Merge pull request #272 from ao508/molecular-accession-number

Molecular accession number

Author: ao508

frontend/src/generated/graphql.ts

@@ -36,7 +36,7 @@ import { NoteAddOutlined } from "@material-ui/icons";
 const QUERY_NAME = "dashboardSamples";
 const INITIAL_SORT_FIELD_NAME = "importDate";
 const RECORD_NAME = "samples";
-const PHI_FIELDS = new Set(["sequencingDate"]);
+const PHI_FIELDS = new Set(["sequencingDate", "molecularAccessionNumber"]);
 
 export function SamplesPage() {
   const [userSearchVal, setUserSearchVal] = useState("");

frontend/src/pages/samples/SamplesPage.tsx

@@ -149,6 +149,11 @@ export const sampleColDefs: Array<ColDef<DashboardSample>> = [
     headerName: "Sequencing Date",
     ...getPhiColDefProps({ widthSize: 260 }),
   },
+  {
+    field: "molecularAccessionNumber",
+    headerName: "Molecular Accession Number",
+    ...getPhiColDefProps({ widthSize: 260 }),
+  },
   {
     field: "cmoPatientId",
     headerName: "CMO Patient ID",

frontend/src/pages/samples/config.tsx

@@ -49,6 +49,7 @@ databricks_phi_id_mapping_table=
 databricks_seq_dates_by_patient_table=
 databricks_seq_dates_by_sample_table=
 databricks_cdsi_demographics_table=
+databricks_phi_mol_accession_table=
 
 [ccs]
 blocked_cohort_ids=

graphql-server/src/env/application.properties.EXAMPLE

@@ -3,7 +3,7 @@ import {
   DashboardSample,
   InputMaybe,
   QueryDashboardSamplesArgs,
-  SeqDateBySampleId,
+  SeqDateAccessionBySampleId,
 } from "../../generated/graphql";
 import { OncotreeCache, PatientDemographicsCache } from "../../utils/cache";
 import { neo4jDriver } from "../../utils/servers";
@@ -215,7 +215,7 @@ export function buildSamplesQueryBody({
         apoc.coll.toSet(
           [sid IN apoc.coll.sortMaps(sampleIdsList, "importDate")
             WHERE sid.cmoSampleName <> latestSm.cmoSampleName AND sid.cmoSampleName <> ""
-            | sid.cmoSampleName + " (" + sid.importDate + ")"
+            | sid.cmoSampleName + " (" + apoc.date.format(sid.importDate, 'ms', 'yyyy-MM-dd') + ")"
           ]
         ),
       ", ") AS historicalCmoSampleNames
@@ -655,33 +655,42 @@ export async function querySeqDatesByDmpSampleId(dmpSampleIds: string[]) {
     .join(",");
   const query = `
     SELECT
-      DMP_SAMPLE_ID,
-      SEQUENCING_DATE
+      ${props.databricks_seq_dates_by_sample_table}.DMP_SAMPLE_ID AS DMP_SAMPLE_ID,
+      ${props.databricks_seq_dates_by_sample_table}.SEQUENCING_DATE AS SEQUENCING_DATE,
+      ${props.databricks_phi_mol_accession_table}.PDRX_ACCESSION_NO AS MOLECULAR_ACCESSION_NUMBER
     FROM
       ${props.databricks_seq_dates_by_sample_table}
+    JOIN
+      ${props.databricks_phi_mol_accession_table} ON ${props.databricks_seq_dates_by_sample_table}.DMP_SAMPLE_ID = ${props.databricks_phi_mol_accession_table}.SAMPLE_ID
     WHERE
-      DMP_SAMPLE_ID IN (${dmpSampleIdsList})
+      ${props.databricks_seq_dates_by_sample_table}.DMP_SAMPLE_ID IN (${dmpSampleIdsList})
   `;
-  return await queryDatabricks<SeqDateBySampleId>(query);
+  return await queryDatabricks<SeqDateAccessionBySampleId>(query);
 }
 
 export function mapPhiToSamplesData({
   samplesData,
   seqDatesBySampleId,
 }: {
   samplesData: Array<DashboardSample>;
-  seqDatesBySampleId: Array<SeqDateBySampleId>;
+  seqDatesBySampleId: Array<SeqDateAccessionBySampleId>;
 }): Array<DashboardSample> {
   const seqDateBySampleIdMap: Record<string, string> = {};
+  const molAccessionBySampleIdMap: Record<string, string> = {};
   seqDatesBySampleId.forEach((seqDate) => {
     seqDateBySampleIdMap[seqDate.DMP_SAMPLE_ID] = seqDate.SEQUENCING_DATE;
+    molAccessionBySampleIdMap[seqDate.DMP_SAMPLE_ID] =
+      seqDate.MOLECULAR_ACCESSION_NUMBER ?? "";
   });
   return samplesData.map((sample) => {
     return {
       ...sample,
       sequencingDate: sample.primaryId
         ? seqDateBySampleIdMap[sample.primaryId]
         : null,
+      molecularAccessionNumber: sample.primaryId
+        ? molAccessionBySampleIdMap[sample.primaryId]
+        : null,
     };
   });
 }

graphql-server/src/generated/graphql.ts

@@ -57,6 +57,9 @@ export const props = {
   databricks_cdsi_demographics_table: properties.get(
     "databricks.databricks_cdsi_demographics_table"
   ),
+  databricks_phi_mol_accession_table: properties.get(
+    "databricks.databricks_phi_mol_accession_table"
+  ),
 
   ccs_blocked_cohort_ids: properties.get("ccs.blocked_cohort_ids"),
 };

graphql-server/src/schemas/queries/samples.ts

@@ -106,6 +106,7 @@ const SAMPLE_FIELDS = `
 
   # Databricks
   sequencingDate: String
+  molecularAccessionNumber: String
   race: String
 
   # results total
@@ -198,9 +199,10 @@ const QUERY_RESULT_TYPEDEFS = gql`
     ANCHOR_ONCOTREE_CODE: String!
   }
 
-  type SeqDateBySampleId {
+  type SeqDateAccessionBySampleId {
     DMP_SAMPLE_ID: String!
     SEQUENCING_DATE: String!
+    MOLECULAR_ACCESSION_NUMBER: String
   }
 
   type TempoCohortSample {