BI-2901: Add backend VCF download endpoint for genotyping imports

src/main/java/org/breedinginsight/api/v1/controller/geno/GenotypeDataUploadController.java

@@ -16,10 +16,13 @@
  */
 package org.breedinginsight.api.v1.controller.geno;
 
+import io.micronaut.http.HttpHeaders;
 import io.micronaut.http.HttpResponse;
+import io.micronaut.http.HttpStatus;
 import io.micronaut.http.MediaType;
 import io.micronaut.http.annotation.*;
 import io.micronaut.http.multipart.CompletedFileUpload;
+import io.micronaut.http.server.types.files.StreamedFile;
 import lombok.extern.slf4j.Slf4j;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.api.auth.*;
@@ -30,6 +33,7 @@
 import org.breedinginsight.api.model.v1.validators.QueryValid;
 import org.breedinginsight.api.v1.controller.metadata.AddMetadata;
 import org.breedinginsight.brapps.importer.model.response.ImportResponse;
+import org.breedinginsight.model.DownloadFile;
 import org.breedinginsight.model.GenotypeImportDetails;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.ProgramService;
@@ -41,6 +45,7 @@
 
 import javax.inject.Inject;
 import javax.validation.Valid;
+import java.io.IOException;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -83,6 +88,30 @@ public HttpResponse<Response<DataResponse<GenotypeImportDetails>>> getGenotypeIm
         );
     }
 
+    @Get("programs/{programId}/geno/imports/{genotypeImportId}/download")
+    @ProgramSecured(roleGroups = ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES)
+    @Produces(value = {"application/octet-stream"})
+    public HttpResponse<StreamedFile> downloadGenotypeImport(@PathVariable UUID programId, @PathVariable UUID genotypeImportId) {
+        Optional<Program> program = programService.getById(programId);
+        if (program.isEmpty()) {
+            log.info("programId not found: {}", programId.toString());
+            return HttpResponse.notFound();
+        }
+
+        try {
+            Optional<DownloadFile> downloadFile = genoService.downloadGenotypeImport(programId, genotypeImportId);
+            if (downloadFile.isEmpty()) {
+                return HttpResponse.notFound();
+            }
+
+            return HttpResponse.ok(downloadFile.get().getStreamedFile())
+                    .header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename=" + downloadFile.get().getFileName());
+        } catch (IOException e) {
+            log.error("Error downloading genotype import", e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error downloading genotype import");
+        }
+    }
+
     @Post("programs/{programId}/submissions/{submissionId}/geno/import")
     @Consumes(MediaType.MULTIPART_FORM_DATA)
     @Produces(MediaType.APPLICATION_JSON)

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

@@ -21,13 +21,15 @@
 import org.breedinginsight.dao.db.tables.daos.GenotypeImportDao;
 import org.breedinginsight.dao.db.tables.pojos.GenotypeImportEntity;
 import org.breedinginsight.model.GenotypeImportDetails;
+import org.breedinginsight.model.GenotypeImportDownloadDetails;
 import org.jooq.Configuration;
 import org.jooq.DSLContext;
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
 import java.time.OffsetDateTime;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 
 import static org.breedinginsight.dao.db.Tables.*;
@@ -62,6 +64,7 @@ public List<GenotypeImportDetails> getGenotypeImportsByProgramId(UUID programId)
         BiUserTable genotypingImportByUser = BI_USER.as("genotypingImportByUser");
 
         return dsl.select(
+                        GENOTYPE_IMPORT.ID,
                         SAMPLE_SUBMISSION.ID,
                         SAMPLE_SUBMISSION.NAME,
                         sampleSubmissionCreatedByUser.NAME,
@@ -82,4 +85,19 @@ public List<GenotypeImportDetails> getGenotypeImportsByProgramId(UUID programId)
                         .parseSqlRecord(record, sampleSubmissionCreatedByUser, genotypingImportByUser));
     }
 
+    public Optional<GenotypeImportDownloadDetails> getDownloadableGenotypeImportById(UUID programId, UUID genotypeImportId) {
+        return dsl.select(
+                        GENOTYPE_IMPORT.SAMPLE_SUBMISSION_ID,
+                        GENOTYPE_IMPORT.IMPORTER_IMPORT_ID,
+                        IMPORTER_IMPORT.UPLOAD_FILE_NAME)
+                .from(GENOTYPE_IMPORT)
+                .join(SAMPLE_SUBMISSION).on(GENOTYPE_IMPORT.SAMPLE_SUBMISSION_ID.eq(SAMPLE_SUBMISSION.ID))
+                .join(IMPORTER_IMPORT).on(GENOTYPE_IMPORT.IMPORTER_IMPORT_ID.eq(IMPORTER_IMPORT.ID))
+                .join(IMPORTER_PROGRESS).on(IMPORTER_IMPORT.IMPORTER_PROGRESS_ID.eq(IMPORTER_PROGRESS.ID))
+                .where(GENOTYPE_IMPORT.ID.eq(genotypeImportId))
+                .and(SAMPLE_SUBMISSION.PROGRAM_ID.eq(programId))
+                .and(IMPORTER_IMPORT.PROGRAM_ID.eq(programId))
+                .and(IMPORTER_PROGRESS.STATUSCODE.eq((short) HttpStatus.OK.getCode()))
+                .fetchOptional(GenotypeImportDownloadDetails::parseSqlRecord);
+    }
 }

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

@@ -33,6 +33,7 @@
 
 import static org.breedinginsight.dao.db.Tables.IMPORTER_IMPORT;
 import static org.breedinginsight.dao.db.Tables.SAMPLE_SUBMISSION;
+import static org.breedinginsight.dao.db.Tables.GENOTYPE_IMPORT;
 
 @Getter
 @Setter
@@ -43,6 +44,7 @@
 @Introspected
 @Jacksonized
 public class GenotypeImportDetails {
+    private UUID genotypeImportId;
     private UUID sampleSubmissionId;
     private String projectNameForSampleSubmission;
     private String sampleSubmissionCreatedBy;
@@ -54,6 +56,7 @@ public static GenotypeImportDetails parseSqlRecord(Record record,
                                                        BiUserTable sampleSubmissionCreatedByUser,
                                                        BiUserTable genotypingImportByUser) {
         return GenotypeImportDetails.builder()
+                .genotypeImportId(record.get(GENOTYPE_IMPORT.ID))
                 .sampleSubmissionId(record.get(SAMPLE_SUBMISSION.ID))
                 .projectNameForSampleSubmission(record.get(SAMPLE_SUBMISSION.NAME))
                 .sampleSubmissionCreatedBy(record.get(sampleSubmissionCreatedByUser.NAME))

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

@@ -0,0 +1,54 @@
+/*
+ * 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.model;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+import lombok.experimental.Accessors;
+import lombok.experimental.SuperBuilder;
+import lombok.extern.jackson.Jacksonized;
+import org.jooq.Record;
+
+import java.util.UUID;
+
+import static org.breedinginsight.dao.db.Tables.GENOTYPE_IMPORT;
+import static org.breedinginsight.dao.db.Tables.IMPORTER_IMPORT;
+
+@Getter
+@Setter
+@Accessors(chain = true)
+@ToString
+@SuperBuilder
+@NoArgsConstructor
+@Introspected
+@Jacksonized
+public class GenotypeImportDownloadDetails {
+    private UUID sampleSubmissionId;
+    private UUID importerImportId;
+    private String genotypeFileName;
+
+    public static GenotypeImportDownloadDetails parseSqlRecord(Record record) {
+        return GenotypeImportDownloadDetails.builder()
+                .sampleSubmissionId(record.get(GENOTYPE_IMPORT.SAMPLE_SUBMISSION_ID))
+                .importerImportId(record.get(GENOTYPE_IMPORT.IMPORTER_IMPORT_ID))
+                .genotypeFileName(record.get(IMPORTER_IMPORT.UPLOAD_FILE_NAME))
+                .build();
+    }
+}

src/main/java/org/breedinginsight/services/geno/GenotypeService.java

@@ -19,12 +19,15 @@
 import io.micronaut.http.multipart.CompletedFileUpload;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.brapps.importer.model.response.ImportResponse;
+import org.breedinginsight.model.DownloadFile;
 import org.breedinginsight.model.GermplasmGenotype;
 import org.breedinginsight.services.exceptions.AuthorizationException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.model.GenotypeImportDetails;
 
+import java.io.IOException;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 
 public interface GenotypeService {
@@ -33,4 +36,6 @@ public interface GenotypeService {
     GermplasmGenotype retrieveGenotypeData(UUID programId, UUID germplasmId) throws DoesNotExistException, AuthorizationException, ApiException;
 
     List<GenotypeImportDetails> getGenotypeImports(UUID programId);
+
+    Optional<DownloadFile> downloadGenotypeImport(UUID programId, UUID genotypeImportId)throws IOException;
 }

src/main/java/org/breedinginsight/services/geno/impl/GigwaGenotypeServiceImpl.java

@@ -8,6 +8,7 @@
 import io.micronaut.http.HttpStatus;
 import io.micronaut.http.multipart.CompletedFileUpload;
 import io.micronaut.http.server.exceptions.InternalServerException;
+import io.micronaut.http.server.types.files.StreamedFile;
 import lombok.extern.slf4j.Slf4j;
 import okhttp3.*;
 import org.apache.commons.lang3.tuple.Pair;
@@ -46,10 +47,7 @@
 import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.daos.SampleSubmissionDAO;
 import org.breedinginsight.daos.UserDAO;
-import org.breedinginsight.model.GenotypeImportDetails;
-import org.breedinginsight.model.GermplasmGenotype;
-import org.breedinginsight.model.Program;
-import org.breedinginsight.model.User;
+import org.breedinginsight.model.*;
 import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
 import org.breedinginsight.services.exceptions.AuthorizationException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
@@ -66,6 +64,7 @@
 import javax.inject.Singleton;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.time.LocalDateTime;
 import java.time.OffsetDateTime;
 import java.util.*;
@@ -276,6 +275,52 @@ public List<GenotypeImportDetails> getGenotypeImports(UUID programId) {
         return genotypeImportDAO.getGenotypeImportsByProgramId(programId);
     }
 
+    @Override
+    public Optional<DownloadFile> downloadGenotypeImport(UUID programId, UUID genotypeImportId) {
+        Optional<GenotypeImportDownloadDetails> genotypeImportDownloadDetails = genotypeImportDAO
+                .getDownloadableGenotypeImportById(programId, genotypeImportId);
+
+        if (genotypeImportDownloadDetails.isEmpty()) {
+            return Optional.empty();
+        }
+
+        UUID submissionId = genotypeImportDownloadDetails.get().getSampleSubmissionId();
+        UUID importerImportId = genotypeImportDownloadDetails.get().getImporterImportId();
+        String originalFileName = genotypeImportDownloadDetails.get().getGenotypeFileName();
+
+        Optional<String> storedKey = findStoredGenotypeImportKey(programId, submissionId, importerImportId);
+        if (storedKey.isEmpty()) {
+            return Optional.empty();
+        }
+
+        InputStream inputStream = s3Client.getObject(GetObjectRequest.builder()
+                .bucket(storageService.getDefaultBucketName())
+                .key(storedKey.get())
+                .build());
+
+        return Optional.of(new DownloadFile(
+                originalFileName,
+                new StreamedFile(
+                        inputStream,
+                        new io.micronaut.http.MediaType(io.micronaut.http.MediaType.APPLICATION_OCTET_STREAM)
+                )
+        ));
+    }
+
+    private Optional<String> findStoredGenotypeImportKey(UUID programId, UUID submissionId, UUID importerImportId) {
+        String prefix = programId + "/" + submissionId + "/" + importerImportId;
+
+        ListObjectsV2Response response = s3Client.listObjectsV2(ListObjectsV2Request.builder()
+                .bucket(storageService.getDefaultBucketName())
+                .prefix(prefix)
+                .maxKeys(1)
+                .build());
+
+        return response.contents().stream()
+                .map(S3Object::key)
+                .findFirst();
+    }
+
     private boolean validateSamples(Program program, UUID submissionId, byte[] fileContents, ImportUpload upload) throws DoesNotExistException, ApiException {
         log.debug("Validating samples in submitted VCF file for submission: " + submissionId);