Merge pull request #1408 from phac-nml/metadata-uploader-batch-endpoints

Metadata uploader batch endpoints

doc/user/user/sample-metadata/index.md

@@ -37,23 +37,31 @@ Links to the upload page can be found:
 
 Any CSV or Excel spreadsheet containing metadata for samples in a project can be uploaded through the IRIDA web interface.  One of the column in the table __must__ correspond to the sample name within the project.  In this example spreadsheet, the `NLEP #` column is the sample name.
 
-The first step is to select the CSV or Excel file containing the data.  Either click on the square label `Click or drop Excel/CSV file containing metadata for samples in this project.` or drag and drop the file from your file browser.
+The first step is to select the CSV or Excel file containing the data.  Either click or drag the file into the drop zone from your file browser.
 
 ![Select spreadsheet](images/upload-selection.png)
 
-After uploading a spreadsheet, the column corresponding to the sample name must be selected.  After selecting the column header, press the `Preview the data` button.
+After uploading a spreadsheet, you will be brought to the `Map Columns` step.  The column corresponding to the sample name must be selected. 
 
-![Select name column.](images/upload-column.png)
+![Select name column.](images/upload-column-before.png)
 
-Rows that do not match an existing sample name are identified with the `New` tag.  If selected, these samples will automatically be created.  Rows that do match an existing sample name will be updated.  Only select the rows that are to be uploaded and press the `Upload the data` button.
+Once the sample name column is selected, a table will be displayed listing all the metadata fields.  You can review the existing and target metadata field restrictions here.  Press the `Review the data` button to continue.
+
+![Select name column.](images/upload-column-after.png)
+
+You may select the rows that are to be uploaded on the `Review Data` step. Rows that do not match an existing sample name are identified with the `New` tag.  If selected, these samples will automatically be created.  Rows that match an existing sample name will be updated.
 
 ![Preview Upload](images/upload-preview.png)
 
-Rows that have an invalid sample name will be highlighted in red.  These errors should be fixed within the spreadsheet and re-imported.
+Rows that have an invalid sample name will be highlighted in red.  These errors should be fixed within the spreadsheet and re-imported.  Press the `Upload the data` button to continue.
 
 ![Upload Preview Errors](images/upload-preview-errors.png)
 
-The complete page will be displayed on a successful upload.  Clicking on the `Upload another file` button will redirect to the beginning of a new upload.
+Progress will be displayed while uploading.  Please be patient while uploading large data sets.  Do not close the window or leave the page.
+
+![Upload Preview Errors](images/loading.png)
+
+On a successful upload, you will be brought to the `Complete` step.  Clicking on the `Upload another file` button will redirect to the beginning of a new upload.
 
 ![Upload Preview Success](images/upload-preview-success.png)
 

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/CreateSampleResponse.java

@@ -0,0 +1,25 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto;
+
+/**
+ * UI response to create a new sample
+ */
+public class CreateSampleResponse extends UpdateSampleResponse {
+	private Long sampleId;
+
+	public CreateSampleResponse(String errorMessage) {
+		super(true, errorMessage);
+	}
+
+	public CreateSampleResponse(Long sampleId) {
+		super(false);
+		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/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/dto/UpdateSampleResponse.java

@@ -0,0 +1,37 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto;
+
+/**
+ * UI response to update an existing sample
+ */
+public class UpdateSampleResponse {
+	private boolean error;
+	private String errorMessage;
+
+	public UpdateSampleResponse() {
+	}
+
+	public UpdateSampleResponse(boolean error) {
+		this.error = error;
+	}
+
+	public UpdateSampleResponse(boolean error, String errorMessage) {
+		this.error = error;
+		this.errorMessage = errorMessage;
+	}
+
+	public boolean isError() {
+		return error;
+	}
+
+	public void setError(boolean error) {
+		this.error = error;
+	}
+
+	public String getErrorMessage() {
+		return errorMessage;
+	}
+
+	public void setErrorMessage(String errorMessage) {
+		this.errorMessage = errorMessage;
+	}
+}

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

@@ -0,0 +1,19 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax;
+
+import java.util.Map;
+
+/**
+ * AJAX response to return multiple responses to the client
+ */
+public class AjaxMultipleResponse extends AjaxResponse {
+	private Map<String, Object> responses;
+
+	public AjaxMultipleResponse(Map<String, Object> responses) {
+		this.responses = responses;
+	}
+
+	public Map<String, Object> getResponses() {
+		return responses;
+	}
+}
+

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/ajax/metadata/MetadataAjaxController.java

@@ -115,8 +115,12 @@ public List<ProjectMetadataField> getMetadataFieldsForProject(@RequestParam Long
 	@PostMapping("/fields")
 	public ResponseEntity<AjaxResponse> createMetadataFieldsForProject(@RequestParam Long projectId,
 			@RequestBody List<ProjectMetadataField> fields, Locale locale) {
-		return ResponseEntity.ok(
-				new AjaxSuccessResponse(service.createMetadataFieldsForProject(projectId, fields, locale)));
+		try {
+			return ResponseEntity.ok(
+					new AjaxSuccessResponse(service.createMetadataFieldsForProject(projectId, fields, locale)));
+		} catch (Exception e) {
+			return ResponseEntity.status(HttpStatus.CONFLICT).body(new AjaxErrorResponse(e.getMessage()));
+		}
 	}
 
 	/**