Metadata uploader base

CHANGELOG.md

@@ -10,6 +10,7 @@
 * [UI/Developer]: Removed old notification system hack and updated to use only Ant Design notifications. See [PR 1447](https://github.com/phac-nml/irida/pull/1447)
 * [UI]: Fixed bug where the `User` column was named `User Group` on the admin User Groups page. [See PR 1450](https://github.com/phac-nml/irida/pull/1450)
 * [Developer]: Replaced Apache OLTU with Nimbusds for performing OAuth2 authentication flow during syncing and Galaxy exporting. See [PR 1432](https://github.com/phac-nml/irida/pull/1432)
+* [Developer/UI]: Performance enhancements to the metadata uploader. See [PR 1445](https://github.com/phac-nml/irida/pull/1445).
 
 ## [22.09.7] - 2022/01/24
 * [UI]: Fixed bugs on NCBI Export page preventing the NCBI `submission.xml` file from being properly written. See [PR 1451](https://github.com/phac-nml/irida/pull/1451)

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.  Click 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.  Click 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/CreateSampleRequest.java

@@ -2,14 +2,16 @@
 
 import java.util.List;
 
+import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.MetadataEntryModel;
+
 /**
  * UI Request to create a new sample
  */
 public class CreateSampleRequest {
 	private String name;
 	private String organism;
 	private String description;
-	private List<FieldUpdate> metadata;
+	private List<MetadataEntryModel> metadata;
 
 	public CreateSampleRequest() {
 	}
@@ -19,7 +21,7 @@ public CreateSampleRequest(String name, String organism) {
 		this.organism = organism;
 	}
 
-	public CreateSampleRequest(String name, String organism, String description, List<FieldUpdate> metadata) {
+	public CreateSampleRequest(String name, String organism, String description, List<MetadataEntryModel> metadata) {
 		this.name = name;
 		this.organism = organism;
 		this.description = description;
@@ -50,11 +52,11 @@ public void setDescription(String description) {
 		this.description = description;
 	}
 
-	public List<FieldUpdate> getMetadata() {
+	public List<MetadataEntryModel> getMetadata() {
 		return metadata;
 	}
 
-	public void setMetadata(List<FieldUpdate> metadata) {
+	public void setMetadata(List<MetadataEntryModel> metadata) {
 		this.metadata = metadata;
 	}
 }

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

@@ -0,0 +1,21 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto;
+
+import java.util.List;
+
+import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse;
+
+/**
+ * Returns an ajax response with locked sample ids.
+ */
+public class LockedSamplesResponse extends AjaxResponse {
+	private List<Long> sampleIds;
+
+	public LockedSamplesResponse(List<Long> sampleIds) {
+		this.sampleIds = sampleIds;
+	}
+
+	public List<Long> getSampleIds() {
+		return sampleIds;
+	}
+}
+

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

@@ -0,0 +1,37 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto;
+
+/**
+ * UI response to create/update a sample with error
+ */
+public class SampleErrorResponse {
+	private boolean error;
+	private String errorMessage;
+
+	public SampleErrorResponse() {
+	}
+
+	public SampleErrorResponse(boolean error) {
+		this.error = error;
+	}
+
+	public SampleErrorResponse(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/SampleResponse.java

@@ -0,0 +1,25 @@
+package ca.corefacility.bioinformatics.irida.ria.web.ajax.dto;
+
+/**
+ * UI response to create/update a sample with error and sample id
+ */
+public class SampleResponse extends SampleErrorResponse {
+	private Long sampleId;
+
+	public SampleResponse(String errorMessage) {
+		super(true, errorMessage);
+	}
+
+	public SampleResponse(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

@@ -2,11 +2,25 @@
 
 import java.util.List;
 
+import ca.corefacility.bioinformatics.irida.ria.web.ajax.projects.dto.MetadataEntryModel;
+
 /**
  * UI Request to update an existing sample
  */
 public class UpdateSampleRequest extends CreateSampleRequest {
-	public UpdateSampleRequest(String name, String organism, String description, List<FieldUpdate> 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;
 	}
 }