Metadata uploader - PARSE FILE

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

@@ -140,7 +140,7 @@ public ResponseEntity<AjaxResponse> createSample(CreateSampleRequest request, Lo
 			if (!Strings.isNullOrEmpty(request.getDescription())) {
 				sample.setDescription(request.getDescription());
 			}
-			Join<Project, Sample> join = projectService.addSampleToProject(project, sample, true);
+			Join<Project, Sample> join = projectService.addSampleToProjectWithoutEvent(project, sample, true);
 			if (request.getMetadata() != null) {
 				Set<MetadataEntry> metadataEntrySet = request.getMetadata().stream().map(entry -> {
 					MetadataTemplateField field = metadataTemplateService.saveMetadataField(
@@ -169,8 +169,12 @@ public ResponseEntity<AjaxResponse> updateSample(UpdateSampleRequest request, Lo
 		try {
 			Sample sample = sampleService.read(sampleId);
 			sample.setSampleName(request.getName());
-			sample.setOrganism(request.getOrganism());
-			sample.setDescription(request.getDescription());
+			if (!Strings.isNullOrEmpty(request.getOrganism())) {
+				sample.setOrganism(request.getOrganism());
+			}
+			if (request.getDescription() != null) {
+				sample.setDescription(request.getDescription());
+			}
 			if (request.getMetadata() != null) {
 				Set<MetadataEntry> metadataEntrySet = request.getMetadata().stream().map(entry -> {
 					MetadataTemplateField field = metadataTemplateService.saveMetadataField(

src/main/java/ca/corefacility/bioinformatics/irida/service/ProjectService.java

@@ -137,6 +137,17 @@ public Join<Project, UserGroup> updateUserGroupProjectMetadataRole(Project proje
 	 */
 	public Join<Project, Sample> addSampleToProject(Project project, Sample sample, boolean owner);
 
+	/**
+	 * Add the specified {@link Sample} to the {@link Project} without creating an event.
+	 *
+	 * @param project the {@link Project} to add the {@link Sample} to.
+	 * @param sample  the {@link Sample} to add to the {@link Project}. If the {@link Sample} has not previously been
+	 *                persisted, the service will persist the {@link Sample}.
+	 * @param owner   Whether the project will have modification access for this sample
+	 * @return a reference to the relationship resource created between the two entities.
+	 */
+	public Join<Project, Sample> addSampleToProjectWithoutEvent(Project project, Sample sample, boolean owner);
+
 	/**
 	 * Move a {@link Sample} from one {@link Project} to another
 	 *

src/main/java/ca/corefacility/bioinformatics/irida/service/impl/ProjectServiceImpl.java

@@ -23,7 +23,6 @@
 import org.springframework.security.access.prepost.PostFilter;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.security.core.userdetails.UserDetails;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.util.StringUtils;
@@ -411,8 +410,9 @@ public ProjectSampleJoin addSampleToProject(Project project, Sample sample, bool
 		// Check to ensure a sample with this sample name doesn't exist in this
 		// project already
 		if (sampleRepository.getSampleBySampleName(project, sample.getSampleName()) != null) {
-			throw new ExistingSampleNameException("Sample with the name '" + sample.getSampleName()
-					+ "' already exists in project " + project.getId(), sample);
+			throw new ExistingSampleNameException(
+					"Sample with the name '" + sample.getSampleName() + "' already exists in project "
+							+ project.getId(), sample);
 		}
 
 		// the sample hasn't been persisted before, persist it before calling
@@ -438,13 +438,24 @@ public ProjectSampleJoin addSampleToProject(Project project, Sample sample, bool
 		}
 	}
 
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	@Transactional
+	@PreAuthorize("hasAnyRole('ROLE_ADMIN', 'ROLE_SEQUENCER') or (hasPermission(#project, 'isProjectOwner'))")
+	public ProjectSampleJoin addSampleToProjectWithoutEvent(Project project, Sample sample, boolean owner) {
+		return addSampleToProject(project, sample, owner);
+	}
+
 	/**
 	 * {@inheritDoc}
 	 */
 	@Override
 	@Transactional
 	@LaunchesProjectEvent(SampleAddedProjectEvent.class)
-	@PreAuthorize("hasRole('ROLE_ADMIN') or ( hasPermission(#source, 'isProjectOwner') and hasPermission(#destination, 'isProjectOwner'))")
+	@PreAuthorize(
+			"hasRole('ROLE_ADMIN') or ( hasPermission(#source, 'isProjectOwner') and hasPermission(#destination, 'isProjectOwner'))")
 	public ProjectSampleJoin moveSampleBetweenProjects(Project source, Project destination, Sample sample) {
 		//read the existing ProjectSampleJoin to see if we're the owner
 		ProjectSampleJoin projectSampleJoin = psjRepository.readSampleForProject(source, sample);
@@ -608,15 +619,16 @@ public Collection<UserGroupProjectJoin> getUserGroupProjectJoins(User user, Proj
 	 * {@inheritDoc}
 	 */
 	@Override
-	@PreAuthorize("hasRole('ROLE_ADMIN') or hasPermission(#subject,'isProjectOwner') and hasPermission(#relatedProject,'canReadProject')")
+	@PreAuthorize(
+			"hasRole('ROLE_ADMIN') or hasPermission(#subject,'isProjectOwner') and hasPermission(#relatedProject,'canReadProject')")
 	public RelatedProjectJoin addRelatedProject(Project subject, Project relatedProject) {
 		if (subject.equals(relatedProject)) {
 			throw new IllegalArgumentException("Project cannot be related to itself");
 		}
 
 		try {
-			RelatedProjectJoin relation = relatedProjectRepository
-					.save(new RelatedProjectJoin(subject, relatedProject));
+			RelatedProjectJoin relation = relatedProjectRepository.save(
+					new RelatedProjectJoin(subject, relatedProject));
 			return relation;
 		} catch (DataIntegrityViolationException e) {
 			throw new EntityExistsException(
@@ -692,8 +704,8 @@ public Join<Project, ReferenceFile> addReferenceFileToProject(Project project, R
 	@Override
 	@PreAuthorize("hasRole('ROLE_ADMIN') or hasPermission(#project, 'isProjectOwner')")
 	public void removeReferenceFileFromProject(Project project, ReferenceFile file) {
-		List<Join<Project, ReferenceFile>> referenceFilesForProject = prfjRepository
-				.findReferenceFilesForProject(project);
+		List<Join<Project, ReferenceFile>> referenceFilesForProject = prfjRepository.findReferenceFilesForProject(
+				project);
 		Join<Project, ReferenceFile> specificJoin = null;
 		for (Join<Project, ReferenceFile> join : referenceFilesForProject) {
 			if (join.getObject().equals(file)) {
@@ -704,8 +716,9 @@ public void removeReferenceFileFromProject(Project project, ReferenceFile file)
 		if (specificJoin != null) {
 			prfjRepository.delete((ProjectReferenceFileJoin) specificJoin);
 		} else {
-			throw new EntityNotFoundException("Cannot find a join for project [" + project.getName()
-					+ "] and reference file [" + file.getLabel() + "].");
+			throw new EntityNotFoundException(
+					"Cannot find a join for project [" + project.getName() + "] and reference file [" + file.getLabel()
+							+ "].");
 		}
 	}
 
@@ -849,8 +862,8 @@ public Project createProjectWithSamples(Project project, List<Long> sampleIds, b
 	@PostFilter("hasPermission(filterObject, 'canReadProject')")
 	@Override
 	public List<Project> getProjectsUsedInAnalysisSubmission(AnalysisSubmission submission) {
-		Set<SequencingObject> findSequencingObjectsForAnalysisSubmission = sequencingObjectRepository
-				.findSequencingObjectsForAnalysisSubmission(submission);
+		Set<SequencingObject> findSequencingObjectsForAnalysisSubmission = sequencingObjectRepository.findSequencingObjectsForAnalysisSubmission(
+				submission);
 
 		// get available projects
 		Set<Project> projectsInAnalysis = getProjectsForSequencingObjects(findSequencingObjectsForAnalysisSubmission);
@@ -891,7 +904,7 @@ private static final Sort getOrDefaultSort(Sort sort) {
 	 * @param projectRole The {@link ProjectRole} to search for.
 	 * @param user        The user to search
 	 * @return a {@link Specification} to search for {@link Project} where the specified {@link User} has a certain
-	 *         {@link ProjectRole}.
+	 * {@link ProjectRole}.
 	 */
 	private static final Specification<ProjectUserJoin> getProjectJoinsWithRole(User user, ProjectRole projectRole) {
 		return new Specification<ProjectUserJoin>() {

src/main/webapp/resources/js/apis/metadata/sample-utils.ts

@@ -0,0 +1,18 @@
+/*
+ * Utility file for samples
+ */
+
+export const sampleNameRegex = new RegExp("^[A-Za-z0-9-_]{3,}$");
+
+/**
+ * Checks is the sample name is valid
+ * @param sampleName the name of the sample
+ * @returns if the sample name is valid
+ */
+export function validateSampleName(sampleName: string): boolean {
+  if (sampleName) {
+    return sampleNameRegex.test(sampleName);
+  } else {
+    return false;
+  }
+}

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

@@ -5,12 +5,44 @@ import {
 } from "../../types/irida";
 import { getProjectIdFromUrl, setBaseUrl } from "../../utilities/url-utilities";
 import { get, post } from "../requests";
+import axios from "axios";
 
 export interface SequencingFiles {
   singles: SingleEndSequenceFile[];
   pairs: PairedEndSequenceFile[];
 }
 
+export interface ValidateSampleNameModel {
+  ids?: number[];
+  name: string;
+}
+
+export interface ValidateSamplesResponse {
+  samples: ValidateSampleNameModel[];
+}
+
+export interface MetadataItem {
+  [field: string]: string;
+  rowKey: string;
+}
+
+export interface FieldUpdate {
+  field: string;
+  value: string;
+}
+
+export interface SampleRequest {
+  name: string;
+  organism?: string;
+  description?: string;
+  metadata: FieldUpdate[];
+}
+
+export interface ValidateSampleNamesRequest {
+  samples: ValidateSampleNameModel[];
+  associatedProjectIds?: number[];
+}
+
 const PROJECT_ID = getProjectIdFromUrl();
 const URL = setBaseUrl(`/ajax/projects`);
 
@@ -70,6 +102,45 @@ export const {
   useShareSamplesWithProjectMutation,
 } = samplesApi;
 
+export async function validateSamples({
+  projectId,
+  body,
+}: {
+  projectId: string;
+  body: ValidateSampleNamesRequest;
+}): Promise<ValidateSamplesResponse> {
+  const response = await axios.post(
+    `${URL}/${projectId}/samples/validate`,
+    body
+  );
+  return response.data;
+}
+
+export async function createSample({
+  projectId,
+  body,
+}: {
+  projectId: string;
+  body: SampleRequest;
+}) {
+  return await axios.post(`${URL}/${projectId}/samples/add-sample`, body);
+}
+
+export async function updateSample({
+  projectId,
+  sampleId,
+  body,
+}: {
+  projectId: string;
+  sampleId: number;
+  body: SampleRequest;
+}) {
+  return await axios.patch(
+    `${URL}/${projectId}/samples/add-sample/${sampleId}`,
+    body
+  );
+}
+
 /**
  * Server side validation of a new sample name.
  * @param name - sample name to validate

src/main/webapp/resources/js/components/ant.design/forms/BlockRadioInput.jsx → src/main/webapp/resources/js/components/ant.design/forms/BlockRadioInput.tsx

@@ -19,6 +19,11 @@ const RadioItem = styled.button`
   }
 `;
 
+interface BlockRadioInputProps
+  extends React.ButtonHTMLAttributes<HTMLButtonElement> {
+  children?: React.ReactNode;
+}
+
 /**
  * React component to Render a Ant Design Radio button in block.
  *
@@ -27,6 +32,9 @@ const RadioItem = styled.button`
  * @returns {JSX.Element}
  * @constructor
  */
-export function BlockRadioInput({ children, ...props }) {
+export function BlockRadioInput({
+  children,
+  ...props
+}: BlockRadioInputProps): JSX.Element {
   return <RadioItem {...props}>{children}</RadioItem>;
 }