Sample details refactor

CHANGELOG.md

@@ -27,6 +27,7 @@
 * [Developer]: Fix issue where large downloads silent failed due to async request timeout. See [PR 1368](https://github.com/phac-nml/irida/pull/1368)
 * [Developer]: Update to Spring Boot 2.7.3 and update various other dependencies. See [PR 1369](https://github.com/phac-nml/irida/pull/1369)
 * [Developer]: Fixed issue with disabled user accounts requesting a password reset. See [PR 1373](https://github.com/phac-nml/irida/pull/1373)
+* [Developer/UI]: Updated sample details view to use Ant Design and moved into a modal which can be launched from anywhere the sample name is listed. See [PR 1370](https://github.com/phac-nml/irida/pull/1370)
 
 ## [22.05.5] - 2022/06/28
 * [UI]: Fixed bug preventing export of project samples table due to invalid url. [PR 1331](https://github.com/phac-nml/irida/pull/1331)

doc/_includes/tutorials/common/samples/download-sequence-file.md

@@ -1 +1 @@
-You can download a sequence file by clicking on the <span class="fa fa-fw fa-download"></span> icon, on the right-hand side of the row for the sequence file.
+You can download a sequence file by clicking on the **Download** button, on the right-hand side of the row for the sequence file.

doc/_includes/tutorials/common/samples/view-individual-sample.md

@@ -2,6 +2,6 @@ To view details about an individual sample, start by [viewing the samples in a p
 
 ![Sample name button.]({{ site.baseurl }}/images/tutorials/common/samples/sample-name-button.png)
 
-The sample details page shows all of the details that are currently known about a sample:
+The sample details viewer shows all of the details that are currently known about a sample:
 
-![Sample details page.]({{ site.baseurl }}/images/tutorials/common/samples/sample-details.png)
+![Sample details viewer.]({{ site.baseurl }}/images/tutorials/common/samples/sample-detail-viewer.png)

doc/_includes/tutorials/common/samples/view-sequence-files.md

@@ -1,6 +1,6 @@
 Start by [viewing the details of an individual sample]({{ site.baseurl }}/user/user/samples/#viewing-individual-sample-details). On the sample details page, click on the "Files" tab, just above the sample details panel:
 
-![Sample details file tab.]({{ site.baseurl }}/images/tutorials/common/samples/sample-details-file-tab.png)
+![Sample details file tab.]({{ site.baseurl }}/images/tutorials/common/samples/sample-detail-viewer-files-tab.png)
 
 Sequence files may have been uploaded as paired-end files or as single-end files, depending on how the isolate was sequenced.
 

doc/_includes/tutorials/common/uploading-sample-files.md

@@ -1,16 +1,14 @@
 ### Sequence Files & Assemblies
 
-Sequence files can be uploaded by hovering over the "Upload Files" above the sequence file table, and selecting the button for the appropriate file type.
+Sequence files can be uploaded by either dragging and dropping the files into the upload section, or by clicking the section and selecting the files. Sequence, fast5, and assembly files can be uploaded at the same time.
 
-![Upload sequence file.]({{ site.baseurl }}/images/tutorials/common/samples/upload-sample-file-btn.png)
+![Upload sequence file.]({{ site.baseurl }}/images/tutorials/common/samples/sample-detail-viewer-files-upload-btn.png)
 
 * **Upload Sequence Files** - Files must have the extension `.fastq` or `.fastq.gz`, all other formats will be ignored.  You can select single or multiple files in the system file selection window.  If you are uploading paired end data, ensure they are selected in the same upload.
 * **Upload Fast5 Files**  - Files must have the extension `.fast5` or `.fast5.tar.gz`.
 
 * **Upload Assembly** - Assembly files must have the extension `.fasta` or `.fna`.
 
-Files will upload will begin immediately.  A notification will open in the bottom right corner of the screen displaying the status of the upload.  If you need to cancel an upload click the <img class="inline" src="{{ site.baseurl }}/images/tutorials/common/samples/upload-sample-cancel-btn.png" alt="Cancel Upload Button" /> button.  **Do not leave or refresh the page as this will cancel the upload**, a warning will be display if you attempt to do this.
-
-![Cancel upload]({{ site.baseurl }}/images/tutorials/common/samples/upload-sample-progress-cancel.png)
-
+Uploading of files will begin immediately. A progress bar for each of the file types (sequence, assembly, and fast5 files) will be displayed with the status of the upload. Also, expandable panels for each of the file types will be displayed below each progress bar which can be expanded to show the files that are uploading.  If you need to cancel an upload click the **Cancel Upload** button.  **Do not close the sample details viewer or refresh the page as this will cancel the upload**.
 
+![Cancel upload]({{ site.baseurl }}/images/tutorials/common/samples/sample-detail-viewer-upload-cancel-btn.png)

doc/developer/interface/index.md

@@ -155,7 +155,7 @@ Example:
     <script id="cart-translations" th:inline="javascript" th:fragment="i18n">
         window.translations = window.translations || [];
         window.translations.unshift({
-            "SampleDetailsSidebar.removeFromCart": /*[[#{SampleDetailsSidebar.removeFromCart}]]*/ "",
+            "SampleDetailsViewer.removeFromCart": /*[[#{SampleDetailsViewer.removeFromCart}]]*/ "",
             "SampleDetails.metadata": /*[[#{SampleDetails.metadata}]]*/ "",
             "SampleDetails.files": /*[[#{SampleDetails.files}]]*/ "",
             "SampleFiles.singles": /*[[#{SampleFiles.singles}]]*/ "",
@@ -188,7 +188,7 @@ Example:
     <script id="cart-translations">
         window.translations = window.translations || [];
         window.translations.unshift({
-            "SampleDetailsSidebar.removeFromCart": "Remove From Cart",
+            "SampleDetailsViewer.removeFromCart": "Remove From Cart",
             "SampleDetails.metadata": "Metadata",
             "SampleDetails.files": "Files",
             "SampleFiles.singles": "Single End Data",

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

@@ -145,6 +145,12 @@ Metadata Fields have:
 * **Type**: Indicates the type of data that the field can be.  Usually this will be just "text".
 * **Restrictions**: Indicates the metadata role required to view that field and any fields with levels below this restriction level.
 
+#### Individual Sample Metadata
+
+You can view the metadata for a sample from the **Metadata** tab of the sample details viewer which can be launched from anywhere the sample is listed by clicking the sample name. Only a user with a project **Manager** role can add/edit sample metadata.
+
+![Sample metadata](images/sample-detail-viewer-metadata.png)
+
 #### Metadata Field Security
 
 Metadata Fields can be restricted at the project level by metadata role. There are 4 restriction levels which can be applied to a field (Level 1, Level 2, Level 3, Level 4 (with Level 4 being the highest restriction level and Level 1 the lowest)). A project **Manager** has a default metadata role of `Level 4` and can view all the project sample metadata. A **Collaborator** can have any of the metadata roles applied to them and will only be able to view fields with their metadata role and lower.

doc/user/user/samples/index.md

@@ -31,21 +31,25 @@ The samples listing shows high-level sample details, such as:
 
 ### Viewing individual sample details
 
+**Note: Details for individual samples can be viewed from anywhere a sample is listed (such as from the recent activity, analysis results, analysis output files, sharing of samples, etc) by clicking on the sample name. This will launch the sample details viewer. Only a user with the project Manager role will be able to modify sample details, metadata, and files.**
+
+![Sample details page.]({{ site.baseurl }}/images/tutorials/common/samples/sample-detail-viewer.png)
+
 All of the sample details that are in IRIDA are currently provided by a user with the project **Manager** role. To view details about an individual sample, start by [viewing the samples in a project](#viewing-samples-in-a-project), then click on the sample name in the samples table:
 
 ![Sample name button.]({{ site.baseurl }}/images/tutorials/common/samples/sample-name-button.png)
 
-The sample details page shows all of the details that are currently known about a sample:
+The sample details viewer shows all of the details that are currently known about a sample:
 
-![Sample details page.]({{ site.baseurl }}/images/tutorials/common/samples/sample-details.png)
+![Sample details page.]({{ site.baseurl }}/images/tutorials/common/samples/sample-detail-viewer.png)
 
 ### Editing sample details
 
-Start by [viewing the details of an individual sample](#viewing-individual-sample-details). On the samples details page, click on the "Edit" button in the top, right-hand corner:
+Start by [viewing the details of an individual sample](#viewing-individual-sample-details). On the **Details** tab of the sample details viewer, click on the <img src="images/sample-details-edit-btn.png" alt="Edit icon" class="inline"> button next to the details you would like to update:
 
 ![Sample details edit button.](images/sample-details-edit.png)
 
-You can provide as many or as few sample details that you want -- the sample details are not used by any workflows in IRIDA (except the sample name in the SNVPhyl workflow), and (with the exception of the sample name) none of the sample details are required fields. When you've finished updating the sample details, you can click on the "Update" button at the bottom, right-hand side of the page.
+You can provide as many or as few sample details that you want -- the sample details are not used by any workflows in IRIDA (except the sample name in the SNVPhyl workflow), and (with the exception of the sample name) none of the sample details are required fields.
 
 ### Viewing contained files
 
@@ -73,40 +77,43 @@ You can download all sequence files in a sample by following the instructions in
 
 #### Deleting a sequence file
 
-If you need to delete a sequence file from IRIDA, you can do so by clicking on the <img src="images/delete-icon.png" alt="Delete icon" class="inline"> icon, on the right-hand side of the row for the sequence file.
+If you need to delete a sequence file from IRIDA, you can do so by clicking on the <img src="images/ellipsis-menu.png" class="inline" alt="Ellipsis menu icon."> button on the right-hand side of the row for the sequencing object/genome assembly and then clicking **Remove**.
 
 You can only delete a sequence file from a sample if you have the project <img src="images/manager-icon.png" class="inline" alt="Manager role icon."> **Manager** role on the project.
 
 #### Concatenating sequence files
 
-In cases where a top-up run or any other additional data is added to a sample, you may want to combine the sequence files into a single *concatenated* file.  IRIDA allows you to do this under the *Concatenate Files* page.
+In cases where a top-up run or any other additional data is added to a sample, you may want to combine the sequence files into a single *concatenated* file.  IRIDA allows you to do this from the files tab of the sample details viewer.
+You must select 2 or more sequence file objects **of the same type** to concatenate.  If you have selected a collection of files which cannot be concatenated, a warning will be displayed once the **Concatenate** button is clicked.
 
-![Concatenate link]({{ site.baseurl }}/images/tutorials/common/samples/concatenate-link.png)
+![Concatenate link]({{ site.baseurl }}/images/tutorials/common/samples/sequence-file-concatenate.png)
 
-In the concatenation page you must select 2 or more sequence file objects **of the same type** to concatenate.  If you have selected a collection of files which cannot be concatenated, a warning will be displayed.
+If two different types of collections are selected then you will see the following warning in the upper right corner:
 
-![Concatenate page]({{ site.baseurl }}/images/tutorials/common/samples/concatenate-page.png)
+![Concatenate warning]({{ site.baseurl }}/images/tutorials/common/samples/sequence-file-concatenate-warning.png)
 
-Once you have selected your files to concatenate, you have the following options:
+Once you have selected your files (same type of collections) to concatenate, and clicked the **Concatenate** button, a modal is displayed. The modal will display the files you have selected to concatenate. You have the following options:
 
-* *New filename* - This will set the base name of the new concatenated files.  For paired-end data a modifier will be appended to determine the forward and reverse files.
-* *Remove originals* - This will remove the original files from the sample, leaving only the new concatenated file.
+* *New File Name* - This will set the base name of the new concatenated files.  For paired-end data a modifier will be appended to determine the forward and reverse files.
+* *Keep Originals / Remove originals* - This will allow you to select if you want to remove or keep the original files from the sample, leaving only the new concatenated file if remove originals is selected.
 
-Once you have selected your files and selected your options, click *Submit* to begin the concatenation.  This may take a while, so you should stay on this page until the process is complete.  Once your files are concatenated, you will be redirected back to the sample-files page.
+Once you have provided a file name and selected if you want to keep/remove the original files, click *Concatenate* to begin the concatenation.  This process may take a while. Once your files are concatenated, they will be listed in the files tab of the sample details viewer.
+
+![Concatenate page]({{ site.baseurl }}/images/tutorials/common/samples/sequence-file-concatenate-modal.png)
 
 #### Viewing genome assemblies
 
 Samples can also contain assembled genomes.
 
-![sample-automated-assembly](images/sample-automated-assembly.png)
+![sample-automated-assembly](images/sample-contained-files.png)
 
 Genome assemblies can be linked to samples in the following ways:
 
 1. By uploading assemblies to the sample through the [file upload interface](#sequence-files--assemblies)
 2. By enabling the assembly pipeline as an [automated pipeline](../project/#automated-pipelines), which will be triggered on upload of sequencing files in the appropriate project.
 3. Or by selecting the option to save assemblies back to a sample from the [Launch Pipelines](../pipelines/#saving-pipeline-results-to-a-sample) page.
 
-The assembled genome file can be downloaded by clicking the <span class="fa fa-fw fa-download"></span> icon.
+The assembled genome file can be downloaded by clicking the **Download** button on the right-hand side of the row for the assembly.
 
 If the project manager has enabled automated assemblies for uploaded data an assembly will also be shown associated with the particular sequence files used to generate the assembled genome.
 
@@ -118,9 +125,7 @@ See the [project documentation](../project#automated-pipelines) for information
 
 #### Deleting genome assemblies
 
-Assembled genomes may be deleted from a sample by selecting the <img src="images/delete-icon.png" alt="Delete icon" class="inline"> icon.
-
-![delete-sample-assembly](images/delete-sample-assembly.png)
+Assembled genomes may be deleted from a sample by clicking the <img src="images/ellipsis-menu.png" class="inline" alt="Ellipsis menu icon."> button on the right-hand side of the row for the assembly and then selecting **Remove**.
 
 Adding a new sample
 -------------------

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

@@ -18,12 +18,14 @@
 
 import ca.corefacility.bioinformatics.irida.model.IridaRepresentationModel;
 import ca.corefacility.bioinformatics.irida.model.MutableIridaThing;
+import ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly;
 import ca.corefacility.bioinformatics.irida.model.event.SampleAddedProjectEvent;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin;
 import ca.corefacility.bioinformatics.irida.model.remote.RemoteStatus;
 import ca.corefacility.bioinformatics.irida.model.remote.RemoteSynchronizable;
 import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
+import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
 import ca.corefacility.bioinformatics.irida.validators.annotations.Latitude;
 import ca.corefacility.bioinformatics.irida.validators.annotations.Longitude;
 import ca.corefacility.bioinformatics.irida.validators.annotations.ValidSampleName;
@@ -144,6 +146,14 @@ public class Sample extends IridaRepresentationModel
 	@Longitude
 	private String longitude;
 
+	@OneToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+	@JoinColumn(name = "default_sequencing_object")
+	private SequencingObject defaultSequencingObject;
+
+	@OneToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL)
+	@JoinColumn(name = "default_genome_assembly")
+	private GenomeAssembly defaultGenomeAssembly;
+
 	@OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.REMOVE, mappedBy = "sample")
 	private List<ProjectSampleJoin> projects;
 
@@ -346,4 +356,18 @@ public RemoteStatus getRemoteStatus() {
 	public void setRemoteStatus(RemoteStatus status) {
 		this.remoteStatus = status;
 	}
+
+	public SequencingObject getDefaultSequencingObject() {
+		return defaultSequencingObject;
+	}
+
+	public void setDefaultSequencingObject(SequencingObject sequencingObject) {
+		this.defaultSequencingObject = sequencingObject;
+	}
+
+	public GenomeAssembly getDefaultGenomeAssembly() { return defaultGenomeAssembly; }
+
+	public void setDefaultGenomeAssembly(GenomeAssembly genomeAssembly) {
+		this.defaultGenomeAssembly = genomeAssembly;
+	}
 }

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/analysis/ProjectSampleAnalysisOutputInfo.java

@@ -27,13 +27,14 @@ public class ProjectSampleAnalysisOutputInfo {
 	private String userFirstName;
 	private String userLastName;
 	private IridaWorkflowDescription workflowDescription;
+	private Long projectId;
 
 	public ProjectSampleAnalysisOutputInfo() {}
 
 	public ProjectSampleAnalysisOutputInfo(Long sampleId, String sampleName, Long analysisId,
 			String analysisOutputFileKey, String filePath, Long analysisOutputFileId, AnalysisType analysisType,
 			UUID workflowId, Date createdDate, String analysisSubmissionName, Long analysisSubmissionId, Long userId,
-			String userFirstName, String userLastName) {
+			String userFirstName, String userLastName, Long projectId) {
 		this.sampleId = sampleId;
 		this.sampleName = sampleName;
 		this.analysisId = analysisId;
@@ -49,6 +50,7 @@ public ProjectSampleAnalysisOutputInfo(Long sampleId, String sampleName, Long an
 		this.userFirstName = userFirstName;
 		this.userLastName = userLastName;
 		this.workflowDescription = null;
+		this.projectId = projectId;
 	}
 
 	@Override
@@ -59,7 +61,7 @@ public String toString() {
 				+ ", analysisType=" + analysisType + ", workflowId=" + workflowId + ", createdDate=" + createdDate
 				+ ", analysisSubmissionName='" + analysisSubmissionName + '\'' + ", analysisSubmissionId="
 				+ analysisSubmissionId + ", userId=" + userId + ", userFirstName='" + userFirstName + '\''
-				+ ", userLastName='" + userLastName + '\'' + '}';
+				+ ", userLastName='" + userLastName + ", projectId='" + projectId +  '\'' + '}';
 	}
 
 	@Override
@@ -78,7 +80,8 @@ public boolean equals(Object o) {
 				getAnalysisSubmissionName(), that.getAnalysisSubmissionName()) && Objects.equals(
 				getAnalysisSubmissionId(), that.getAnalysisSubmissionId()) && Objects.equals(getUserId(),
 				that.getUserId()) && Objects.equals(getUserFirstName(), that.getUserFirstName()) && Objects.equals(
-				getUserLastName(), that.getUserLastName());
+				getUserLastName(), that.getUserLastName()) && Objects.equals(
+				getProjectId(), that.getProjectId());
 	}
 
 	@Override
@@ -87,7 +90,7 @@ public int hashCode() {
 		return Objects.hash(getSampleId(), getSampleName(), getAnalysisId(), getAnalysisOutputFileKey(), getFilePath(),
 				getAnalysisOutputFileId(), getAnalysisType(), getWorkflowId(), getCreatedDate(),
 				getAnalysisSubmissionName(), getAnalysisSubmissionId(), getUserId(), getUserFirstName(),
-				getUserLastName());
+				getUserLastName(), getProjectId());
 	}
 
 	public Long getSampleId() {
@@ -217,4 +220,12 @@ public void setWorkflowDescription(IridaWorkflowDescription iridaWorkflowDescrip
 	public IridaWorkflowDescription getWorkflowDescription() {
 		return workflowDescription;
 	}
+
+	public Long getProjectId() {
+		return projectId;
+	}
+
+	public void setProjectId(Long projectId) {
+		this.projectId = projectId;
+	}
 }