Merge pull request #1353 from phac-nml/unify-sample-validation

Unify validate sample names

CHANGELOG.md

@@ -19,6 +19,7 @@
 * [Developer]: Updated OAuth2 implementation to use Spring Security 5 OAuth2 libraries. See [PR 1339](https://github.com/phac-nml/irida/pull/1339)
 * [Developer]: Add identifier to project drop-downs. See [PR 1352](https://github.com/phac-nml/irida/pull/1352)
 * [UI]: Fixed issue with Biohansel pipeline being launched without selecting an option for a required parameter. See [PR 1356](https://github.com/phac-nml/irida/pull/1356)
+* [Developer]: Unified validate sample names into one endpoint. See [PR 1353](https://github.com/phac-nml/irida/pull/1353)
 
 ## [22.05.5] - 2022/06/28
 * [UI]: Fixed bug preventing export of project samples table due to invalid url. [PR 1331](https://github.com/phac-nml/irida/pull/1331)

src/main/java/ca/corefacility/bioinformatics/irida/repositories/sample/SampleRepository.java

@@ -4,6 +4,8 @@
 import java.util.List;
 import java.util.Set;
 
+import javax.persistence.Tuple;
+
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.EntityGraph;
@@ -34,7 +36,7 @@ public interface SampleRepository extends IridaJpaRepository<Sample, Long>, Samp
 	public List<Sample> getSamplesForProjectShallow(Project project);
 
 	/**
-	 * Get a {@link Sample} with the given string sample identifier from a specific project.
+	 * Get a {@link Sample} with the given string sample name from a specific project.
 	 *
 	 * @param p          The {@link Project} that the {@link Sample} belongs to.
 	 * @param sampleName The string sample name for a sample
@@ -44,6 +46,18 @@ public interface SampleRepository extends IridaJpaRepository<Sample, Long>, Samp
 	@Query("select j.sample from ProjectSampleJoin j where j.project = ?1 and j.sample.sampleName = ?2")
 	public Sample getSampleBySampleName(Project p, String sampleName) throws EntityNotFoundException;
 
+	/**
+	 * Get the {@link Sample} identifiers with the given list of sample names from a list of projects.
+	 *
+	 * @param projectIds  The {@link Project} identifiers that the {@link Sample} belongs to.
+	 * @param sampleNames The list of sample names
+	 * @return A list of {@link Sample} identifiers
+	 * @throws EntityNotFoundException if a sample with this identifier doesn't exist
+	 */
+	@Query("select j.sample.sampleName, j.sample.id from ProjectSampleJoin j where j.project.id in ?1 and j.sample.sampleName in ?2")
+	public List<Tuple> getSampleIdsBySampleNameInProjects(List<Long> projectIds, List<String> sampleNames)
+			throws EntityNotFoundException;
+
 	/**
 	 * Get a {@link Page} of {@link Sample}s based on a list of {@link Sample} names
 	 *

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/ajax/projects/ProjectSamplesAjaxController.java

@@ -12,13 +12,13 @@
 import org.springframework.web.bind.annotation.*;
 import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
 
-import ca.corefacility.bioinformatics.irida.model.sample.Sample;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleFilesResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxErrorResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxSuccessResponse;
+import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIShareSamplesException;
 import ca.corefacility.bioinformatics.irida.ria.web.models.tables.AntTableResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.projects.dto.DownloadRequest;
@@ -119,8 +119,7 @@ public ResponseEntity<AjaxResponse> mergeSamples(@PathVariable Long projectId, @
 			String response = uiSampleService.mergeSamples(projectId, request, locale);
 			return ResponseEntity.ok(new AjaxSuccessResponse(response));
 		} catch (SampleMergeException e) {
-			return ResponseEntity.status(HttpStatus.BAD_REQUEST)
-					.body(new AjaxErrorResponse(e.getMessage()));
+			return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new AjaxErrorResponse(e.getMessage()));
 		}
 	}
 
@@ -169,28 +168,6 @@ public void downloadSamplesSpreadsheet(@PathVariable long projectId, @RequestPar
 		uiSampleService.downloadSamplesSpreadsheet(projectId, type, request, response, locale);
 	}
 
-	/**
-	 * Get a list of all {@link Sample} identifiers within a specific project
-	 *
-	 * @param id Identifier for a Project
-	 * @return {@link List} of {@link Sample} identifiers
-	 */
-	@GetMapping("/identifiers")
-	public List<Long> getSampleIdsForProject(@RequestParam Long id) {
-		return uiSampleService.getSampleIdsForProject(id);
-	}
-
-	/**
-	 * Get a list of all {@link Sample} names within a specific project
-	 *
-	 * @param id Identifier for a Project
-	 * @return {@link List} of {@link Sample} names
-	 */
-	@GetMapping("/names")
-	public List<String> getSampleNamesForProject(@RequestParam Long id) {
-		return uiSampleService.getSampleNamesForProject(id);
-	}
-
 	/**
 	 * Share / Move samples between projects
 	 *
@@ -205,8 +182,7 @@ public ResponseEntity<AjaxResponse> shareSamplesWithProject(@RequestBody ShareSa
 			uiSampleService.shareSamplesWithProject(request, locale);
 			return ResponseEntity.ok(new AjaxSuccessResponse(""));
 		} catch (UIShareSamplesException e) {
-			return ResponseEntity.status(HttpStatus.FORBIDDEN)
-					.body(new AjaxErrorResponse(e.getLocalizedMessage()));
+			return ResponseEntity.status(HttpStatus.FORBIDDEN).body(new AjaxErrorResponse(e.getLocalizedMessage()));
 		}
 	}
 
@@ -221,4 +197,18 @@ public ResponseEntity<AjaxResponse> shareSamplesWithProject(@RequestBody ShareSa
 	public SampleFilesResponse getFilesForSamples(@RequestParam List<Long> ids, @PathVariable Long projectId) {
 		return uiSampleService.getFilesForSamples(ids, projectId);
 	}
+
+	/**
+	 * Validate a list of samples names
+	 *
+	 * @param projectId project identifier
+	 * @param request   {@link ValidateSampleNamesRequest} details about the sample names to validate
+	 * @return a list of validated sample names
+	 */
+	@PostMapping("/validate")
+	public ResponseEntity<AjaxResponse> validateSampleNames(@PathVariable Long projectId,
+			@RequestBody ValidateSampleNamesRequest request) {
+		return ResponseEntity.ok(uiProjectSampleService.validateSampleNames(projectId, request));
+	}
+
 }

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/ajax/projects/dto/ValidateSampleNameModel.java

@@ -0,0 +1,32 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto;
+
+import java.util.List;
+
+/**
+ * Model for UI to represent a sample.
+ */
+public class ValidateSampleNameModel {
+	private List<Long> ids;
+	private String name;
+
+	public ValidateSampleNameModel(List<Long> ids, String name) {
+		this.ids = ids;
+		this.name = name;
+	}
+
+	public List<Long> getIds() {
+		return ids;
+	}
+
+	public void setIds(List<Long> ids) {
+		this.ids = ids;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/ajax/projects/dto/ValidateSampleNamesRequest.java

@@ -0,0 +1,30 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto;
+
+import java.util.List;
+
+/**
+ * UI request to validate sample names.
+ */
+public class ValidateSampleNamesRequest {
+	private List<ValidateSampleNameModel> samples;
+	private List<Long> associatedProjectIds;
+
+	public ValidateSampleNamesRequest() {
+	}
+
+	public List<ValidateSampleNameModel> getSamples() {
+		return samples;
+	}
+
+	public void setSamples(List<ValidateSampleNameModel> samples) {
+		this.samples = samples;
+	}
+
+	public List<Long> getAssociatedProjectIds() {
+		return associatedProjectIds;
+	}
+
+	public void setAssociatedProjectIds(List<Long> associatedProjectIds) {
+		this.associatedProjectIds = associatedProjectIds;
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/ajax/projects/dto/ValidateSampleNamesResponse.java

@@ -0,0 +1,20 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto;
+
+import java.util.List;
+
+import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse;
+
+/**
+ * Return a list of sample names.
+ */
+public class ValidateSampleNamesResponse extends AjaxResponse {
+	private List<ValidateSampleNameModel> samples;
+
+	public ValidateSampleNamesResponse(List<ValidateSampleNameModel> samples) {
+		this.samples = samples;
+	}
+
+	public List<ValidateSampleNameModel> getSamples() {
+		return samples;
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/samples/SamplesAjaxController.java

@@ -22,8 +22,6 @@
 import ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleNameCheckRequest;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleNameCheckResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService;
 import ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService;
 import ca.corefacility.bioinformatics.irida.service.SequencingObjectService;
@@ -101,7 +99,7 @@ public ResponseEntity<String> uploadSequenceFiles(@PathVariable Long sampleId, M
 	 */
 	@RequestMapping(value = "/{sampleId}/fast5/upload", method = RequestMethod.POST)
 	public ResponseEntity<String> uploadFast5Files(@PathVariable Long sampleId, MultipartHttpServletRequest request,
-												   Locale locale) {
+			Locale locale) {
 		Sample sample = sampleService.read(sampleId);
 		Iterator<String> fileNames = request.getFileNames();
 		List<MultipartFile> files = new ArrayList<>();
@@ -114,7 +112,7 @@ public ResponseEntity<String> uploadFast5Files(@PathVariable Long sampleId, Mult
 				createFast5FileInSample(file, sample);
 			}
 			return ResponseEntity.ok(messageSource.getMessage("server.SampleFileUploader.success",
-					new Object[]{sample.getSampleName()}, locale));
+					new Object[] { sample.getSampleName() }, locale));
 		} catch (IOException e) {
 			return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("");
 		}
@@ -181,17 +179,6 @@ public ResponseEntity<AjaxResponse> getFilesForSample(@PathVariable Long id,
 		return ResponseEntity.ok(uiSampleService.getSampleFiles(id, projectId));
 	}
 
-	/**
-	 * Check if a list of sample names exist within a project
-	 *
-	 * @param request {@link SampleNameCheckRequest} containing the project id and sample names
-	 * @return {@link SampleNameCheckResponse} containing list of valid and invalid sample names
-	 */
-	@PostMapping("/validate")
-	public SampleNameCheckResponse checkSampleNames(@RequestBody SampleNameCheckRequest request) {
-		return uiSampleService.checkSampleNames(request);
-	}
-
 	/**
 	 * Create {@link SequenceFile}'s then add them as {@link SequenceFilePair} to a {@link Sample}
 	 *
@@ -230,8 +217,7 @@ private void createFast5FileInSample(MultipartFile file, Sample sample) throws I
 	}
 
 	/**
-	 * Private method to move the sequence file into the correct directory and
-	 * create the {@link SequenceFile} object.
+	 * Private method to move the sequence file into the correct directory and create the {@link SequenceFile} object.
 	 *
 	 * @param file {@link MultipartFile} sequence file uploaded.
 	 * @return {@link SequenceFile}