Support #35538 - Molecular Analysis Run view page bug and test coverage

- Created an enum for the different usage types for molecular analysis run items. - Refactored all usage types to use the new enums. - Added a mock for the run items. - Tweaked what should happen if no run items are loaded in.
AAFC-BICoE · Jan 14, 2025 · aac4766 · aac4766
1 parent 6394cfb
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diff --git a/...ges/dina-ui/components/molecular-analysis/useMetagenomicsWorkflowMolecularAnalysisRun.tsx b/...ges/dina-ui/components/molecular-analysis/useMetagenomicsWorkflowMolecularAnalysisRun.tsx
@@ -1,5 +1,8 @@
 import { PcrBatchItem } from "../../types/seqdb-api";
-import { MolecularAnalysisRunItem } from "../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
+import {
+  MolecularAnalysisRunItem,
+  MolecularAnalysisRunItemUsageType
+} from "../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 import { useEffect, useState } from "react";
 import {
   BulkGetOptions,
@@ -405,7 +408,8 @@ export function useMetagenomicsWorkflowMolecularAnalysisRun({
             type: "molecular-analysis-run-item",
             resource: {
               type: "molecular-analysis-run-item",
-              usageType: "metagenomics-batch-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.METAGENOMICS_BATCH_ITEM,
               ...(molecularAnalysisRunItemName && {
                 name: molecularAnalysisRunItemName
               }),

diff --git a/packages/dina-ui/components/molecular-analysis/useMolecularAnalysisRun.tsx b/packages/dina-ui/components/molecular-analysis/useMolecularAnalysisRun.tsx
@@ -12,7 +12,10 @@ import { KitsuResource, PersistedResource } from "kitsu";
 import { MaterialSampleSummary } from "../../types/collection-api";
 import { useDinaIntl } from "../../intl/dina-ui-intl";
 import { ColumnDef } from "@tanstack/react-table";
-import { MolecularAnalysisRunItem } from "packages/dina-ui/types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
+import {
+  MolecularAnalysisRunItem,
+  MolecularAnalysisRunItemUsageType
+} from "../../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";
 import { useMolecularAnalysisRunColumns } from "./useMolecularAnalysisRunColumns";
@@ -440,7 +443,7 @@ export function useMolecularAnalysisRun({
             type: "molecular-analysis-run-item",
             resource: {
               type: "molecular-analysis-run-item",
-              usageType: "seq-reaction",
+              usageType: MolecularAnalysisRunItemUsageType.SEQ_REACTION,
               ...(molecularAnalysisRunItemName && {
                 name: molecularAnalysisRunItemName
               }),

diff --git a/packages/dina-ui/components/molecular-analysis/useMolecularAnalysisRunView.tsx b/packages/dina-ui/components/molecular-analysis/useMolecularAnalysisRunView.tsx
@@ -4,7 +4,10 @@ import { filterBy, useApiClient, useQuery } from "common-ui";
 import { PersistedResource } from "kitsu";
 import { attachGenericMolecularAnalysisItems } from "../seqdb/molecular-analysis-workflow/useGenericMolecularAnalysisRun";
 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 {
+  MolecularAnalysisRunItem,
+  MolecularAnalysisRunItemUsageType
+} from "../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 import { MetagenomicsBatchItem } from "packages/dina-ui/types/seqdb-api/resources/metagenomics/MetagenomicsBatchItem";
 import {
   attachMaterialSampleSummaryMetagenomics,
@@ -35,18 +38,24 @@ export function useMolecularAnalysisRunView({
   molecularAnalysisRunId
 }: UseMolecularAnalysisRunViewProps) {
   const { apiClient, bulkGet } = useApiClient();
+
   const [columns, setColumns] = useState<any[]>([]);
+
   // Run Items
   const [sequencingRunItems, setSequencingRunItems] =
     useState<SequencingRunItem[]>();
+
   const [loading, setLoading] = useState<boolean>(true);
 
   // Quality control items
   const [qualityControls, setQualityControls] = useState<QualityControl[]>([]);
+
+  // Quality control type vocabulary options, mainly used for localization.
   const { loading: loadingVocabularyItems, vocabOptions: qualityControlTypes } =
     useVocabularyOptions({
       path: "seqdb-api/vocabulary/qualityControlType"
     });
+
   const molecularAnalysisRunItemQuery = useQuery<MolecularAnalysisRunItem[]>(
     {
       path: `seqdb-api/molecular-analysis-run-item`,
@@ -77,7 +86,11 @@ export function useMolecularAnalysisRunView({
 
         async function fetchGenericMolecularAnalysisItems() {
           const fetchPaths = molecularAnalysisRunItems
-            .filter((runItem) => runItem.usageType !== "quality-control")
+            .filter(
+              (runItem) =>
+                runItem.usageType !==
+                MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
+            )
             .map(
               (molecularAnalysisRunItem) =>
                 `seqdb-api/generic-molecular-analysis-item?include=storageUnitUsage,materialSample,molecularAnalysisRunItem&filter[rsql]=molecularAnalysisRunItem.uuid==${molecularAnalysisRunItem.id}`
@@ -111,14 +124,13 @@ export function useMolecularAnalysisRunView({
           return metagenomicsBatchItems;
         }
 
-        const usageType = molecularAnalysisRunItems.filter(
-          (runItem) => runItem.usageType !== "quality-control"
-        )?.[0]?.usageType;
-
-        if (!usageType) {
-          setLoading(false);
-          return;
-        }
+        const usageType =
+          molecularAnalysisRunItems.filter(
+            (runItem) =>
+              runItem.usageType !==
+              MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
+          )?.[0]?.usageType ??
+          MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM;
 
         setColumns(
           useMolecularAnalysisRunColumns({
@@ -127,7 +139,7 @@ export function useMolecularAnalysisRunView({
           })
         );
 
-        if (usageType === "seq-reaction") {
+        if (usageType === MolecularAnalysisRunItemUsageType.SEQ_REACTION) {
           let seqReactions = await fetchSeqReactions();
           seqReactions = seqReactions.filter((item) => item !== undefined);
 
@@ -150,7 +162,10 @@ export function useMolecularAnalysisRunView({
           // All finished loading.
           setSequencingRunItems(sequencingRunItemsChain);
           setLoading(false);
-        } else if (usageType === "generic-molecular-analysis-item") {
+        } else if (
+          usageType ===
+          MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM
+        ) {
           let genericMolecularAnalysisItems =
             await fetchGenericMolecularAnalysisItems();
           genericMolecularAnalysisItems = genericMolecularAnalysisItems.filter(
@@ -172,7 +187,9 @@ export function useMolecularAnalysisRunView({
           );
 
           const qualityControlRunItems = molecularAnalysisRunItems.filter(
-            (runItem) => runItem.usageType === "quality-control"
+            (runItem) =>
+              runItem.usageType ===
+              MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
           );
 
           // Get quality controls
@@ -212,7 +229,10 @@ export function useMolecularAnalysisRunView({
           // All finished loading.
           setSequencingRunItems(sequencingRunItemsChain);
           setLoading(false);
-        } else if (usageType === "metagenomics-batch-item") {
+        } else if (
+          usageType ===
+          MolecularAnalysisRunItemUsageType.METAGENOMICS_BATCH_ITEM
+        ) {
           let metagenomicsBatchItems = await fetchMetagenomicsBatchItems();
           metagenomicsBatchItems = metagenomicsBatchItems.filter(
             (item) => item !== undefined
@@ -242,6 +262,7 @@ export function useMolecularAnalysisRunView({
       }
     }
   );
+
   return {
     loading:
       molecularAnalysisRunItemQuery.loading ||

diff --git a/...-ui/components/seqdb/molecular-analysis-workflow/MolecularAnalysisSampleSelectionStep.tsx b/...-ui/components/seqdb/molecular-analysis-workflow/MolecularAnalysisSampleSelectionStep.tsx
@@ -18,7 +18,10 @@ import { SeqdbMessage } from "../../../intl/seqdb-intl";
 import { useMaterialSampleRelationshipColumns } from "../../collection/material-sample/useMaterialSampleRelationshipColumns";
 import { GenericMolecularAnalysis } from "packages/dina-ui/types/seqdb-api/resources/GenericMolecularAnalysis";
 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 {
+  MolecularAnalysisRunItem,
+  MolecularAnalysisRunItemUsageType
+} from "../../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 
 export interface MolecularAnalysisSampleSelectionStepProps {
   molecularAnalysisId: string;
@@ -235,7 +238,8 @@ export function MolecularAnalysisSampleSelectionStep({
             itemsToCreate.map((_) => ({
               resource: {
                 type: "molecular-analysis-run-item",
-                usageType: "generic-molecular-analysis-item",
+                usageType:
+                  MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
                 relationships: {
                   run: {
                     data: {

diff --git a/.../dina-ui/components/seqdb/molecular-analysis-workflow/__mocks__/MolecularAnalysisMocks.ts b/.../dina-ui/components/seqdb/molecular-analysis-workflow/__mocks__/MolecularAnalysisMocks.ts
@@ -10,7 +10,10 @@ import { Metadata } from "packages/dina-ui/types/objectstore-api";
 import { GenericMolecularAnalysis } from "packages/dina-ui/types/seqdb-api/resources/GenericMolecularAnalysis";
 import { GenericMolecularAnalysisItem } from "packages/dina-ui/types/seqdb-api/resources/GenericMolecularAnalysisItem";
 import { MolecularAnalysisRun } from "packages/dina-ui/types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRun";
-import { MolecularAnalysisRunItem } from "packages/dina-ui/types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
+import {
+  MolecularAnalysisRunItem,
+  MolecularAnalysisRunItemUsageType
+} from "../../../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 import { QualityControl } from "packages/dina-ui/types/seqdb-api/resources/QualityControl";
 import { Group } from "packages/dina-ui/types/user-api";
 
@@ -609,14 +612,14 @@ export const TEST_QUALITY_CONTROL_RUN_ITEMS: PersistedResource<MolecularAnalysis
       type: "molecular-analysis-run-item",
       createdBy: "dina-admin",
       createdOn: "2024-12-11T20:52:48.43824Z",
-      usageType: "quality-control"
+      usageType: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
     },
     {
       id: "e9e39b72-ece7-454b-893a-2fc2d075e7b7",
       type: "molecular-analysis-run-item",
       createdBy: "dina-admin",
       createdOn: "2024-12-11T20:52:48.43824Z",
-      usageType: "quality-control"
+      usageType: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
     }
   ];
 

diff --git a/...components/seqdb/molecular-analysis-workflow/__tests__/MolecularAnalysisGridStep.test.tsx b/...components/seqdb/molecular-analysis-workflow/__tests__/MolecularAnalysisGridStep.test.tsx
@@ -22,6 +22,7 @@ import "@testing-library/jest-dom";
 import { waitForElementToBeRemoved } from "@testing-library/react";
 import { useState, useEffect } from "react";
 import userEvent from "@testing-library/user-event";
+import { MolecularAnalysisRunItemUsageType } from "../../../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 
 const onSavedMock = jest.fn();
 const mockSetEditMode = jest.fn();
@@ -284,7 +285,8 @@ describe("Molecular Analysis Workflow - Step 3 - Molecular Analysis Coordinate S
                 type: "storage-unit"
               },
               type: "storage-unit-usage",
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               wellColumn: 1,
               wellRow: "A"
             },
@@ -298,7 +300,8 @@ describe("Molecular Analysis Workflow - Step 3 - Molecular Analysis Coordinate S
                 type: "storage-unit"
               },
               type: "storage-unit-usage",
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               wellColumn: 2,
               wellRow: "A"
             },
@@ -312,7 +315,8 @@ describe("Molecular Analysis Workflow - Step 3 - Molecular Analysis Coordinate S
                 type: "storage-unit"
               },
               type: "storage-unit-usage",
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               wellColumn: 3,
               wellRow: "A"
             },

diff --git a/.../components/seqdb/molecular-analysis-workflow/__tests__/MolecularAnalysisRunStep.test.tsx b/.../components/seqdb/molecular-analysis-workflow/__tests__/MolecularAnalysisRunStep.test.tsx
@@ -28,6 +28,7 @@ import {
   MolecularAnalysisRunStep,
   MolecularAnalysisRunStepProps
 } from "../MolecularAnalysisRunStep";
+import { MolecularAnalysisRunItemUsageType } from "../../../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 
 const mockGet = jest.fn<any, any>(async (path, params) => {
   switch (path) {
@@ -51,7 +52,8 @@ const mockGet = jest.fn<any, any>(async (path, params) => {
       switch (params.filter.rsql) {
         case "run.uuid==" +
           TEST_MOLECULAR_ANALYSIS_RUN_ID +
-          ";usageType==quality-control":
+          ";usageType==" +
+          MolecularAnalysisRunItemUsageType.QUALITY_CONTROL:
           return { data: TEST_QUALITY_CONTROL_RUN_ITEMS };
       }
 
@@ -365,7 +367,8 @@ describe("Molecular Analysis Workflow - Step 4 - Molecular Analysis Run Step", (
                   }
                 }
               },
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               type: "molecular-analysis-run-item"
             },
             type: "molecular-analysis-run-item"
@@ -381,7 +384,8 @@ describe("Molecular Analysis Workflow - Step 4 - Molecular Analysis Run Step", (
                   }
                 }
               },
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               type: "molecular-analysis-run-item"
             },
             type: "molecular-analysis-run-item"
@@ -396,7 +400,8 @@ describe("Molecular Analysis Workflow - Step 4 - Molecular Analysis Run Step", (
                   }
                 }
               },
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               type: "molecular-analysis-run-item"
             },
             type: "molecular-analysis-run-item"
@@ -475,7 +480,7 @@ describe("Molecular Analysis Workflow - Step 4 - Molecular Analysis Run Step", (
                 }
               },
               type: "molecular-analysis-run-item",
-              usageType: "quality-control"
+              usageType: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
             },
             type: "molecular-analysis-run-item"
           }
@@ -644,7 +649,7 @@ describe("Molecular Analysis Workflow - Step 4 - Molecular Analysis Run Step", (
                 }
               },
               type: "molecular-analysis-run-item",
-              usageType: "quality-control"
+              usageType: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
             },
             type: "molecular-analysis-run-item"
           }

diff --git a/...seqdb/molecular-analysis-workflow/__tests__/MolecularAnalysisSampleSelectionStep.test.tsx b/...seqdb/molecular-analysis-workflow/__tests__/MolecularAnalysisSampleSelectionStep.test.tsx
@@ -19,6 +19,7 @@ import {
   TEST_MOLECULAR_ANALYSIS_RUN_ID,
   TEST_SEARCH_RESPONSE
 } from "../__mocks__/MolecularAnalysisMocks";
+import { MolecularAnalysisRunItemUsageType } from "../../../../types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
 
 const onSavedMock = jest.fn();
 const mockSetEditMode = jest.fn();
@@ -266,7 +267,8 @@ describe("Molecular Analysis Workflow - Step 2 - Molecular Analysis Sample Selec
               }
             },
             type: "molecular-analysis-run-item",
-            usageType: "generic-molecular-analysis-item"
+            usageType:
+              MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM
           },
           type: "molecular-analysis-run-item"
         }

diff --git a/...s/dina-ui/components/seqdb/molecular-analysis-workflow/useGenericMolecularAnalysisRun.tsx b/...s/dina-ui/components/seqdb/molecular-analysis-workflow/useGenericMolecularAnalysisRun.tsx
@@ -6,7 +6,10 @@ import { MaterialSampleSummary } from "packages/dina-ui/types/collection-api";
 import { useDinaIntl } from "../../../intl/dina-ui-intl";
 import { GenericMolecularAnalysisItem } from "packages/dina-ui/types/seqdb-api/resources/GenericMolecularAnalysisItem";
 import { GenericMolecularAnalysis } from "packages/dina-ui/types/seqdb-api/resources/GenericMolecularAnalysis";
-import { MolecularAnalysisRunItem } from "packages/dina-ui/types/seqdb-api/resources/molecular-analysis/MolecularAnalysisRunItem";
+import {
+  MolecularAnalysisRunItem,
+  MolecularAnalysisRunItemUsageType
+} from "../../../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";
 import { QualityControl } from "packages/dina-ui/types/seqdb-api/resources/QualityControl";
@@ -437,7 +440,7 @@ export function useGenericMolecularAnalysisRun({
         group: "",
         name: "",
         qcType: "",
-        type: "quality-control"
+        type: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
       }
     ]);
   }
@@ -526,7 +529,7 @@ export function useGenericMolecularAnalysisRun({
               {
                 selector: "usageType",
                 comparison: "==",
-                arguments: "quality-control"
+                arguments: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL
               }
             ]
           })("")
@@ -621,7 +624,8 @@ export function useGenericMolecularAnalysisRun({
             type: "molecular-analysis-run-item",
             resource: {
               type: "molecular-analysis-run-item",
-              usageType: "generic-molecular-analysis-item",
+              usageType:
+                MolecularAnalysisRunItemUsageType.GENERIC_MOLECULAR_ANALYSIS_ITEM,
               ...(molecularAnalysisRunItemName && {
                 name: molecularAnalysisRunItemName
               }),
@@ -668,7 +672,7 @@ export function useGenericMolecularAnalysisRun({
           type: "molecular-analysis-run-item",
           resource: {
             type: "molecular-analysis-run-item",
-            usageType: "quality-control",
+            usageType: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL,
             relationships: {
               run: {
                 data: {
@@ -808,7 +812,7 @@ export function useGenericMolecularAnalysisRun({
               type: "molecular-analysis-run-item",
               resource: {
                 type: "molecular-analysis-run-item",
-                usageType: "quality-control",
+                usageType: MolecularAnalysisRunItemUsageType.QUALITY_CONTROL,
                 relationships: {
                   run: {
                     data: {