Merge pull request #274 from ao508/search-by-man

Enable querying by molecular accession number when in sample PHI mode

Author: ao508

graphql-server/src/schemas/custom.ts

@@ -9,6 +9,7 @@ import {
   QueryDashboardPatientsArgs,
   QueryDashboardRequestsArgs,
   QueryDashboardSamplesArgs,
+  SeqDateAccessionBySampleId,
   TempoCohortRequestInput,
 } from "../generated/graphql";
 import { props } from "../utils/constants";
@@ -359,6 +360,34 @@ export async function buildCustomSchema(ogm: OGM) {
           PATIENT_DEMOGRAPHICS_CACHE_KEY
         ) as PatientDemographicsCache;
 
+        // if phi enabled, query for possible mapped sample ids to add to search vals list while removing phi searchables from search vals list
+        let dmpSampleSeqDateAccessions: Array<SeqDateAccessionBySampleId> = [];
+        if (searchVals && canSearchPhiData({ phiEnabled, searchVals })) {
+          dmpSampleSeqDateAccessions = await querySeqDatesByDmpSampleId(
+            searchVals
+          );
+          let mappedSampleIds: string[] = [];
+          let toRemove: string[] = [];
+          dmpSampleSeqDateAccessions.forEach((v) => {
+            if (
+              v.DMP_SAMPLE_ID &&
+              searchVals &&
+              !searchVals.includes(v.DMP_SAMPLE_ID)
+            ) {
+              mappedSampleIds.push(v.DMP_SAMPLE_ID);
+            }
+            if (
+              v.MOLECULAR_ACCESSION_NUMBER &&
+              searchVals &&
+              searchVals.includes(v.MOLECULAR_ACCESSION_NUMBER)
+            ) {
+              toRemove.push(v.MOLECULAR_ACCESSION_NUMBER);
+            }
+          });
+          searchVals.push(...mappedSampleIds);
+          searchVals = searchVals.filter((val) => !toRemove.includes(val));
+        }
+
         const addlOncotreeCodes = getAddlOtCodesMatchingCtOrCtdVals({
           searchVals,
           oncotreeCache,

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

@@ -690,10 +690,8 @@ function getPlatformByInstrumentModel(
     : null;
 }
 
-export async function querySeqDatesByDmpSampleId(dmpSampleIds: string[]) {
-  const dmpSampleIdsList = dmpSampleIds
-    .map((dmpSampleId) => `'${dmpSampleId}'`)
-    .join(",");
+export async function querySeqDatesByDmpSampleId(searchVals: string[]) {
+  const searchValList = searchVals.map((value) => `'${value}'`).join(",");
   const query = `
     SELECT
       ${props.databricks_seq_dates_by_sample_table}.DMP_SAMPLE_ID AS DMP_SAMPLE_ID,
@@ -704,7 +702,8 @@ export async function querySeqDatesByDmpSampleId(dmpSampleIds: string[]) {
     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
-      ${props.databricks_seq_dates_by_sample_table}.DMP_SAMPLE_ID IN (${dmpSampleIdsList})
+      ${props.databricks_seq_dates_by_sample_table}.DMP_SAMPLE_ID IN (${searchValList})
+      OR ${props.databricks_phi_mol_accession_table}.PDRX_ACCESSION_NO IN (${searchValList})
   `;
   return await queryDatabricks<SeqDateAccessionBySampleId>(query);
 }