Merge branch 'main' into rob/2783-fix-errors-generated-by-eslintrcjson

query-connector/flyway/sql/V01_06__add_dibbsConceptType.sql

@@ -1,5 +1,5 @@
 ALTER TABLE valuesets
-ADD COLUMN dibbsConceptType text GENERATED ALWAYS AS (
+ADD COLUMN dibbs_concept_type text GENERATED ALWAYS AS (
     CASE
         WHEN type IN ('lotc', 'lrtc', 'ostc') THEN 'labs'
         WHEN type = 'mrtc' THEN 'medications'

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

@@ -18,7 +18,7 @@ import {
 import { handleRequestError } from "./error-handling-service";
 import {
   getSavedQueryByName,
-  mapQueryRowsToValueSetItems,
+  mapQueryRowsToConceptValueSets,
 } from "@/app/database-service";
 
 /**
@@ -92,7 +92,7 @@ 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 vsItems = await mapQueryRowsToValueSetItems(queryResults);
+  const valueSets = await mapQueryRowsToConceptValueSets(queryResults);
 
   // Add params & patient identifiers to UseCaseRequest
   const UseCaseRequest: UseCaseQueryRequest = {
@@ -111,7 +111,7 @@ export async function POST(request: NextRequest) {
 
   const UseCaseQueryResponse: QueryResponse = await UseCaseQuery(
     UseCaseRequest,
-    vsItems,
+    valueSets,
   );
 
   // Bundle data

query-connector/src/app/constants.ts

@@ -302,38 +302,6 @@ export const metadata = {
   description: "Try out TEFCA with queries for public health use cases.",
 };
 
-// TODO: Remove ValueSetItem, ValueSet, and valueSetTypeToClincalServiceTypeMap once
-// ticket #2789 is resolved
-
-/*Type to specify the expected components for each item in a value set that will be 
-displayed in the CustomizeQuery component*/
-export interface ValueSetItem {
-  code: string;
-  display: string;
-  system: string;
-  include: boolean;
-  author: string;
-  clinicalServiceType: string;
-  valueSetName: string;
-}
-
-/*Type to specify the expected expected types of valueset items that will be displayed 
-as separate tabs in the CusomizeQuery component*/
-export interface ValueSet {
-  labs: ValueSetItem[];
-  medications: ValueSetItem[];
-  conditions: ValueSetItem[];
-}
-
-export type ValueSetType = keyof ValueSet;
-
-export const valueSetTypeToClincalServiceTypeMap = {
-  labs: ["ostc", "lotc", "lrtc"],
-  medications: ["mrtc"],
-  conditions: ["dxtc", "sdtc"],
-};
-/// TODO: Remove the above once ticket #2789 is resolved
-
 /*
  * The expected type of a ValueSet concept.
  */
@@ -346,17 +314,17 @@ export interface Concept {
 /*
  * The expected type of a ValueSet.
  */
-// export interface ValueSet {
-//   valueset_id: string;
-//   valueset_version: string;
-//   valueset_name: string;
-//   author: string;
-//   system: string;
-//   ersdConceptType?: string;
-//   dibbsConceptType: string;
-//   includeValueSet: boolean;
-//   concepts: Concept[];
-// }
+export interface ValueSet {
+  valueSetId: string;
+  valueSetVersion: string;
+  valueSetName: string;
+  author: string;
+  system: string;
+  ersdConceptType?: string;
+  dibbsConceptType: string;
+  includeValueSet: boolean;
+  concepts: Concept[];
+}
 
 /*
  * The expected type of ValueSets grouped by dibbsConceptType for the purpose of display.
@@ -366,6 +334,8 @@ export interface ValueSetDisplay {
   medications: ValueSet[];
   conditions: ValueSet[];
 }
+export type DibbsValueSetType = keyof ValueSetDisplay;
+
 
 // Define the type guard for FHIR resources
 // Define the FHIR Resource types

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

@@ -1,11 +1,11 @@
 "use server";
 import { Pool, PoolConfig, QueryResultRow } from "pg";
 import { Bundle, OperationOutcome } from "fhir/r4";
-import { ValueSetItem, valueSetTypeToClincalServiceTypeMap } from "./constants";
 import { encode } from "base-64";
+import { ValueSet } from "./constants";
 
 const getQuerybyNameSQL = `
-select q.query_name, q.id, qtv.valueset_id, vs.name as valueset_name, vs.author as author, vs.type, qic.concept_id, qic.include, c.code, c.code_system, c.display 
+select q.query_name, q.id, qtv.valueset_id, vs.name as valueset_name, vs.version, vs.author as author, vs.type, vs.dibbs_concept_type as dibbs_concept_type, qic.concept_id, qic.include, c.code, c.code_system, c.display 
   from query q 
   left join query_to_valueset qtv on q.id = qtv.query_id 
   left join valuesets vs on qtv.valueset_id = vs.id
@@ -48,45 +48,48 @@ export const getSavedQueryByName = async (name: string) => {
 };
 
 /**
- * Helper function to filter the valueset-mapped rows of results returned from
- * the DB for particular types of related clinical services.
- * @param vsItems A list of value sets mapped from DB rows.
- * @param type One of "labs", "medications", or "conditions".
- * @returns A list of rows containing only the predicate service type.
+ * Maps the results returned from the DIBBs value set and coding system database
+ * into a collection of value sets, each containing one or more Concepts build out
+ * of the coding information in the DB.
+ * @param rows The Rows returned from the DB Query.
+ * @returns A list of ValueSets, which hold the Concepts pulled from the DB.
  */
-export const filterValueSets = async (
-  vsItems: ValueSetItem[],
-  type: "labs" | "medications" | "conditions",
+export const mapQueryRowsToConceptValueSets = async (
+  rows: QueryResultRow[],
 ) => {
-  // Assign clinical code type based on desired filter
-  // Mapping is established in TCR, so follow that convention
-  let valuesetFilters = valueSetTypeToClincalServiceTypeMap[type];
-  const results = vsItems.filter((vs) =>
-    valuesetFilters.includes(vs.clinicalServiceType),
-  );
-  return results;
-};
+  // Create groupings of rows (each of which is a single Concept) by their ValueSet ID
+  const vsIdGroupedRows = rows.reduce((conceptsByVSId, r) => {
+    if (!(r["valueset_id"] in conceptsByVSId)) {
+      conceptsByVSId[r["valueset_id"]] = [];
+    }
+    conceptsByVSId[r["valueset_id"]].push(r);
+    return conceptsByVSId;
+  }, {});
 
-/**
- * Helper function that transforms and groups a set of database rows into a list of
- * ValueSet items grouped by author and code_system for display on the CustomizeQuery page.
- * @param rows The rows returned from the DB.
- * @returns A list of ValueSetItems grouped by author and system.
- */
-export const mapQueryRowsToValueSetItems = async (rows: QueryResultRow[]) => {
-  const vsItems = rows.map((r) => {
-    const vsTranslation: ValueSetItem = {
-      code: r["code"],
-      display: r["display"],
-      system: r["code_system"],
-      include: r["include"],
-      author: r["author"],
-      valueSetName: r["valueset_name"],
-      clinicalServiceType: r["type"],
+  // Each "prop" of the struct is now a ValueSet ID
+  // Iterate over them to create formal Concept Groups attached to a formal VS
+  const valueSets = Object.keys(vsIdGroupedRows).map((vsID) => {
+    const conceptGroup: QueryResultRow[] = vsIdGroupedRows[vsID];
+    const valueSet: ValueSet = {
+      valueSetId: conceptGroup[0]["valueset_id"],
+      valueSetVersion: conceptGroup[0]["version"],
+      valueSetName: conceptGroup[0]["valueset_name"],
+      author: conceptGroup[0]["author"],
+      system: conceptGroup[0]["code_system"],
+      ersdConceptType: conceptGroup[0]["type"],
+      dibbsConceptType: conceptGroup[0]["dibbs_concept_type"],
+      includeValueSet: conceptGroup.find((c) => c["include"]) ? true : false,
+      concepts: conceptGroup.map((c) => {
+        return {
+          code: c["code"],
+          display: c["display"],
+          include: c["include"],
+        };
+      }),
     };
-    return vsTranslation;
+    return valueSet;
   });
-  return vsItems;
+  return valueSets;
 };
 
 /*

query-connector/src/app/format-service.tsx

@@ -6,7 +6,7 @@ import {
   ContactPoint,
   Identifier,
 } from "fhir/r4";
-import { ValueSetItem } from "./constants";
+import { ValueSet } from "./constants";
 import { QueryStruct } from "./query-service";
 
 /**
@@ -261,29 +261,38 @@ export async function GetPhoneQueryFormats(phone: string) {
 }
 
 /**
- * Formats a statefully updated list of value set items into a JSON structure
+ * Formats a statefully updated list of value sets into a JSON structure
  * used for executing custom queries.
  * @param useCase The base use case being queried for.
- * @param vsItems The list of value set items the user wants included.
+ * @param valueSets The list of value sets the user wants included.
  * @returns A structured specification of a query that can be executed.
  */
-export const formatValueSetItemsAsQuerySpec = async (
+export const formatValueSetsAsQuerySpec = async (
   useCase: string,
-  vsItems: ValueSetItem[],
+  valueSets: ValueSet[],
 ) => {
   let secondEncounter: boolean = false;
   if (["cancer", "chlamydia", "gonorrhea", "syphilis"].includes(useCase)) {
     secondEncounter = true;
   }
-  const labCodes: string[] = vsItems
+  const labCodes: string[] = valueSets
     .filter((vs) => vs.system === "http://loinc.org")
-    .map((vs) => vs.code);
-  const snomedCodes: string[] = vsItems
+    .reduce((acc, vs) => {
+      vs.concepts.forEach((concept) => acc.push(concept.code));
+      return acc;
+    }, [] as string[]);
+  const snomedCodes: string[] = valueSets
     .filter((vs) => vs.system === "http://snomed.info/sct")
-    .map((vs) => vs.code);
-  const rxnormCodes: string[] = vsItems
+    .reduce((acc, vs) => {
+      vs.concepts.forEach((concept) => acc.push(concept.code));
+      return acc;
+    }, [] as string[]);
+  const rxnormCodes: string[] = valueSets
     .filter((vs) => vs.system === "http://www.nlm.nih.gov/research/umls/rxnorm")
-    .map((vs) => vs.code);
+    .reduce((acc, vs) => {
+      vs.concepts.forEach((concept) => acc.push(concept.code));
+      return acc;
+    }, [] as string[]);
 
   const spec: QueryStruct = {
     labCodes: labCodes,

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

@@ -6,13 +6,14 @@ import FHIRClient from "./fhir-servers";
 import {
   USE_CASES,
   FHIR_SERVERS,
-  ValueSetItem,
+  ValueSet,
   isFhirResource,
   FhirResource,
 } from "./constants";
+
 import { CustomQuery } from "./CustomQuery";
 import { GetPhoneQueryFormats } from "./format-service";
-import { formatValueSetItemsAsQuerySpec } from "./format-service";
+import { formatValueSetsAsQuerySpec } from "./format-service";
 
 /**
  * The query response when the request source is from the Viewer UI.
@@ -146,7 +147,7 @@ async function patientQuery(
  */
 export async function UseCaseQuery(
   request: UseCaseQueryRequest,
-  queryValueSets: ValueSetItem[],
+  queryValueSets: ValueSet[],
   queryResponse: QueryResponse = {},
 ): Promise<QueryResponse> {
   const fhirClient = new FHIRClient(request.fhir_server);
@@ -187,15 +188,12 @@ export async function UseCaseQuery(
  */
 async function generalizedQuery(
   useCase: USE_CASES,
-  queryValueSets: ValueSetItem[],
+  queryValueSets: ValueSet[],
   patientId: string,
   fhirClient: FHIRClient,
   queryResponse: QueryResponse,
 ): Promise<QueryResponse> {
-  const querySpec = await formatValueSetItemsAsQuerySpec(
-    useCase,
-    queryValueSets,
-  );
+  const querySpec = await formatValueSetsAsQuerySpec(useCase, queryValueSets);
   const builtQuery = new CustomQuery(querySpec, patientId);
   let response: fetch.Response | fetch.Response[];
 

query-connector/src/app/query/SelectQuery.tsx

@@ -1,6 +1,6 @@
 "use client";
 import React, { useEffect, useState } from "react";
-import { FHIR_SERVERS, USE_CASES, ValueSetItem } from "../constants";
+import { FHIR_SERVERS, USE_CASES, ValueSet } from "../constants";
 import CustomizeQuery from "./components/CustomizeQuery";
 import SelectSavedQuery from "./components/selectQuery/SelectSavedQuery";
 
@@ -57,8 +57,8 @@ const SelectQuery: React.FC<SelectQueryProps> = ({
   setFhirServer,
   setShowCustomizeQuery,
 }) => {
-  const [queryValueSets, setQueryValueSets] = useState<ValueSetItem[]>(
-    [] as ValueSetItem[],
+  const [queryValueSets, setQueryValueSets] = useState<ValueSet[]>(
+    [] as ValueSet[],
   );
   const [loadingQueryValueSets, setLoadingQueryValueSets] =
     useState<boolean>(false);
@@ -97,6 +97,7 @@ const SelectQuery: React.FC<SelectQueryProps> = ({
   }
 
   const displayLoading = loadingResultResponse || loadingQueryValueSets;
+
   return (
     <div>
       {displayLoading && <LoadingView loading={loadingResultResponse} />}