Support #35284 - Add attachments on MolecularAnalysisRun

- Started working on implementing this for the sanger workflow. - Tests will need to be updated.
AAFC-BICoE · Dec 3, 2024 · 558bcae · 558bcae
1 parent 3f2119a
commit 558bcae
Show file tree

Hide file tree

Showing 3 changed files with 99 additions and 11 deletions.
diff --git a/packages/dina-ui/components/molecular-analysis/useMolecularAnalysisRun.tsx b/packages/dina-ui/components/molecular-analysis/useMolecularAnalysisRun.tsx
@@ -20,6 +20,7 @@ import { attachGenericMolecularAnalysisItems } from "../seqdb/molecular-analysis
 import { GenericMolecularAnalysisItem } from "packages/dina-ui/types/seqdb-api/resources/GenericMolecularAnalysisItem";
 import { MolecularAnalysisRunItem } from "packages/dina-ui/types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 import { MolecularAnalysisRun } from "packages/dina-ui/types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRun";
+import { ResourceIdentifierObject } from "jsonapi-typescript";
 
 export interface UseMolecularAnalysisRunProps {
   seqBatchId: string;
@@ -88,6 +89,23 @@ export interface UseMolecularAnalysisRunReturn {
   sequencingRunItems?: SequencingRunItem[];
 
   columns: ColumnDef<SequencingRunItem>[];
+
+  /**
+   * UUID of the sequencing run.
+   */
+  sequencingRunId?: string;
+
+  /**
+   * Displays the current attachments. This is used since the run not might exist yet and can't
+   * be saved directly.
+   */
+  attachments: ResourceIdentifierObject[];
+
+  /**
+   * Set the current attachments. This is used since the run not might exist yet and can't
+   * be saved directly.
+   */
+  setAttachments: (newMetadatas: ResourceIdentifierObject[]) => void;
 }
 
 /**
@@ -222,7 +240,7 @@ export function useMolecularAnalysisRun({
   performSave,
   setPerformSave
 }: UseMolecularAnalysisRunProps): UseMolecularAnalysisRunReturn {
-  const { bulkGet, save } = useApiClient();
+  const { bulkGet, save, apiClient } = useApiClient();
   const { formatMessage } = useDinaIntl();
   const { compareByStringAndNumber } = useStringComparator();
   const columns = getMolecularAnalysisRunColumns(
@@ -244,6 +262,11 @@ export function useMolecularAnalysisRun({
   const [sequencingRunItems, setSequencingRunItems] =
     useState<SequencingRunItem[]>();
 
+  // Sequencing run attachments
+  const [attachments, setAttachments] = useState<ResourceIdentifierObject[]>(
+    []
+  );
+
   // Network Requests, starting with the SeqReaction
   useQuery<SeqReaction[]>(
     {
@@ -305,6 +328,25 @@ export function useMolecularAnalysisRun({
           if (firstSequencingRun) {
             setSequencingRun(firstSequencingRun);
             setSequencingRunName(firstSequencingRun.name);
+            await findMolecularAnalysisRunAttachments(firstSequencingRun);
+          }
+        }
+
+        async function findMolecularAnalysisRunAttachments(
+          run: MolecularAnalysisRun
+        ) {
+          // Only perform the request if a sequencing run exists.
+          if (run?.id) {
+            const runQuery = await apiClient.get(
+              `seqdb-api/molecular-analysis-run/${run?.id}`,
+              {
+                include: "attachments"
+              }
+            );
+
+            if (runQuery && (runQuery as any)?.data?.attachments) {
+              setAttachments((runQuery as any)?.data?.attachments);
+            }
           }
         }
 
@@ -365,8 +407,15 @@ export function useMolecularAnalysisRun({
           resource: {
             type: "molecular-analysis-run",
             name: sequencingRunName,
-            group: groupName
-          }
+            group: groupName,
+            ...(attachments.length > 0 && {
+              relationships: {
+                attachments: {
+                  data: attachments
+                }
+              }
+            })
+          } as any
         }
       ];
       const savedMolecularAnalysisRun = await save(
@@ -444,7 +493,7 @@ export function useMolecularAnalysisRun({
     }
   }
 
-  async function updateSequencingName() {
+  async function updateSequencingRun() {
     // Sequencing run needs an id to update.
     if (!sequencingRun?.id) {
       setPerformSave(false);
@@ -461,8 +510,13 @@ export function useMolecularAnalysisRun({
           resource: {
             id: sequencingRun.id,
             type: "molecular-analysis-run",
-            name: sequencingRunName
-          }
+            name: sequencingRunName,
+            relationships: {
+              attachments: {
+                data: attachments
+              }
+            }
+          } as any
         }
       ];
       await save(molecularAnalysisRunSaveArg, {
@@ -507,7 +561,7 @@ export function useMolecularAnalysisRun({
 
       // Determine if a new run should be created or update the existing one.
       if (sequencingRun) {
-        updateSequencingName();
+        updateSequencingRun();
       } else {
         createNewRun();
       }
@@ -521,7 +575,10 @@ export function useMolecularAnalysisRun({
     sequencingRunName,
     setSequencingRunName,
     sequencingRunItems,
-    columns
+    columns,
+    attachments,
+    setAttachments,
+    sequencingRunId: sequencingRun?.id
   };
 }
 

diff --git a/...s/dina-ui/components/seqdb/molecular-analysis-workflow/useGenericMolecularAnalysisRun.tsx b/...s/dina-ui/components/seqdb/molecular-analysis-workflow/useGenericMolecularAnalysisRun.tsx
@@ -239,7 +239,7 @@ export function useGenericMolecularAnalysisRun({
           if (firstSequencingRun) {
             setSequencingRun(firstSequencingRun);
             setSequencingRunName(firstSequencingRun.name);
-            findMolecularAnalysisRunAttachments(firstSequencingRun);
+            await findMolecularAnalysisRunAttachments(firstSequencingRun);
           }
         }
 

diff --git a/packages/dina-ui/components/seqdb/seq-workflow/SangerRunStep.tsx b/packages/dina-ui/components/seqdb/seq-workflow/SangerRunStep.tsx
@@ -4,9 +4,11 @@ import {
   SequencingRunItem,
   useMolecularAnalysisRun
 } from "../../molecular-analysis/useMolecularAnalysisRun";
-import { LoadingSpinner, ReactTable } from "common-ui";
+import { DinaForm, LoadingSpinner, ReactTable } from "common-ui";
 import { Alert } from "react-bootstrap";
 import { DinaMessage } from "../../../intl/dina-ui-intl";
+import { AttachmentsEditor } from "../../object-store/attachment-list/AttachmentsField";
+import { AttachmentReadOnlySection } from "../../object-store/attachment-list/AttachmentReadOnlySection";
 
 export interface SangerRunStepProps {
   seqBatchId: string;
@@ -31,7 +33,10 @@ export function SangerRunStep({
     setSequencingRunName,
     sequencingRunName,
     sequencingRunItems,
-    columns
+    columns,
+    attachments,
+    setAttachments,
+    sequencingRunId
   } = useMolecularAnalysisRun({
     editMode,
     setEditMode,
@@ -124,6 +129,32 @@ export function SangerRunStep({
               sort={[{ id: "wellCoordinates", desc: false }]}
             />
           </div>
+          <div className="col-12 mt-3">
+            <DinaForm initialValues={{}}>
+              {editMode ? (
+                <AttachmentsEditor
+                  attachmentPath={``}
+                  name="attachments"
+                  onChange={setAttachments}
+                  value={attachments}
+                  title={
+                    <DinaMessage id="molecularAnalysisRunStep_attachments" />
+                  }
+                />
+              ) : (
+                <>
+                  {sequencingRunId && (
+                    <AttachmentReadOnlySection
+                      attachmentPath={`seqdb-api/molecular-analysis-run/${sequencingRunId}/attachments`}
+                      title={
+                        <DinaMessage id="molecularAnalysisRunStep_attachments" />
+                      }
+                    />
+                  )}
+                </>
+              )}
+            </DinaForm>
+          </div>
         </div>
       ) : (
         <div className="row">