Metadata uploader batch endpoints

src/main/java/ca/corefacility/bioinformatics/irida/model/sample/MetadataTemplateField.java

@@ -1,19 +1,22 @@
 package ca.corefacility.bioinformatics.irida.model.sample;
 
-import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
-import org.hibernate.envers.Audited;
-import org.springframework.data.jpa.domain.support.AuditingEntityListener;
+import java.util.List;
+import java.util.Objects;
 
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
-import java.util.List;
-import java.util.Objects;
+
+import org.hibernate.envers.Audited;
+import org.springframework.data.jpa.domain.support.AuditingEntityListener;
+
+import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
 
 /**
  * Describes an individual field in a {@link MetadataTemplate}.
  */
 @Entity
-@Table(name = "metadata_field")
+@Table(name = "metadata_field",
+		uniqueConstraints = @UniqueConstraint(columnNames = { "label" }, name = "UK_METADATA_FIELD_LABEL"))
 @Audited
 @EntityListeners(AuditingEntityListener.class)
 public class MetadataTemplateField {

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

@@ -8,7 +8,19 @@
  * UI Request to update an existing sample
  */
 public class UpdateSampleRequest extends CreateSampleRequest {
-	public UpdateSampleRequest(String name, String organism, String description, List<MetadataEntryModel> metadata) {
+	private Long sampleId;
+
+	public UpdateSampleRequest(Long sampleID, String name, String organism, String description,
+			List<MetadataEntryModel> metadata) {
 		super(name, organism, description, metadata);
+		this.sampleId = sampleID;
+	}
+
+	public Long getSampleId() {
+		return sampleId;
+	}
+
+	public void setSampleId(Long sampleId) {
+		this.sampleId = sampleId;
 	}
 }

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

@@ -14,10 +14,9 @@
 
 import ca.corefacility.bioinformatics.irida.model.sample.Sample;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.*;
-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.dto.ajax.*;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest;
+import ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIMetadataImportException;
 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;
@@ -62,31 +61,40 @@ public ResponseEntity<SampleNameValidationResponse> validateNewSampleName(@Reque
 	}
 
 	/**
-	 * Create a new sample within a project
+	 * Create new samples within a project
 	 *
-	 * @param request   Details about the sample
+	 * @param requests  Details about the samples
 	 * @param projectId current project identifier
 	 * @param locale    current users locale
-	 * @return result of creating the project
+	 * @return result of creating the samples
 	 */
 	@PostMapping("/add-sample")
-	public ResponseEntity<AjaxResponse> createSampleInProject(@RequestBody CreateSampleRequest request,
+	public ResponseEntity<AjaxResponse> createSamplesInProject(@RequestBody CreateSampleRequest[] requests,
 			@PathVariable long projectId, Locale locale) {
-		return uiProjectSampleService.createSample(request, projectId, locale);
+		try {
+			return ResponseEntity.ok(new AjaxUpdateItemSuccessResponse(
+					uiProjectSampleService.createSamples(requests, projectId, locale)));
+		} catch (UIMetadataImportException e) {
+			return ResponseEntity.status(HttpStatus.CONFLICT).body(new AjaxFormErrorResponse(e.getErrors()));
+		}
 	}
 
 	/**
-	 * Update a sample within a project
+	 * Update samples within a project
 	 *
-	 * @param request  Details about the sample
-	 * @param sampleId sample identifier
+	 * @param requests Details about the samples
 	 * @param locale   current users locale
-	 * @return result of creating the project
+	 * @return result of updating the samples
 	 */
-	@PatchMapping("/add-sample/{sampleId}")
-	public ResponseEntity<AjaxResponse> updateSampleInProject(@RequestBody UpdateSampleRequest request,
-			@PathVariable Long projectId, @PathVariable long sampleId, Locale locale) {
-		return uiProjectSampleService.updateSample(request, sampleId, locale);
+	@PatchMapping("/add-sample")
+	public ResponseEntity<AjaxResponse> updateSamplesInProject(@RequestBody UpdateSampleRequest[] requests,
+			Locale locale) {
+		try {
+			return ResponseEntity.ok(
+					new AjaxUpdateItemSuccessResponse(uiProjectSampleService.updateSamples(requests, locale)));
+		} catch (UIMetadataImportException e) {
+			return ResponseEntity.status(HttpStatus.CONFLICT).body(new AjaxFormErrorResponse(e.getErrors()));
+		}
 	}
 
 	/**

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/exceptions/UIMetadataImportException.java

@@ -0,0 +1,19 @@
+package ca.corefacility.bioinformatics.irida.ria.web.exceptions;
+
+import java.util.Map;
+
+/**
+ * Exception to be thrown by the UI when there are errors during a metadata import.
+ */
+public class UIMetadataImportException extends Exception {
+	private final Map<String, String> errors;
+
+	public UIMetadataImportException(Map<String, String> errors) {
+		super("Metadata Import Exception");
+		this.errors = errors;
+	}
+
+	public Map<String, String> getErrors() {
+		return this.errors;
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UIProjectSampleService.java

@@ -3,6 +3,8 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+import javax.validation.ConstraintViolationException;
+
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.MessageSource;
 import org.springframework.http.HttpStatus;
@@ -20,14 +22,11 @@
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.LockedSamplesResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.UpdateSampleRequest;
-import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxCreateItemSuccessResponse;
-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.AjaxUpdateItemSuccessResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.MetadataEntryModel;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNameModel;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.ValidateSampleNamesResponse;
+import ca.corefacility.bioinformatics.irida.ria.web.exceptions.UIMetadataImportException;
 import ca.corefacility.bioinformatics.irida.service.ProjectService;
 import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
 import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
@@ -123,65 +122,107 @@ public ResponseEntity<SampleNameValidationResponse> validateNewSampleName(String
 	}
 
 	/**
-	 * Create a new sample in a project
+	 * Create new samples in a project
 	 *
-	 * @param request   {@link CreateSampleRequest} details about the sample to create
+	 * @param requests  Each {@link CreateSampleRequest} contains details about the sample to create
 	 * @param projectId Identifier for the current project
 	 * @param locale    Users current locale
 	 * @return result of creating the sample
+	 * @throws UIMetadataImportException if there are errors creating the project samples
 	 */
-	@Transactional
-	public ResponseEntity<AjaxResponse> createSample(CreateSampleRequest request, Long projectId, Locale locale) {
-		try {
-			Project project = projectService.read(projectId);
-			Sample sample = new Sample(request.getName());
-			if (!Strings.isNullOrEmpty(request.getOrganism())) {
-				sample.setOrganism(request.getOrganism());
+	public String createSamples(CreateSampleRequest[] requests, Long projectId, Locale locale)
+			throws UIMetadataImportException {
+		Map<String, String> errors = new HashMap<>();
+		for (CreateSampleRequest request : requests) {
+			try {
+				createSample(projectId, request);
+			} catch (Exception e) {
+				errors.put(request.getName(), e.getMessage());
 			}
-			if (!Strings.isNullOrEmpty(request.getDescription())) {
-				sample.setDescription(request.getDescription());
-			}
-			Join<Project, Sample> join = projectService.addSampleToProjectWithoutEvent(project, sample, true);
-			if (request.getMetadata() != null) {
-				Set<MetadataEntry> metadataEntrySet = createMetadata(request.getMetadata());
-				sampleService.updateSampleMetadata(sample, metadataEntrySet);
+		}
+		if (errors.isEmpty()) {
+			return messageSource.getMessage("server.AddSample.success", null, locale);
+		} else {
+			throw new UIMetadataImportException(errors);
+		}
+	}
+
+	/**
+	 * Create a new sample in a project
+	 *
+	 * @param request   {@link CreateSampleRequest} contains details about the sample to create
+	 * @param projectId Identifier for the current project
+	 * @return result of creating the sample
+	 * @throws EntityNotFoundException if the identifier does not exist in the database
+	 */
+	@Transactional
+	public Long createSample(Long projectId, CreateSampleRequest request) throws EntityNotFoundException {
+		Project project = projectService.read(projectId);
+		Sample sample = new Sample(request.getName());
+		if (!Strings.isNullOrEmpty(request.getOrganism())) {
+			sample.setOrganism(request.getOrganism());
+		}
+		if (!Strings.isNullOrEmpty(request.getDescription())) {
+			sample.setDescription(request.getDescription());
+		}
+		Join<Project, Sample> join = projectService.addSampleToProjectWithoutEvent(project, sample, true);
+		if (request.getMetadata() != null) {
+			Set<MetadataEntry> metadataEntrySet = createMetadata(request.getMetadata());
+			sampleService.mergeSampleMetadata(sample, metadataEntrySet);
+		}
+		return join.getObject().getId();
+	}
+
+	/**
+	 * Update samples in a project
+	 *
+	 * @param requests Each {@link UpdateSampleRequest} contains details about the sample to update
+	 * @param locale   Users current locale
+	 * @return result of creating the samples
+	 * @throws UIMetadataImportException if there are errors creating the project samples
+	 */
+	public String updateSamples(UpdateSampleRequest[] requests, Locale locale) throws UIMetadataImportException {
+		Map<String, String> errors = new HashMap<>();
+		for (UpdateSampleRequest request : requests) {
+			try {
+				updateSample(request);
+			} catch (Exception e) {
+				errors.put(request.getName(), e.getMessage());
 			}
-			return ResponseEntity.ok(new AjaxCreateItemSuccessResponse(join.getObject().getId()));
-		} catch (EntityNotFoundException e) {
-			return ResponseEntity.ok(new AjaxErrorResponse(
-					messageSource.getMessage("server.AddSample.error.exists", new Object[] {}, locale)));
+		}
+		if (errors.isEmpty()) {
+			return messageSource.getMessage("server.AddSample.success", null, locale);
+		} else {
+			throw new UIMetadataImportException(errors);
 		}
 	}
 
 	/**
 	 * Update a sample in a project
 	 *
-	 * @param request  {@link UpdateSampleRequest} details about the sample to update
-	 * @param sampleId Identifier for the sample
-	 * @param locale   Users current locale
+	 * @param request {@link UpdateSampleRequest} contains details about the sample to update
 	 * @return result of creating the sample
+	 * @throws EntityNotFoundException      if the identifier does not exist in the database
+	 * @throws ConstraintViolationException if the entity being updated contains constraint violations
 	 */
 	@Transactional
-	public ResponseEntity<AjaxResponse> updateSample(UpdateSampleRequest request, Long sampleId, Locale locale) {
-		try {
-			Sample sample = sampleService.read(sampleId);
-			sample.setSampleName(request.getName());
-			if (!Strings.isNullOrEmpty(request.getOrganism())) {
-				sample.setOrganism(request.getOrganism());
-			}
-			if (request.getDescription() != null) {
-				sample.setDescription(request.getDescription());
-			}
-			if (request.getMetadata() != null) {
-				Set<MetadataEntry> metadataEntrySet = createMetadata(request.getMetadata());
-				sampleService.mergeSampleMetadata(sample, metadataEntrySet);
-			}
-			sampleService.update(sample);
-			return ResponseEntity.ok(new AjaxUpdateItemSuccessResponse(
-					messageSource.getMessage("server.AddSample.success", null, locale)));
-		} catch (Exception e) {
-			return ResponseEntity.status(HttpStatus.CONFLICT).body(new AjaxErrorResponse(e.getMessage()));
+	public Sample updateSample(UpdateSampleRequest request)
+			throws EntityNotFoundException, ConstraintViolationException {
+		Long sampleId = request.getSampleId();
+		Sample sample = sampleService.read(sampleId);
+		sample.setSampleName(request.getName());
+		if (!Strings.isNullOrEmpty(request.getOrganism())) {
+			sample.setOrganism(request.getOrganism());
+		}
+		if (request.getDescription() != null) {
+			sample.setDescription(request.getDescription());
 		}
+		if (request.getMetadata() != null) {
+			Set<MetadataEntry> metadataEntrySet = createMetadata(request.getMetadata());
+			sampleService.updateSampleMetadata(sample, metadataEntrySet);
+		}
+		return sampleService.update(sample);
+
 	}
 
 	/**

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/unreleased/all-changes.xml

@@ -1,4 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <databaseChangeLog xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
-         http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd"></databaseChangeLog>
+         http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
+    <include file="metadata-field-add-label-constraint.xml" relativeToChangelogFile="true" />
+</databaseChangeLog>

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/unreleased/metadata-field-add-label-constraint.xml

@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+         http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.3.xsd">
+    <changeSet id="metadata-field-add-label-constraint" author="katherine">
+        <addUniqueConstraint columnNames="label" tableName="metadata_field" constraintName="UK_METADATA_FIELD_LABEL" />
+    </changeSet>
+</databaseChangeLog>

src/main/webapp/resources/js/apis/projects/samples.ts

@@ -129,29 +129,24 @@ export async function getLockedSamples({
   return response.data;
 }
 
-export async function createSample({
+export async function createSamples({
   projectId,
   body,
 }: {
   projectId: string;
-  body: SampleRequest;
+  body: SampleRequest[];
 }) {
   return await axios.post(`${URL}/${projectId}/samples/add-sample`, body);
 }
 
-export async function updateSample({
+export async function updateSamples({
   projectId,
-  sampleId,
   body,
 }: {
   projectId: string;
-  sampleId: number;
-  body: SampleRequest;
+  body: SampleRequest[];
 }) {
-  return await axios.patch(
-    `${URL}/${projectId}/samples/add-sample/${sampleId}`,
-    body
-  );
+  return await axios.patch(`${URL}/${projectId}/samples/add-sample`, body);
 }
 
 /**
@@ -168,25 +163,6 @@ export async function validateSampleName(name: string) {
   return response.json();
 }
 
-/**
- * Create a new sample within a project
- * @param name - name of the new sample
- * @param organism - name of the organism (optional)
- * @returns {Promise<Response>}
- */
-export async function createNewSample({
-  name,
-  organism,
-}: {
-  name: string;
-  organism: string;
-}) {
-  return post(`${URL}/${PROJECT_ID}/samples/add-sample`, {
-    name: name.trim(),
-    organism,
-  });
-}
-
 /**
  * Share or move samples with another project.
  * @param currentId - current projectId