Show a Delivery Date column in the cohort samples popup (#116)

* Modify samples query to also return cohort dates * Expose the earliest cohort date of each sample in the cohort samples popup * Display a Delivery Date column in the cohort samples popup * Rename functions that extract data from samples query for clarity * Consolidate field data getters to getSampleCohortDataFromSamplesQuery Remove logic that get specific field data from the column definitions and consolidate it to the getSampleCohortDataFromSamplesQuery function.
mskcc · Mar 27, 2024 · ba77d40 · ba77d40
1 parent 2e8ca2a
commit ba77d40
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Showing 8 changed files with 88 additions and 27 deletions.
diff --git a/frontend/src/generated/graphql.ts b/frontend/src/generated/graphql.ts
@@ -10785,7 +10785,14 @@ export type FindSamplesByInputValueQuery = {
           __typename?: "SampleCohortsHasCohortSampleConnection";
           edges: Array<{
             __typename?: "SampleCohortsHasCohortSampleRelationship";
-            node: { __typename?: "Cohort"; cohortId: string };
+            node: {
+              __typename?: "Cohort";
+              cohortId: string;
+              hasCohortCompleteCohortCompletes: Array<{
+                __typename?: "CohortComplete";
+                date: string;
+              }>;
+            };
           }>;
         };
         hasTempoTempos: Array<{
@@ -11280,6 +11287,9 @@ export const FindSamplesByInputValueDocument = gql`
             edges {
               node {
                 cohortId
+                hasCohortCompleteCohortCompletes {
+                  date
+                }
               }
             }
           }

diff --git a/frontend/src/pages/cohorts/CohortsPage.tsx b/frontend/src/pages/cohorts/CohortsPage.tsx
@@ -11,7 +11,7 @@ import {
   CohortsListColumns,
   cohortSampleFilterWhereVariables,
   defaultReadOnlyColDef,
-  getCohortDataFromSamples,
+  getSampleCohortDataFromSamplesQuery,
   handleSearch,
 } from "../../shared/helpers";
 import RecordsList from "../../components/RecordsList";
@@ -141,7 +141,7 @@ export default function CohortsPage() {
           sampleQueryParamValue &&
           `${sampleQueryParamHeaderName} "${sampleQueryParamValue}"`
         }
-        getSamplesRowData={getCohortDataFromSamples}
+        getSamplesRowData={getSampleCohortDataFromSamplesQuery}
         samplesParentWhereVariables={
           {
             cohortsHasCohortSampleConnection_SOME: {

diff --git a/frontend/src/pages/patients/PatientsPage.tsx b/frontend/src/pages/patients/PatientsPage.tsx
@@ -18,7 +18,7 @@ import {
   PatientsListColumns,
   SampleDetailsColumns,
   defaultEditableColDef,
-  getMetadataFromSamples,
+  getSampleMetadataFromSamplesQuery,
   sampleFilterWhereVariables,
 } from "../../shared/helpers";
 import { getUserEmail } from "../../utils/getUserEmail";
@@ -292,7 +292,7 @@ export default function PatientsPage({
           sampleQueryParamValue &&
           `${sampleQueryParamHeaderName} ${sampleQueryParamValue}`
         }
-        getSamplesRowData={getMetadataFromSamples}
+        getSamplesRowData={getSampleMetadataFromSamplesQuery}
         samplesParentWhereVariables={
           {
             OR: [

diff --git a/frontend/src/pages/requests/RequestsPage.tsx b/frontend/src/pages/requests/RequestsPage.tsx
@@ -8,7 +8,7 @@ import {
   RequestsListColumns,
   SampleDetailsColumns,
   defaultEditableColDef,
-  getMetadataFromSamples,
+  getSampleMetadataFromSamplesQuery,
   handleSearch,
   sampleFilterWhereVariables,
 } from "../../shared/helpers";
@@ -90,7 +90,7 @@ export default function RequestsPage() {
           sampleQueryParamValue &&
           `${sampleQueryParamHeaderName} ${sampleQueryParamValue}`
         }
-        getSamplesRowData={getMetadataFromSamples}
+        getSamplesRowData={getSampleMetadataFromSamplesQuery}
         samplesParentWhereVariables={
           {
             hasMetadataSampleMetadata_SOME: {

diff --git a/frontend/src/pages/samples/SamplesPage.tsx b/frontend/src/pages/samples/SamplesPage.tsx
@@ -3,7 +3,7 @@ import SamplesList from "../../components/SamplesList";
 import {
   SampleDetailsColumns,
   defaultEditableColDef,
-  getMetadataFromSamples,
+  getSampleMetadataFromSamplesQuery,
   sampleFilterWhereVariables,
 } from "../../shared/helpers";
 import { SampleWhere } from "../../generated/graphql";
@@ -16,7 +16,7 @@ export default function SamplesPage() {
       <SamplesList
         columnDefs={SampleDetailsColumns}
         defaultColDef={defaultEditableColDef}
-        getRowData={getMetadataFromSamples}
+        getRowData={getSampleMetadataFromSamplesQuery}
         refetchWhereVariables={(parsedSearchVals) => {
           return {
             hasMetadataSampleMetadata_SOME: {

diff --git a/frontend/src/shared/helpers.tsx b/frontend/src/shared/helpers.tsx
@@ -576,40 +576,44 @@ export const CohortSamplesDetailsColumns: ColDef[] = [
     headerName: "CMO Sample Name",
   },
   {
+    field: "deliveryDate",
+    headerName: "Delivery Date",
+  },
+  {
+    field: "bamCompleteDate",
     headerName: "BAM Complete Date",
-    valueGetter: ({ data }) => data.bamComplete?.date,
   },
   {
+    field: "bamCompleteStatus",
     headerName: "BAM Complete Status",
-    valueGetter: ({ data }) => data.bamComplete?.status,
   },
   {
+    field: "mafCompleteDate",
     headerName: "MAF Complete Date",
-    valueGetter: ({ data }) => data.mafComplete?.date,
   },
   {
+    field: "mafCompleteNormalPrimaryId",
     headerName: "MAF Complete Normal Primary ID",
-    valueGetter: ({ data }) => data.mafComplete?.normalPrimaryId,
   },
   {
+    field: "mafCompleteStatus",
     headerName: "MAF Complete Status",
-    valueGetter: ({ data }) => data.mafComplete?.status,
   },
   {
+    field: "qcCompleteDate",
     headerName: "QC Complete Date",
-    valueGetter: ({ data }) => data.qcComplete?.date,
   },
   {
+    field: "qcCompleteResult",
     headerName: "QC Complete Result",
-    valueGetter: ({ data }) => data.qcComplete?.result,
   },
   {
+    field: "qcCompleteReason",
     headerName: "QC Complete Reason",
-    valueGetter: ({ data }) => data.qcComplete?.reason,
   },
   {
+    field: "qcCompleteStatus",
     headerName: "QC Complete Status",
-    valueGetter: ({ data }) => data.qcComplete?.status,
   },
 ];
 
@@ -823,23 +827,57 @@ export function cohortSampleFilterWhereVariables(
   ];
 }
 
-export function getMetadataFromSamples(samples: Sample[]) {
-  return samples.map((s: any) => {
+export function getSampleMetadataFromSamplesQuery(samples: Sample[]) {
+  return samples.map((s) => {
     return {
       ...s.hasMetadataSampleMetadata[0],
       revisable: s.revisable,
     };
   });
 }
 
-export function getCohortDataFromSamples(samples: Sample[]) {
-  return samples.map((s: any) => {
+export function getSampleCohortDataFromSamplesQuery(samples: Sample[]) {
+  return samples.map((s) => {
+    const cohorts = s.cohortsHasCohortSampleConnection?.edges;
+    const cohortDates = cohorts?.flatMap((c) => {
+      return c.node.hasCohortCompleteCohortCompletes.map((cc) => {
+        return cc.date;
+      });
+    });
+    const deliveryDate = cohortDates?.sort()[0]; // earliest cohort date
+
+    const tempo = s.hasTempoTempos?.[0];
+    const bamComplete = tempo?.hasEventBamCompletes?.[0];
+    const { date: bamCompleteDate, status: bamCompleteStatus } =
+      bamComplete ?? {};
+
+    const mafComplete = tempo?.hasEventMafCompletes?.[0];
+    const {
+      date: mafCompleteDate,
+      status: mafCompleteStatus,
+      normalPrimaryId: mafCompleteNormalPrimaryId,
+    } = mafComplete ?? {};
+
+    const qcComplete = tempo?.hasEventQcCompletes?.[0];
+    const {
+      date: qcCompleteDate,
+      result: qcCompleteResult,
+      reason: qcCompleteReason,
+      status: qcCompleteStatus,
+    } = qcComplete ?? {};
+
     return {
       ...s.hasMetadataSampleMetadata[0],
-      revisable: s.revisable,
-      bamComplete: s.hasTempoTempos[0].hasEventBamCompletes[0],
-      mafComplete: s.hasTempoTempos[0].hasEventMafCompletes[0],
-      qcComplete: s.hasTempoTempos[0].hasEventQcCompletes[0],
+      deliveryDate,
+      bamCompleteDate,
+      bamCompleteStatus,
+      mafCompleteDate,
+      mafCompleteStatus,
+      mafCompleteNormalPrimaryId,
+      qcCompleteDate,
+      qcCompleteResult,
+      qcCompleteReason,
+      qcCompleteStatus,
     };
   });
 }

diff --git a/graphql-server/src/generated/graphql.ts b/graphql-server/src/generated/graphql.ts
@@ -10784,7 +10784,14 @@ export type FindSamplesByInputValueQuery = {
           __typename?: "SampleCohortsHasCohortSampleConnection";
           edges: Array<{
             __typename?: "SampleCohortsHasCohortSampleRelationship";
-            node: { __typename?: "Cohort"; cohortId: string };
+            node: {
+              __typename?: "Cohort";
+              cohortId: string;
+              hasCohortCompleteCohortCompletes: Array<{
+                __typename?: "CohortComplete";
+                date: string;
+              }>;
+            };
           }>;
         };
         hasTempoTempos: Array<{
@@ -11181,6 +11188,9 @@ export const FindSamplesByInputValueDocument = gql`
             edges {
               node {
                 cohortId
+                hasCohortCompleteCohortCompletes {
+                  date
+                }
               }
             }
           }

diff --git a/graphql/operations.graphql b/graphql/operations.graphql
@@ -87,6 +87,9 @@ query FindSamplesByInputValue(
           edges {
             node {
               cohortId
+              hasCohortCompleteCohortCompletes {
+                date
+              }
             }
           }
         }