Release/1.4

docker-compose.yml

@@ -176,6 +176,9 @@ services:
           - localstack
     environment:
       - LOCALSTACK_HOST=localstack
+      - PERSISTENCE=1
+    volumes:
+      - localstack_data:/var/lib/localstack
 
 networks:
   backend:
@@ -187,3 +190,5 @@ volumes:
     name: ${GIGWA_CONTAINER_NAME:-gigwa}_data
   gigwa_mongo_data:
     name: ${GIGWA_CONTAINER_NAME:-gigwa}_mongo_data
+  localstack_data:
+    name: localstack_data

pom.xml

@@ -89,7 +89,7 @@
         <guava.version>31.0.1-jre</guava.version>
         <okhttp.version>4.9.3</okhttp.version>
         <mockito.version>4.3.1</mockito.version>
-        <brapi-java-client.version>2.2.0</brapi-java-client.version>
+        <brapi-java-client.version>2.2.1</brapi-java-client.version>
         <commons-io.version>2.11.0</commons-io.version>
         <tika-app.version>2.2.1</tika-app.version>
         <!-- Version of apache-poi depends on version of tika. Tika uses these. -->
@@ -464,6 +464,11 @@
             <artifactId>micronaut-amazon-awssdk-s3</artifactId>
             <version>2.0.5-micronaut-2.0</version>
         </dependency>
+        <dependency>
+            <groupId>com.github.samtools</groupId>
+            <artifactId>htsjdk</artifactId>
+            <version>2.24.1</version>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

settings.xml

@@ -49,6 +49,12 @@
                     <releases><enabled>true</enabled></releases>
                     <snapshots><enabled>true</enabled></snapshots>
                 </repository>
+                <repository>
+                    <id>central-snapshots</id>
+                    <url>https://central.sonatype.com/repository/maven-snapshots/</url>
+                    <releases><enabled>false</enabled></releases>
+                    <snapshots><enabled>true</enabled></snapshots>
+                </repository>
                 <repository>
                     <id>github-fannypack</id>
                     <name>FannyPack github repository</name>

src/main/java/org/breedinginsight/api/model/v1/request/query/GenotypeImportQuery.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.model.v1.request.query;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+import org.apache.commons.lang3.StringUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Getter
+@Introspected
+public class GenotypeImportQuery extends QueryParams {
+
+    private String sampleSubmissionId;
+    private String projectNameForSampleSubmission;
+    private String sampleSubmissionCreatedBy;
+    private String genotypingFileName;
+    private String genotypingImportDate;
+    private String genotypingImportBy;
+
+    public SearchRequest constructSearchRequest() {
+        List<FilterRequest> filters = new ArrayList<>();
+
+        if (!StringUtils.isBlank(getSampleSubmissionId())) {
+            filters.add(constructFilterRequest("sampleSubmissionId", getSampleSubmissionId()));
+        }
+        if (!StringUtils.isBlank(getProjectNameForSampleSubmission())) {
+            filters.add(constructFilterRequest("projectNameForSampleSubmission", getProjectNameForSampleSubmission()));
+        }
+        if (!StringUtils.isBlank(getSampleSubmissionCreatedBy())) {
+            filters.add(constructFilterRequest("sampleSubmissionCreatedBy", getSampleSubmissionCreatedBy()));
+        }
+        if (!StringUtils.isBlank(getGenotypingFileName())) {
+            filters.add(constructFilterRequest("genotypingFileName", getGenotypingFileName()));
+        }
+        if (!StringUtils.isBlank(getGenotypingImportDate())) {
+            filters.add(constructFilterRequest("genotypingImportDate", getGenotypingImportDate()));
+        }
+        if (!StringUtils.isBlank(getGenotypingImportBy())) {
+            filters.add(constructFilterRequest("genotypingImportBy", getGenotypingImportBy()));
+        }
+
+        return new SearchRequest(filters);
+    }
+
+    private FilterRequest constructFilterRequest(String field, String value) {
+        return FilterRequest.builder()
+                .field(field)
+                .value(value)
+                .build();
+    }
+}

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

@@ -1,46 +1,126 @@
+/*
+ * 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 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.AuthenticatedUser;
-import org.breedinginsight.api.auth.ProgramSecured;
-import org.breedinginsight.api.auth.ProgramSecuredRole;
-import org.breedinginsight.api.auth.SecurityService;
+import org.breedinginsight.api.auth.*;
+import org.breedinginsight.api.model.v1.request.query.GenotypeImportQuery;
+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.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;
 import org.breedinginsight.services.exceptions.AuthorizationException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.services.geno.GenotypeService;
+import org.breedinginsight.utilities.response.ResponseUtils;
+import org.breedinginsight.utilities.response.mappers.GenotypeImportQueryMapper;
 
 import javax.inject.Inject;
+import javax.validation.Valid;
+import java.io.IOException;
+import java.util.Optional;
 import java.util.UUID;
 
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
 public class GenotypeDataUploadController {
     private final GenotypeService genoService;
     private final SecurityService securityService;
+    private final ProgramService programService;
+    private final GenotypeImportQueryMapper genotypeImportQueryMapper;
 
     @Inject
-    public GenotypeDataUploadController(GenotypeService genoService, SecurityService securityService) {
+    public GenotypeDataUploadController(GenotypeService genoService, SecurityService securityService,
+                                        ProgramService programService, GenotypeImportQueryMapper genotypeImportQueryMapper) {
         this.genoService = genoService;
         this.securityService = securityService;
+        this.programService = programService;
+        this.genotypeImportQueryMapper = genotypeImportQueryMapper;
     }
 
-    @Post("programs/{programId}/experiments/{experimentId}/geno/import")
+    @Get("programs/{programId}/geno/imports{?genotypeImportQuery*}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES)
+    public HttpResponse<Response<DataResponse<GenotypeImportDetails>>> getGenotypeImports(
+            @PathVariable UUID programId,
+            @QueryValue @QueryValid(using = GenotypeImportQueryMapper.class) @Valid GenotypeImportQuery genotypeImportQuery) {
+        Optional<Program> program = programService.getById(programId);
+        if (program.isEmpty()) {
+            log.info("programId not found: {}", programId.toString());
+            return HttpResponse.notFound();
+        }
+
+        SearchRequest searchRequest = genotypeImportQuery.constructSearchRequest();
+
+        return ResponseUtils.getQueryResponse(
+                genoService.getGenotypeImports(programId),
+                genotypeImportQueryMapper,
+                searchRequest,
+                genotypeImportQuery
+        );
+    }
+
+    @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)
     @AddMetadata
     @ProgramSecured(roles = {ProgramSecuredRole.PROGRAM_ADMIN})
-    public HttpResponse<Response<ImportResponse>> uploadData(@PathVariable UUID programId, @PathVariable UUID experimentId, @Part("file") CompletedFileUpload upload) {
+    public HttpResponse<Response<ImportResponse>> uploadData(@PathVariable UUID programId, @PathVariable UUID submissionId, @Part("file") CompletedFileUpload upload) {
         AuthenticatedUser actingUser = securityService.getUser();
         try {
-            ImportResponse result = genoService.submitGenotypeData(actingUser.getId(), programId, experimentId, upload);
+            ImportResponse result = genoService.submitGenotypeData(actingUser.getId(), programId, submissionId, upload);
             Response<ImportResponse> response = new Response<>(result);
             return HttpResponse.ok(response);
         } catch (DoesNotExistException e) {

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

@@ -54,6 +54,11 @@
 @Secured(SecurityRule.IS_AUTHENTICATED)
 public class SampleSubmissionController {
 
+    public static final String DELETE_STATUS_NOT_ALLOWED_ERROR_MESSAGE =
+            "Sample submission cannot be deleted because status is submitted or completed";
+    public static final String DELETE_GENOTYPE_DATA_NOT_ALLOWED_ERROR_MESSAGE =
+            "Sample submission cannot be deleted because associated genotype data exists";
+
     private final boolean brapiSubmissionEnabled;
     private final SampleSubmissionService sampleSubmissionService;
     private final ProgramService programService;
@@ -303,20 +308,20 @@ public HttpResponse deleteSubmissionById(@PathVariable UUID programId, @PathVari
             return HttpResponse.notFound();
         }
 
-        // sample status validation
-        Optional<SampleSubmission> submissionOpt = sampleSubmissionService.getSampleSubmission(program.get(), submissionId, false);
-
-        if(submissionOpt.isEmpty()) {
-            return HttpResponse.notFound();
-        }
-        SampleSubmission submission = submissionOpt.get();
-        if (!submission.isDeletable()) {
-            return HttpResponse.notAllowed();
+        SampleSubmissionService.DeleteResult result = sampleSubmissionService.deleteSampleSubmission(program.get(), submissionId);
+        switch (result) {
+            case NOT_FOUND:
+                return HttpResponse.notFound();
+            case STATUS_NOT_ALLOWED:
+                return HttpResponse.notAllowed()
+                        .body(DELETE_STATUS_NOT_ALLOWED_ERROR_MESSAGE);
+            case GENOTYPE_DATA_NOT_ALLOWED:
+                return HttpResponse.notAllowed()
+                        .body(DELETE_GENOTYPE_DATA_NOT_ALLOWED_ERROR_MESSAGE);
+            case DELETED:
+            default:
+                return HttpResponse.ok();
         }
-
-        sampleSubmissionService.deleteSampleSubmission(program.get(), submissionId);
-
-        return HttpResponse.ok();
     }
 
 }

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

@@ -439,7 +439,8 @@ public HttpResponse<Response<GermplasmGenotype>> getGermplasmGenotype(@PathVaria
 
         try {
             BrAPIGermplasm germplasm = germplasmDAO.getGermplasmByUUID(germplasmId, programId);
-            GermplasmGenotype germplasmGenotype = genoService.retrieveGenotypeData(programId, germplasm);
+
+            GermplasmGenotype germplasmGenotype = genoService.retrieveGenotypeData(programId, UUID.fromString(germplasmId));
 
             Response<GermplasmGenotype> response = new Response(germplasmGenotype);
             return HttpResponse.ok(response);

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java

@@ -204,8 +204,7 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
                     germplasm.setAdditionalInfo(additionalInfo);
                 }
 
-                // TODO: BI-1883 to cleanup this workaround for the pedigree string
-                String pedigree = processBreedbasePedigree(germplasm.getPedigree());
+                String pedigree = germplasm.getPedigree();
                 additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE, pedigree);
 
                 String gidPedigreeString = "";
@@ -281,34 +280,6 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
         return programGermplasmMap;
     }
 
-    // TODO: hack for now, probably should update breedbase
-    // Made a JIRA card BI-1883 for this
-    // Breedbase will return NA/NA for no pedigree or NA/father, mother/NA
-    // strip NAs before saving RAW_PEDIGREE, if there was a germplasm with name NA it would be in format NA [program key]
-    // so that case should be ok if we just strip NA/NA, NA/, or /NA<\0>
-    private String processBreedbasePedigree(String pedigree) {
-
-        if (pedigree != null) {
-            if (pedigree.equals("NA/NA")) {
-                return "";
-            }
-
-            // Technically processGermplasmForDisplay should handle ok without stripping these NAs but will strip anyways
-            // for consistency.
-            // We only allow the /NA case for single parent as we require a female parent in the pedigree
-            // keep the leading slash, will be handled by processGermplasmForDisplay
-            if (pedigree.endsWith("/NA")) {
-                return pedigree.substring(0, pedigree.length()-2);
-            }
-
-            // shouldn't have this case in our data but just in case
-            if (pedigree.startsWith("NA/")) {
-                return pedigree.substring(2);
-            }
-        }
-        return pedigree;
-    }
-
     public List<BrAPIGermplasm> createBrAPIGermplasm(List<BrAPIGermplasm> postBrAPIGermplasmList, UUID programId, ImportUpload upload) {
         GermplasmApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), GermplasmApi.class);
         var program = programDAO.fetchOneById(programId);

src/main/java/org/breedinginsight/brapi/v2/model/request/query/GermplasmQuery.java

@@ -22,6 +22,7 @@ public class GermplasmQuery extends BrapiQuery {
     private String femaleParentGID;
     private String maleParentGID;
     private String createdDate;
+    private String externalUID;
     private String createdByUserName;
     private String synonym;
     // This is a meta-parameter, it describes the display format of any date fields.
@@ -56,9 +57,15 @@ public SearchRequest constructSearchRequest() {
         if (!StringUtils.isBlank(getMaleParentGID())) {
             filters.add(constructFilterRequest("maleParentGID", getMaleParentGID()));
         }
+
         if (!StringUtils.isBlank(getCreatedDate())) {
             filters.add(constructFilterRequest("createdDate", getCreatedDate()));
         }
+
+        if (!StringUtils.isBlank(getExternalUID())) {
+            filters.add(constructFilterRequest("externalUID", getExternalUID()));
+        }
+
         if (!StringUtils.isBlank(getCreatedByUserName())) {
             filters.add(constructFilterRequest("createdByUserName", getCreatedByUserName()));
         }