Sample details refactor/ default assembly

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

@@ -18,6 +18,7 @@
 
 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;
@@ -149,6 +150,10 @@ public class Sample extends IridaRepresentationModel
 	@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;
 
@@ -359,4 +364,10 @@ public SequencingObject getDefaultSequencingObject() {
 	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/ria/web/samples/SamplesAjaxController.java

@@ -172,6 +172,26 @@ public ResponseEntity<AjaxResponse> updateDefaultSequencingObjectForSample(@Path
 		}
 	}
 
+	/**
+	 * Update the default genome assembly for the sample
+	 *
+	 * @param id                 {@link Long} identifier for the sample
+	 * @param genomeAssemblyId The genome assembly identifier
+	 * @param locale             {@link Locale} for the currently logged in user
+	 * @return {@link ResponseEntity} explaining to the user the results of the update.
+	 */
+	@PutMapping(value = "/{id}/default-genome-assembly")
+	public ResponseEntity<AjaxResponse> updateDefaultGenomeAssemblyForSample(@PathVariable Long id,
+			@RequestParam Long genomeAssemblyId, Locale locale) {
+		try {
+			return ResponseEntity.ok(new AjaxSuccessResponse(
+					uiSampleService.updateDefaultGenomeAssemblyForSample(id, genomeAssemblyId, locale)));
+		} catch (EntityNotFoundException e) {
+			return ResponseEntity.status(HttpStatus.BAD_REQUEST)
+					.body(new AjaxErrorResponse(e.getMessage()));
+		}
+	}
+
 	/**
 	 * Get analyses for sample
 	 *

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/unreleased/add-default-genome-assembly-to-sample.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+         http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
+
+    <changeSet id="add-default-genome-assembly-to-sample" author="deep">
+        <addColumn tableName="sample">
+            <column name="default_genome_assembly" type="bigint(20)">
+                <constraints foreignKeyName="FK_SAMPLE_GENOME_ASSEMBLY"
+                             referencedColumnNames="id" referencedTableName="genome_assembly" />
+            </column>
+        </addColumn>
+
+        <addColumn tableName="sample_AUD">
+            <column name="default_genome_assembly" type="bigint(20)" />
+        </addColumn>
+
+    </changeSet>
+</databaseChangeLog>

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/unreleased/all-changes.xml

@@ -6,4 +6,5 @@
          http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
   <include file="user-account-drop-phone-constraint.xml" relativeToChangelogFile="true" />
   <include file="add-default-sequencing-object-to-sample.xml" relativeToChangelogFile="true" />
+  <include file="add-default-genome-assembly-to-sample.xml" relativeToChangelogFile="true" />
 </databaseChangeLog>

src/main/resources/i18n/messages.properties

@@ -2273,13 +2273,16 @@ SampleFilesList.download=Download
 SampleFilesList.removeGenomeAssembly=Are you sure you want to delete this genome assembly from the sample?
 SampleFilesList.removeSequencingObject=Are you sure you want to delete this sequencing object from the sample?
 SampleFilesList.tooltip.setAsDefault=Set this paired end sequencing object as the default for the sample. The sequencing object will be selected by default when running a pipeline.
+SampleFilesList.tooltip.setAsDefaultAssembly=Set this genome assembly as the default for the sample. The genome assembly will be selected by default when running a pipeline which accepts assemblies.
 SampleFilesList.tooltip.remove=This will remove this complete sequencing object (paired end, single end, fast5) from the sample.
 SampleFilesList.default=Default
 SampleFilesList.setAsDefault=Set as Default
 SampleFilesList.defaultSelected=Default paired end sequencing object to be selected when running a pipeline
+SampleFilesList.defaultSelectedAssembly=Default genome assembly to be selected when running a pipeline
 
 server.SampleFilesList.successfully.set.default.seq.object=Successfully set default sequencing object for sample
 server.SampleFilesList.unable.to.update.sample=Unable to update sample as it was not found
+server.SampleFilesList.successfully.set.default.genome.assembly=Successfully set default genome assembly for sample
 
 # ========================================================================================== #
 # SAMPLE FILES CONCATENATE COMPONENT                                                         #

src/main/webapp/resources/css/app.css

@@ -19,6 +19,17 @@
   --grey-11: #1f1f1f;
   --grey-12: #141414;
   --grey-13: #000000;
+
+  --blue-1: #e6f7ff;
+  --blue-2: #bae7ff;
+  --blue-3: #91d5ff;
+  --blue-4: #69c0ff;
+  --blue-5: #40a9ff;
+  --blue-6: #1890ff;
+  --blue-7: #096dd9;
+  --blue-8: #0050b3;
+  --blue-9: #003a8c;
+  --blue-10: #002766;
 }
 
 html,

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

@@ -105,6 +105,13 @@ export const sampleApi = createApi({
       }),
       invalidatesTags: ["SampleDetails"],
     }),
+    updateDefaultSampleGenomeAssembly: build.mutation({
+      query: ({ sampleId, genomeAssemblyId }) => ({
+        url: `/${sampleId}/default-genome-assembly?genomeAssemblyId=${genomeAssemblyId}`,
+        method: "PUT",
+      }),
+      invalidatesTags: ["SampleDetails"],
+    }),
   }),
 });
 
@@ -116,6 +123,7 @@ export const {
   useUpdateSampleMetadataMutation,
   useRemoveSampleFilesMutation,
   useConcatenateSequencingObjectsMutation,
+  useUpdateDefaultSampleGenomeAssemblyMutation,
   useUpdateDefaultSampleSequencingObjectMutation,
 } = sampleApi;
 

src/main/webapp/resources/js/components/samples/components/GenomeAssemblyList.jsx

@@ -1,11 +1,13 @@
 import React from "react";
-import { Button, notification, Popconfirm } from "antd";
-import { useSelector } from "react-redux";
+import { Button, notification, Popconfirm, Tag, Tooltip } from "antd";
+import { useDispatch, useSelector } from "react-redux";
 
 import { SequenceFileTypeRenderer } from "./SequenceFileTypeRenderer";
 import { downloadGenomeAssemblyFile } from "../../../apis/samples/samples";
 import { GenomeAssemblyListItem } from "../../sequence-files/GenomeAssemblyListItem";
 import { DEFAULT_ACTION_WIDTH } from "../sampleFilesSlice";
+import { useUpdateDefaultSampleGenomeAssemblyMutation } from "../../../apis/samples/samples";
+import { setDefaultGenomeAssembly } from "../sampleSlice";
 
 /**
  * React component to display, remove, download genome assemblies
@@ -14,11 +16,14 @@ import { DEFAULT_ACTION_WIDTH } from "../sampleFilesSlice";
  * @constructor
  */
 export function GenomeAssemblyList({ removeSampleFiles = () => {} }) {
+  const [updateSampleDefaultGenomeAssembly] =
+    useUpdateDefaultSampleGenomeAssemblyMutation();
   const { sample, modifiable: isModifiable } = useSelector(
     (state) => state.sampleReducer
   );
   const { files } = useSelector((state) => state.sampleFilesReducer);
   const ACTION_MARGIN_RIGHT = isModifiable ? 0 : 5;
+  const dispatch = useDispatch();
 
   /*
    Download genome assembly files
@@ -30,20 +35,86 @@ export function GenomeAssemblyList({ removeSampleFiles = () => {} }) {
     downloadGenomeAssemblyFile({ sampleId, genomeAssemblyId });
   };
 
+  /*
+  Set default genome assembly for sample to be used for analyses
+   */
+  const updateDefaultGenomeAssembly = (genomeAssembly) => {
+    const { fileInfo: genomeAssemblyObj } = genomeAssembly;
+
+    updateSampleDefaultGenomeAssembly({
+      sampleId: sample.identifier,
+      genomeAssemblyId: genomeAssemblyObj.identifier,
+    })
+      .then(({ data }) => {
+        dispatch(setDefaultGenomeAssembly(genomeAssemblyObj));
+        notification.success({ message: data.message });
+      })
+      .catch((error) => {
+        notification.error({ message: error });
+      });
+  };
+
   /*
    Get the actions required for a Genome Assembly
    */
-  const getActionsForGenomeAssembly = (genomeAssembly) => {
-    let actions = [
+  const getActionsForGenomeAssembly = (genomeAssembly, index) => {
+    const { fileInfo: genomeAssemblyObj } = genomeAssembly;
+    let actions = [];
+
+    if (isModifiable) {
+      if (
+        (sample.defaultGenomeAssembly !== null &&
+          genomeAssemblyObj.identifier ===
+            sample.defaultGenomeAssembly.identifier) ||
+        (sample.defaultGenomeAssembly === null && index === 0)
+      ) {
+        actions.push(
+          <Tooltip
+            title={i18n("SampleFilesList.defaultSelectedAssembly")}
+            placement="top"
+            key={`default-tag-tooltip-ga-${genomeAssemblyObj.identifier}`}
+          >
+            <Tag
+              color={`var(--blue-6)`}
+              key={`default-tag-ga-${genomeAssemblyObj.identifier}`}
+              className="t-default-genome-assembly-tag"
+            >
+              {i18n("SampleFilesList.default")}
+            </Tag>
+          </Tooltip>
+        );
+      } else {
+        actions.push(
+          <Tooltip
+            title={i18n("SampleFilesList.tooltip.setAsDefaultAssembly")}
+            placement="top"
+            key={`set-default-tooltip-ga-${genomeAssemblyObj.identifier}`}
+          >
+            <Button
+              size="small"
+              key={`set-default-ga-${genomeAssemblyObj.identifier}`}
+              onClick={() => updateDefaultGenomeAssembly(genomeAssembly)}
+              type="link"
+              className="t-set-default-genome-assembly-button"
+              style={{ width: 100 }}
+            >
+              {i18n("SampleFilesList.setAsDefault")}
+            </Button>
+          </Tooltip>
+        );
+      }
+    }
+
+    actions.push(
       <span
-        key={`${genomeAssembly.fileInfo.identifier}-file-size`}
+        key={`${genomeAssemblyObj.identifier}-file-size`}
         className="t-file-size"
       >
         {genomeAssembly.firstFileSize}
       </span>,
       <Button
         type="link"
-        key={`${genomeAssembly.fileInfo.identifier}-download-btn`}
+        key={`${genomeAssemblyObj.identifier}-download-btn`}
         style={{
           padding: 0,
           width: DEFAULT_ACTION_WIDTH,
@@ -53,13 +124,13 @@ export function GenomeAssemblyList({ removeSampleFiles = () => {} }) {
         onClick={() => {
           downloadAssemblyFile({
             sampleId: sample.identifier,
-            genomeAssemblyId: genomeAssembly.fileInfo.identifier,
+            genomeAssemblyId: genomeAssemblyObj.identifier,
           });
         }}
       >
         {i18n("SampleFilesList.download")}
-      </Button>,
-    ];
+      </Button>
+    );
 
     if (isModifiable) {
       actions.push(
@@ -74,7 +145,7 @@ export function GenomeAssemblyList({ removeSampleFiles = () => {} }) {
           }}
           onConfirm={() => {
             removeSampleFiles({
-              fileObjectId: genomeAssembly.fileInfo.identifier,
+              fileObjectId: genomeAssemblyObj.identifier,
               type: "assembly",
             });
           }}
@@ -83,7 +154,7 @@ export function GenomeAssemblyList({ removeSampleFiles = () => {} }) {
             type="link"
             className="t-remove-file-btn"
             style={{ padding: 0, width: DEFAULT_ACTION_WIDTH }}
-            key={`${genomeAssembly.fileInfo.identifier}-remove-btn`}
+            key={`${genomeAssemblyObj.identifier}-remove-btn`}
           >
             {i18n("SampleFilesList.remove")}
           </Button>
@@ -96,11 +167,11 @@ export function GenomeAssemblyList({ removeSampleFiles = () => {} }) {
 
   return (
     <SequenceFileTypeRenderer title={i18n("SampleFiles.assemblies")}>
-      {files.assemblies.map((assembly) => (
+      {files.assemblies.map((assembly, index) => (
         <GenomeAssemblyListItem
           key={`assembly-${assembly.fileInfo.identifier}`}
           genomeAssembly={assembly}
-          actions={getActionsForGenomeAssembly(assembly)}
+          actions={getActionsForGenomeAssembly(assembly, index)}
         />
       ))}
     </SequenceFileTypeRenderer>

src/main/webapp/resources/js/components/samples/components/SampleFileList.jsx

@@ -1,8 +1,8 @@
 import React from "react";
 import { notification, Space } from "antd";
-import { useDispatch, useSelector } from "react-redux";
 import { useRemoveSampleFilesMutation } from "../../../apis/samples/samples";
 import { removeFileObjectFromSample } from "../sampleFilesSlice";
+import { useDispatch, useSelector } from "react-redux";
 import { setDefaultSequencingObject } from "../sampleSlice";
 import { GenomeAssemblyList } from "./GenomeAssemblyList";
 import { SequencingObjectList } from "./SequencingObjectList";

src/main/webapp/resources/js/components/samples/components/SequencingObjectList.jsx

@@ -21,14 +21,6 @@ import { SequenceObjectListItem } from "../../sequence-files/SequenceObjectListI
 import { primaryColour } from "../../../utilities/theme-utilities";
 import { SPACE_XS } from "../../../styles/spacing";
 
-const fileProcessTranslations = {
-  UNPROCESSED: i18n("SampleFilesList.fileProcessingState.UNPROCESSED"),
-  QUEUED: i18n("SampleFilesList.fileProcessingState.QUEUED"),
-  PROCESSING: i18n("SampleFilesList.fileProcessingState.PROCESSING"),
-  FINISHED: i18n("SampleFilesList.fileProcessingState.FINISHED"),
-  ERROR: i18n("SampleFilesList.fileProcessingState.ERROR"),
-};
-
 import {
   addToConcatenateSelected,
   DEFAULT_ACTION_WIDTH,
@@ -43,6 +35,14 @@ import {
   useUpdateDefaultSampleSequencingObjectMutation,
 } from "../../../apis/samples/samples";
 
+const fileProcessTranslations = {
+  UNPROCESSED: i18n("SampleFilesList.fileProcessingState.UNPROCESSED"),
+  QUEUED: i18n("SampleFilesList.fileProcessingState.QUEUED"),
+  PROCESSING: i18n("SampleFilesList.fileProcessingState.PROCESSING"),
+  FINISHED: i18n("SampleFilesList.fileProcessingState.FINISHED"),
+  ERROR: i18n("SampleFilesList.fileProcessingState.ERROR"),
+};
+
 /**
  * React component to display, remove, download sequencing objects
  * @param {function} removeSampleFiles The function to remove sequencing objects
@@ -204,7 +204,7 @@ export function SequencingObjectList({ removeSampleFiles = () => {} }) {
             key={`default-tag-tooltip-${obj.identifier}`}
           >
             <Tag
-              color="#108ee9"
+              color={`var(--blue-6)`}
               key={`default-tag-${obj.identifier}`}
               className="t-default-seq-obj-tag"
             >

src/main/webapp/resources/js/components/samples/sampleSlice.js

@@ -94,6 +94,16 @@ export const setDefaultSequencingObject = createAction(
   })
 );
 
+/**
+ * Action to set the default genome assembly for a sample
+ */
+export const setDefaultGenomeAssembly = createAction(
+  `sample/setDefaultGenomeAssembly`,
+  (genomeAssembly) => ({
+    payload: { genomeAssembly },
+  })
+);
+
 /**
  * Action to update sample details
  */
@@ -142,6 +152,10 @@ const sampleSlice = createSlice({
       state.sample.defaultSequencingObject = action.payload.sequencingObject;
     });
 
+    builder.addCase(setDefaultGenomeAssembly, (state, action) => {
+      state.sample.defaultGenomeAssembly = action.payload.genomeAssembly;
+    });
+
     builder.addCase(setProjectDetails, (state, action) => {
       state.projectId = action.payload.projectId;
       state.projectName = action.payload.projectName;