fix translation methods between query pages

query-connector/src/app/api/query/route.ts

@@ -17,7 +17,7 @@ import {
 
 import { handleRequestError } from "./error-handling-service";
 import { getSavedQueryByName } from "@/app/database-service";
-import { mapQueryRowsToValueSets } from "@/app/utils";
+import { unnestValueSetsFromQuery } from "@/app/utils";
 
 /**
  * Health check for TEFCA Viewer
@@ -90,7 +90,7 @@ export async function POST(request: NextRequest) {
   // Lookup default parameters for particular use-case search
   const queryName = UseCaseToQueryName[use_case as USE_CASES];
   const queryResults = await getSavedQueryByName(queryName);
-  const valueSets = mapQueryRowsToValueSets(queryResults);
+  const valueSets = unnestValueSetsFromQuery(queryResults);
 
   // Add params & patient identifiers to UseCaseRequest
   const UseCaseRequest: UseCaseQueryRequest = {

query-connector/src/app/database-service.ts

@@ -688,8 +688,7 @@ export async function getCustomQueries(): Promise<CustomUserQuery[]> {
       q.query_data,
       q.conditions_list
     FROM
-      query q
-    WHERE     q.query_name IN ('Gonorrhea case investigation', 'Newborn screening follow-up', 'Syphilis case investigation', 'Cancer case investigation', 'Chlamydia case investigation');
+      query q;
   `;
   // TODO: this will eventually need to take into account user permissions and specific authors
   // We'll probably also need to refactor this to not show up in any user-facing containers

query-connector/src/app/query/components/selectQuery/queryHooks.ts

@@ -5,7 +5,7 @@ import {
   hyperUnluckyPatient,
 } from "@/app/constants";
 import { getSavedQueryByName } from "@/app/database-service";
-import { mapQueryRowsToValueSets } from "@/app/utils";
+import { unnestValueSetsFromQuery } from "@/app/utils";
 import { UseCaseQuery, UseCaseQueryResponse } from "@/app/query-service";
 import { Patient } from "fhir/r4";
 
@@ -18,7 +18,7 @@ type SetStateCallback<T> = React.Dispatch<React.SetStateAction<T>>;
  */
 export async function fetchUseCaseValueSets(queryName: string) {
   const queryResults = await getSavedQueryByName(queryName);
-  const valueSets = mapQueryRowsToValueSets(queryResults);
+  const valueSets = unnestValueSetsFromQuery(queryResults);
 
   return valueSets;
 }

query-connector/src/app/queryBuilding/buildFromTemplates/page.tsx

@@ -13,15 +13,15 @@ import {
 import {
   CategoryNameToConditionOptionMap,
   ConditionIdToValueSetArray,
-  mapFetchedDataToFrontendStructure,
+  groupConditionDataByCategoryName,
 } from "../utils";
 import { ConditionSelection } from "../components/ConditionSelection";
 import { ValueSetSelection } from "../components/ValueSetSelection";
 import SiteAlert from "@/app/query/designSystem/SiteAlert";
 import { BuildStep } from "../../constants";
 import LoadingView from "../../query/components/LoadingView";
 import classNames from "classnames";
-import { mapQueryRowsToValueSets } from "@/app/utils";
+import { groupConditionConceptsIntoValueSets } from "@/app/utils";
 import { batchToggleConcepts } from "../utils";
 
 export type FormError = {
@@ -82,7 +82,8 @@ export default function QueryTemplateSelection() {
     // if there are new ids, we need to query the db
     if (idsToQuery && idsToQuery.length > 0) {
       const results = await getValueSetsAndConceptsByConditionIDs(conditionIds);
-      const formattedResults = results && mapQueryRowsToValueSets(results);
+      const formattedResults =
+        results && groupConditionConceptsIntoValueSets(results);
 
       // when fetching directly from conditions table (as opposed to a saved query),
       // default to including all value sets
@@ -138,7 +139,7 @@ export default function QueryTemplateSelection() {
 
       if (isSubscribed) {
         setFetchedConditions(
-          mapFetchedDataToFrontendStructure(categoryToConditionArrayMap),
+          groupConditionDataByCategoryName(categoryToConditionArrayMap),
         );
       }
     }

query-connector/src/app/queryBuilding/components/ConditionSelection.tsx

@@ -6,7 +6,7 @@ import classNames from "classnames";
 import { getConditionsData } from "@/app/database-service";
 import {
   CategoryNameToConditionOptionMap,
-  mapFetchedDataToFrontendStructure,
+  groupConditionDataByCategoryName,
   ConditionIdToValueSetArray,
 } from "../utils";
 import ConditionColumnDisplay from "../buildFromTemplates/ConditionColumnDisplay";
@@ -78,7 +78,7 @@ export const ConditionSelection: React.FC<ConditionSelectionProps> = ({
 
       if (isSubscribed) {
         setFetchedConditions(
-          mapFetchedDataToFrontendStructure(categoryToConditionArrayMap),
+          groupConditionDataByCategoryName(categoryToConditionArrayMap),
         );
       }
     }

query-connector/src/app/queryBuilding/utils.ts

@@ -49,7 +49,7 @@ export type CategoryNameToConditionOptionMap = {
  * category mapping
  * @returns - The data in a CategoryNameToConditionOptionMap shape
  */
-export function mapFetchedDataToFrontendStructure(fetchedData: {
+export function groupConditionDataByCategoryName(fetchedData: {
   [categoryName: string]: ConditionIdToNameMap[];
 }) {
   const result: CategoryNameToConditionOptionMap = {};

query-connector/src/app/tests/unit/fixtures.ts

@@ -0,0 +1,155 @@
+import categoryToConditionArrayMap from "../assets/aphlCategoryMapping.json";
+import queryTableDefaults from "../../assets/dibbs_db_seed_query.json";
+import { ConditionIdToNameMap } from "@/app/queryBuilding/utils";
+import { QueryResultRow } from "pg";
+
+export const CATEGORY_TO_CONDITION_ARRAY_MAP =
+  categoryToConditionArrayMap as unknown as {
+    [categoryName: string]: ConditionIdToNameMap[];
+  };
+
+export const DEFAULT_CHLAMYDIA_QUERY = [
+  queryTableDefaults.query.find((v) =>
+    v.query_name.includes("Chlamydia case investigation"),
+  ),
+] as QueryResultRow[];
+
+export const EXPECTED_CHLAMYDIA_VALUESET_LENGTH = Object.values(
+  DEFAULT_CHLAMYDIA_QUERY[0].query_data[
+    "Chlamydia trachomatis infection (disorder)"
+  ],
+).length;
+
+export const CANCER_VALUESETS = [
+  {
+    display: "RESULTS",
+    code_system: "http://cap.org/eCC",
+    code: "9484.100004300",
+    valueset_name: "Cancer (Leukemia) Lab Result",
+    valueset_id: "14_20240923",
+    valueset_external_id: "14",
+    version: "20240923",
+    author: "DIBBs",
+    type: "lrtc",
+    dibbs_concept_type: "labs",
+    condition_id: "2",
+  },
+  {
+    display:
+      "Presence of DNA mismatch repair protein MSH2 in primary malignant neoplasm of colon by immunohistochemistry (observable entity)",
+    code_system: "http://snomed.info/sct",
+    code: "1255068005",
+    valueset_name: "Cancer (Leukemia) Lab Result",
+    valueset_id: "14_20240923",
+    valueset_external_id: "14",
+    version: "20240923",
+    author: "DIBBs",
+    type: "lrtc",
+    dibbs_concept_type: "labs",
+    condition_id: "2",
+  },
+  {
+    display: "MSH2 Result",
+    code_system: "http://cap.org/eCC",
+    code: "30000.100004300",
+    valueset_name: "Cancer (Leukemia) Lab Result",
+    valueset_id: "14_20240923",
+    valueset_external_id: "14",
+    version: "20240923",
+    author: "DIBBs",
+    type: "lrtc",
+    dibbs_concept_type: "labs",
+    condition_id: "2",
+  },
+  {
+    display: "Malignant neoplastic disease (disorder)",
+    code_system: "http://snomed.info/sct",
+    code: "363346000",
+    valueset_name: "Suspected Cancer (Leukemia) Diagnosis",
+    valueset_id: "15_20240923",
+    valueset_external_id: "15",
+    version: "20240923",
+    author: "DIBBs",
+    type: "sdtc",
+    dibbs_concept_type: "conditions",
+    condition_id: "2",
+  },
+  {
+    display: "1 ML alemtuzumab 30 MG/ML Injection",
+    code_system: "http://www.nlm.nih.gov/research/umls/rxnorm",
+    code: "828265",
+    valueset_name: "Cancer (Leukemia) Medication",
+    valueset_id: "3_20240909",
+    valueset_external_id: "3",
+    version: "20240909",
+    author: "DIBBs",
+    type: "mrtc",
+    dibbs_concept_type: "medications",
+    condition_id: "2",
+  },
+  {
+    display: "Stage II (localized)",
+    code_system: "http://snomed.info/sct",
+    code: "36929009",
+    valueset_name: "Cancer (Leukemia) Diagnosis Problem",
+    valueset_id: "2_20240909",
+    valueset_external_id: "2",
+    version: "20240909",
+    author: "DIBBs",
+    type: "dxtc",
+    dibbs_concept_type: "conditions",
+    condition_id: "2",
+  },
+  {
+    display: "Stage group.clinical Cancer",
+    code_system: "http://loinc.org",
+    code: "21908-9",
+    valueset_name: "Cancer (Leukemia) Diagnosis Problem",
+    valueset_id: "2_20240909",
+    valueset_external_id: "2",
+    version: "20240909",
+    author: "DIBBs",
+    type: "dxtc",
+    dibbs_concept_type: "conditions",
+    condition_id: "2",
+  },
+  {
+    display: "Pathology Synoptic report",
+    code_system: "http://loinc.org",
+    code: "60568-3",
+    valueset_name: "Cancer (Leukemia) Diagnosis Problem",
+    valueset_id: "2_20240909",
+    valueset_external_id: "2",
+    version: "20240909",
+    author: "DIBBs",
+    type: "dxtc",
+    dibbs_concept_type: "conditions",
+    condition_id: "2",
+  },
+  {
+    display: "Chronic lymphoid leukemia, disease (disorder)",
+    code_system: "http://snomed.info/sct",
+    code: "92814006",
+    valueset_name: "Cancer (Leukemia) Diagnosis Problem",
+    valueset_id: "2_20240909",
+    valueset_external_id: "2",
+    version: "20240909",
+    author: "DIBBs",
+    type: "dxtc",
+    dibbs_concept_type: "conditions",
+    condition_id: "2",
+  },
+  {
+    display: "Allergy to sulfonamide",
+    code_system: "http://snomed.info/sct",
+    code: "418689008",
+    valueset_name: "Cancer (Leukemia) Diagnosis Problem",
+    valueset_id: "2_20240909",
+    valueset_external_id: "2",
+    version: "20240909",
+    author: "DIBBs",
+    type: "dxtc",
+    dibbs_concept_type: "conditions",
+    condition_id: "2",
+  },
+];

query-connector/src/app/tests/unit/utils.test.tsx

@@ -1,12 +1,22 @@
 import React from "react";
 import { render, screen } from "@testing-library/react";
-import { DataDisplay, DataDisplayInfo } from "../../utils";
-import categoryToConditionArrayMap from "../assets/aphlCategoryMapping.json";
 import {
-  ConditionIdToNameMap,
-  mapFetchedDataToFrontendStructure,
+  DataDisplay,
+  DataDisplayInfo,
+  groupConditionConceptsIntoValueSets,
+  unnestValueSetsFromQuery,
+} from "../../utils";
+
+import {
+  groupConditionDataByCategoryName,
   filterSearchByCategoryAndCondition,
 } from "@/app/queryBuilding/utils";
+import {
+  CANCER_VALUESETS,
+  CATEGORY_TO_CONDITION_ARRAY_MAP,
+  DEFAULT_CHLAMYDIA_QUERY,
+  EXPECTED_CHLAMYDIA_VALUESET_LENGTH,
+} from "./fixtures";
 
 describe("DataDisplay Component", () => {
   it("should render the title and value", () => {
@@ -73,14 +83,12 @@ describe("DataDisplay Component", () => {
   });
 });
 
-const TEST_FIXTURE = categoryToConditionArrayMap as unknown as {
-  [categoryName: string]: ConditionIdToNameMap[];
-};
-
 describe("data util methods for query building", () => {
-  describe("mapFetchedDataToFrontendStructure", () => {
+  describe("groupConditionDataByCategoryName", () => {
     it("translates backend query to frontend dictionary structure", () => {
-      const mappedExample = mapFetchedDataToFrontendStructure(TEST_FIXTURE);
+      const mappedExample = groupConditionDataByCategoryName(
+        CATEGORY_TO_CONDITION_ARRAY_MAP,
+      );
       // check a couple of random values to make sure mapping works correctly
       expect(mappedExample["Injuries, NEC"][44301001].name).toBe(
         "Suicide (event)",
@@ -97,8 +105,9 @@ describe("data util methods for query building", () => {
 
   describe("filterSearchByCategoryAndCondition", () => {
     it("filters by category (parent level)", () => {
-      const frontendStructuredData =
-        mapFetchedDataToFrontendStructure(TEST_FIXTURE);
+      const frontendStructuredData = groupConditionDataByCategoryName(
+        CATEGORY_TO_CONDITION_ARRAY_MAP,
+      );
       const filterResults = filterSearchByCategoryAndCondition(
         "Diseases",
         frontendStructuredData,
@@ -107,8 +116,9 @@ describe("data util methods for query building", () => {
       expect(Object.values(filterResults).length).toBe(9);
     });
     it("filters by condition (child level)", () => {
-      const frontendStructuredData =
-        mapFetchedDataToFrontendStructure(TEST_FIXTURE);
+      const frontendStructuredData = groupConditionDataByCategoryName(
+        CATEGORY_TO_CONDITION_ARRAY_MAP,
+      );
       const filterResults = filterSearchByCategoryAndCondition(
         "hepatitis",
         frontendStructuredData,
@@ -123,4 +133,30 @@ describe("data util methods for query building", () => {
       expect(countOfResults[0] + countOfResults[1]).toBe(8);
     });
   });
+
+  describe("unnestValueSetsFromQuery", () => {
+    const unnestedVals = unnestValueSetsFromQuery(DEFAULT_CHLAMYDIA_QUERY);
+    expect(unnestedVals.length).toBe(EXPECTED_CHLAMYDIA_VALUESET_LENGTH);
+  });
+
+  describe("groupConditionConceptsByValueSetId", () => {
+    const formattedValueSets =
+      groupConditionConceptsIntoValueSets(CANCER_VALUESETS);
+    const EXPECTED_CANCER_VALUESET_GROUPS = 4;
+    expect(formattedValueSets.length).toBe(EXPECTED_CANCER_VALUESET_GROUPS);
+    expect(
+      formattedValueSets.find((v) => v.valueSetId === "14_20240923")?.concepts
+        .length,
+    ).toBe(3);
+    expect(
+      formattedValueSets.find((v) => v.valueSetId === "2_20240909")?.concepts
+        .length,
+    ).toBe(5);
+
+    expect(
+      formattedValueSets
+        .find((v) => v.valueSetId === "2_20240909")
+        ?.concepts.every((v) => Boolean(v)),
+    ).toBeTrue();
+  });
 });