PathVariable UUID submissionId, @QueryValue(value = "vendor") @NotBlank String vendorName) {
+        if(!brapiSubmissionEnabled) {
+            return HttpResponse.notFound();
+        }
+
+        try {
+            GenotypeVendor vendor = GenotypeVendor.fromName(vendorName);
+            if(vendor != null) {
+                Optional<Program> program = programService.getById(programId);
+                if (program.isEmpty()) {
+                    return HttpResponse.notFound();
+                }
+
+                AuthenticatedUser actingUser = securityService.getUser();
+                Optional<User> user = userService.getById(actingUser.getId());
+                if (user.isEmpty()) {
+                    return HttpResponse.unauthorized();
+                }
+
+                Optional<BrAPIVendorOrderSubmission> order = sampleSubmissionService.submitOrder(program.get(), submissionId, user.get(), vendor);
+                if (order.isEmpty()) {
+                    return HttpResponse.notFound();
+                }
+
+                Metadata metadata = new Metadata(new Pagination(1, 1, 1, 0),
+                        List.of(new Status(StatusCode.INFO, "Successful submission")));
+                Response<BrAPIVendorOrderSubmission> response = new Response<>(metadata, order.get());
+                return HttpResponse.ok(response);
+            } else {
+                HttpResponse response = HttpResponse.badRequest("Unrecognized vendor");
+                return response;
+            }
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        }
+    }
+
+    @Get("programs/{programId}/submissions/{submissionId}/status")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN})
+    public HttpResponse<Response<SampleSubmission>> checkVendorStatus(@PathVariable UUID programId, @PathVariable UUID submissionId) {
+        if(!brapiSubmissionEnabled) {
+            return HttpResponse.notFound();
+        }
+
+        Optional<Program> program = programService.getById(programId);
+        if(program.isEmpty()) {
+            log.info(String.format("programId not found: %s", programId.toString()));
+            return HttpResponse.notFound();
+        }
+
+        try {
+            Optional<SampleSubmission> submission = sampleSubmissionService.checkVendorStatus(program.get(), submissionId);
+
+            if(submission.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+
+            Metadata metadata = new Metadata(new Pagination(1, 1, 1, 0),
+                    List.of(new Status(StatusCode.INFO, "Successful Query")));
+            Response<SampleSubmission> response = new Response<>(metadata, submission.get());
+            return HttpResponse.ok(response);
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        }
+    }
+}

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

@@ -97,19 +97,21 @@ 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/brapi/v2/constants/BrAPIAdditionalInfoFields.java

@@ -48,4 +48,10 @@ public final class BrAPIAdditionalInfoFields {
 	public static final String TREATMENTS = "treatments";
     public static final String GID = "gid";
     public static final String ENV_YEAR = "envYear";
+    public static final String GERMPLASM_UUID = "germplasmId";
+    public static final String SAMPLE_ORGANISM = "organism";
+    public static final String SAMPLE_SPECIES = "species";
+    public static final String OBS_UNIT_ID = "obsUnitID";
+    public static final String GERMPLASM_NAME = "germplasmName";
+    public static final String SUBMISSION_NAME = "submissionName";
 }