WIP: Create samples from sequence run

src/main/java/ca/corefacility/bioinformatics/irida/repositories/ProjectRepository.java

@@ -79,6 +79,15 @@ public Page<Project> findManageableProjectsByName(final @Param("projectName") St
 	@Query("FROM Project p WHERE p.remoteStatus != NULL")
 	public List<Project> getRemoteProjects();
 
+	/**
+	 * Get a list of all {@link Project}s for a {@link User}
+	 *
+	 * @param user the user account to load projects for
+	 * @return a list of {@link Project}s
+	 */
+	@Query("FROM Project p WHERE " + PROJECT_MANAGER_PERMISSION)
+	public List<Project> getProjectsForUser(final @Param("forUser") User user);
+
 	/**
 	 * Get a count of all {@link Project}s created within time period
 	 *

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

@@ -61,6 +61,17 @@ public ResponseEntity<SampleNameValidationResponse> validateNewSampleName(@Reque
 		return uiProjectSampleService.validateNewSampleName(name, projectId, locale);
 	}
 
+	/**
+	 * Get a drop-down list of samples for a project
+	 *
+	 * @param projectId Identifier for the current project
+	 * @return a list of sample names
+	 */
+	@RequestMapping("/dropdown")
+	public ResponseEntity<AjaxResponse> getSampleNamesAndIdsForProject(@PathVariable Long projectId) {
+		return ResponseEntity.ok(uiSampleService.getSampleNamesAndIdsForProject(projectId));
+	}
+
 	/**
 	 * Create a new sample within a project
 	 *

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

@@ -0,0 +1,30 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto;
+
+/**
+ * Model for UI to represent a project list item.
+ */
+public class SampleNameListItemModel {
+	private Long id;
+	private String name;
+
+	public SampleNameListItemModel(Long id, String name) {
+		this.id = id;
+		this.name = name;
+	}
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	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/SampleNameListResponse.java

@@ -0,0 +1,22 @@
+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 samples.
+ */
+public class SampleNameListResponse extends AjaxResponse {
+
+	private List<SampleNameListItemModel> samples;
+
+	public SampleNameListResponse(List<SampleNameListItemModel> samples) {
+		this.samples = samples;
+	}
+
+	public List<SampleNameListItemModel> getSamples() {
+		return samples;
+	}
+
+}

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

@@ -37,18 +37,29 @@ public ProjectsAjaxController(UIProjectsService UIProjectsService, MessageSource
 	 * Create a new project.
 	 *
 	 * @param request {@link CreateProjectRequest} containing the name for the project and any other details
-	 * @param locale {@link Locale} for the currently logged-in user
+	 * @param locale  {@link Locale} for the currently logged-in user
 	 * @return Response will contain the created project identifier, or an error message
 	 */
 	@PostMapping("/new")
 	public AjaxResponse createNewProject(@RequestBody CreateProjectRequest request, Locale locale) {
 		try {
 			return new AjaxCreateItemSuccessResponse(projectsService.createProject(request));
 		} catch (Exception e) {
-			return new AjaxErrorResponse(messageSource.getMessage("server.CreateProject.error", new Object[]{}, locale));
+			return new AjaxErrorResponse(
+					messageSource.getMessage("server.CreateProject.error", new Object[] {}, locale));
 		}
 	}
 
+	/**
+	 * Handle request for getting a list of projects for a user
+	 *
+	 * @return {@link List} of {@link Project}s
+	 */
+	@RequestMapping("/names")
+	public ResponseEntity<AjaxResponse> getProjectNamesForUser() {
+		return ResponseEntity.ok(projectsService.getProjectNameForUser());
+	}
+
 	/**
 	 * Handle request for getting a filtered and sorted list of projects for a user or administrator
 	 *
@@ -73,13 +84,6 @@ public ResponseEntity<List<Role>> getProjectRoles(Locale locale) {
 		return ResponseEntity.ok(projectsService.getProjectRoles(locale));
 	}
 
-	/**
-	 * Get a list of projects that the user can share sample to.
-	 *
-	 * @param currentId Current project identifier
-	 * @return {@link List} of {@link Project}s
-	 */
-
 	/**
 	 * Get a list of projects that the user can share sample to.
 	 *

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

@@ -0,0 +1,30 @@
+package ca.corefacility.bioinformatics.irida.ria.web.projects.dto;
+
+/**
+ * Model for UI to represent a project list item.
+ */
+public class ProjectNameListItemModel {
+	private Long id;
+	private String name;
+
+	public ProjectNameListItemModel(Long id, String name) {
+		this.id = id;
+		this.name = name;
+	}
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+}

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

@@ -0,0 +1,22 @@
+package ca.corefacility.bioinformatics.irida.ria.web.projects.dto;
+
+import java.util.List;
+
+import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse;
+
+/**
+ * Return a list of projects.
+ */
+public class ProjectNameListResponse extends AjaxResponse {
+
+	private List<ProjectNameListItemModel> projects;
+
+	public ProjectNameListResponse(List<ProjectNameListItemModel> projects) {
+		this.projects = projects;
+	}
+
+	public List<ProjectNameListItemModel> getProjects() {
+		return projects;
+	}
+
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/sequencingRuns/SequencingRunAjaxController.java

@@ -10,10 +10,7 @@
 
 import ca.corefacility.bioinformatics.irida.model.run.SequencingRun;
 import ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableResponse;
-import ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequenceFileDetails;
-import ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunDetails;
-import ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunModel;
-import ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.SequencingRunsListRequest;
+import ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto.*;
 import ca.corefacility.bioinformatics.irida.ria.web.services.UISequencingRunService;
 
 /**
@@ -76,6 +73,17 @@ public TableResponse<SequencingRunModel> listSequencingRuns(
 		return service.listSequencingRuns(sequencingRunsListRequest, locale);
 	}
 
+	/**
+	 * Update or create new samples with sequence files
+	 *
+	 * @param request - details about the samples
+	 * @return a success message
+	 */
+	@PostMapping("/samples")
+	public ResponseEntity<String> createSamples(@RequestBody CreateSampleRequest request) {
+		return ResponseEntity.ok(service.createSamples(request));
+	}
+
 	/**
 	 * Delete a sequencing run.
 	 *

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/sequencingRuns/dto/CreateSampleRequest.java

@@ -0,0 +1,26 @@
+package ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto;
+
+import java.util.List;
+
+/**
+ * UI request to update or create new samples.
+ */
+public class CreateSampleRequest {
+
+	private List<SampleModel> samples;
+
+	public CreateSampleRequest() {
+	}
+
+	public CreateSampleRequest(List<SampleModel> samples) {
+		this.samples = samples;
+	}
+
+	public List<SampleModel> getSamples() {
+		return samples;
+	}
+
+	public void setSamples(List<SampleModel> samples) {
+		this.samples = samples;
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/sequencingRuns/dto/SampleModel.java

@@ -0,0 +1,55 @@
+package ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto;
+
+import java.util.List;
+
+/**
+ * Represents a sample on the UI sequencing run create samples page.
+ */
+public class SampleModel {
+	private Long projectId;
+	private Long sampleId;
+	private String sampleName;
+	private List<SequenceFilePairModel> pairs;
+
+	public SampleModel() {
+	}
+
+	public SampleModel(Long projectId, Long sampleId, String sampleName, List<SequenceFilePairModel> pairs) {
+		this.projectId = projectId;
+		this.sampleId = sampleId;
+		this.sampleName = sampleName;
+		this.pairs = pairs;
+	}
+
+	public Long getProjectId() {
+		return projectId;
+	}
+
+	public void setProjectId(Long projectId) {
+		this.projectId = projectId;
+	}
+
+	public Long getSampleId() {
+		return sampleId;
+	}
+
+	public void setSampleId(Long sampleId) {
+		this.sampleId = sampleId;
+	}
+
+	public String getSampleName() {
+		return sampleName;
+	}
+
+	public void setSampleName(String sampleName) {
+		this.sampleName = sampleName;
+	}
+
+	public List<SequenceFilePairModel> getPairs() {
+		return pairs;
+	}
+
+	public void setPairs(List<SequenceFilePairModel> pairs) {
+		this.pairs = pairs;
+	}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/sequencingRuns/dto/SequenceFileDetails.java

@@ -11,12 +11,17 @@
 public class SequenceFileDetails implements Comparable<SequenceFileDetails> {
 	private Long id;
 	private Long sequencingObjectId;
+	private String sequencingObjectType;
 	private String fileName;
 	private String fileSize;
 
-	public SequenceFileDetails(SequenceFile file, Long sequencingObjectId) {
+	public SequenceFileDetails() {
+	}
+
+	public SequenceFileDetails(SequenceFile file, Long sequencingObjectId, String sequencingObjectType) {
 		this.id = file.getId();
 		this.sequencingObjectId = sequencingObjectId;
+		this.sequencingObjectType = sequencingObjectType;
 		this.fileName = file.getFileName();
 		this.fileSize = file.getFileSize();
 	}
@@ -29,6 +34,10 @@ public Long getSequencingObjectId() {
 		return sequencingObjectId;
 	}
 
+	public String getSequencingObjectType() {
+		return sequencingObjectType;
+	}
+
 	public String getFileName() {
 		return fileName;
 	}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/sequencingRuns/dto/SequenceFilePairModel.java

@@ -0,0 +1,38 @@
+package ca.corefacility.bioinformatics.irida.ria.web.sequencingRuns.dto;
+
+import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile;
+
+/**
+ * Represents a {@link SequenceFile} on the UI sequencing run create samples page.
+ */
+public class SequenceFilePairModel {
+
+	private SequenceFileDetails forward;
+
+	private SequenceFileDetails reverse;
+
+	public SequenceFilePairModel() {
+	}
+
+	public SequenceFilePairModel(SequenceFileDetails forward, SequenceFileDetails reverse) {
+		this.forward = forward;
+		this.reverse = reverse;
+	}
+
+	public SequenceFileDetails getForward() {
+		return forward;
+	}
+
+	public void setForward(SequenceFileDetails forward) {
+		this.forward = forward;
+	}
+
+	public SequenceFileDetails getReverse() {
+		return reverse;
+	}
+
+	public void setReverse(SequenceFileDetails reverse) {
+		this.reverse = reverse;
+	}
+}
+