Merge branch 'develop' into MAT-6475

MeasureAuthoringTool · Dec 11, 2023 · 00b854d · 00b854d
2 parents ecd7127 + a339621
commit 00b854d
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Showing 25 changed files with 1,921 additions and 131 deletions.
diff --git a/.husky/pre-commit b/.husky/pre-commit
@@ -1,4 +1,4 @@
 /bin/sh
 . "$(dirname "$0")/_/husky.sh"
 
-npm exec pretty-quick --staged && npm exec concurrently npm:test npm:lint
+npm exec pretty-quick --staged && npm exec concurrently "npm:lint" "npm:test -- --silent"
diff --git a/src/api/CqmModelConversionService.ts b/src/api/CqmModelConversionService.ts
@@ -14,6 +14,7 @@ import {
   PopulationSet,
   MeasurePeriod,
   ValueSet,
+  CodeSystem,
 } from "cqm-models";
 import { ServiceConfig } from "./ServiceContext";
 import useServiceConfig from "./useServiceConfig";
@@ -282,6 +283,9 @@ export class CqmConversionService {
     elmJson.library?.valueSets?.def.forEach((valueSet: ValueSet) => {
       valueSet.id = valueSet.id.replace("urn:oid:", "");
     });
+    elmJson.library?.codeSystems?.def.forEach((codeSystem: CodeSystem) => {
+      codeSystem.id = codeSystem.id.replace("urn:oid:", "");
+    });
     const cqlLibrary = new CQLLibrary();
     cqlLibrary.library_name = elmJson.library?.identifier.id;
     cqlLibrary.library_version = elmJson.library?.identifier.version;

diff --git a/src/api/TerminologyServiceApi.test.ts b/src/api/TerminologyServiceApi.test.ts
@@ -4,7 +4,7 @@ import { officeVisitValueSet } from "./__mocks__/OfficeVisitValueSet";
 import { officeVisitMeasureBundle } from "./__mocks__/OfficeVisitMeasureBundle";
 import { cqm_measure_basic } from "../mockdata/qdm/CMS108/cqm_measure_basic";
 import { cqm_measure_basic_valueset } from "../mockdata/qdm/CMS108/cqm_measure_basic_valueset";
-import { Measure as CqmMeasure } from "cqm-models";
+import { Measure as CqmMeasure, ValueSet } from "cqm-models";
 import * as _ from "lodash";
 
 jest.mock("axios");
@@ -81,7 +81,7 @@ describe("TerminologyServiceApi Tests", () => {
 
     terminologyService
       .getQdmValueSetsExpansion(cqm_measure_basic)
-      .then((data) => {
+      .then((data: ValueSet[]) => {
         expect(data.length).toEqual(2);
         expect(data[0].display_name).toEqual("Encounter Inpatient");
         expect(data[0].oid).toEqual("2.16.840.1.113883.3.666.5.307");
@@ -136,15 +136,18 @@ describe("TerminologyServiceApi Tests", () => {
     const result = terminologyService.getCqlCodesForDRCs(cqm_measure_basic);
     expect(result.length).toBe(3);
 
-    expect(result[0].code).toBe("drc-bdb8b89536181a411ad034378b7ceef6");
-    expect(result[0].system).toBe("LOINC");
-    expect(result[0].display).toBe("Housing status");
-    expect(result[1].code).toBe("160734000");
-    expect(result[1].system).toBe("SNOMEDCT");
-    expect(result[1].display).toBe("Lives in a nursing home (finding)");
-    expect(result[2].code).toBe("98181-1");
-    expect(result[2].system).toBe("LOINC");
-    expect(result[2].display).toBe("Medical equipment used");
+    expect(result[0].cqlCode.code).toBe("drc-bdb8b89536181a411ad034378b7ceef6");
+    expect(result[0].cqlCode.system).toBe("LOINC");
+    expect(result[0].cqlCode.display).toBe("Housing status");
+    expect(result[0].codeSystemOid).toBe("2.16.840.1.113883.6.1");
+    expect(result[1].cqlCode.code).toBe("160734000");
+    expect(result[1].cqlCode.system).toBe("SNOMEDCT");
+    expect(result[1].cqlCode.display).toBe("Lives in a nursing home (finding)");
+    expect(result[1].codeSystemOid).toBe("2.16.840.1.113883.6.96");
+    expect(result[2].cqlCode.code).toBe("98181-1");
+    expect(result[2].cqlCode.system).toBe("LOINC");
+    expect(result[2].cqlCode.display).toBe("Medical equipment used");
+    expect(result[2].codeSystemOid).toBe("2.16.840.1.113883.6.1");
   });
 
   it("test getCqlCodesForDRCs no codes", () => {
@@ -161,7 +164,8 @@ describe("TerminologyServiceApi Tests", () => {
   });
 
   it("test getValueSetsForDRCs", () => {
-    const result = terminologyService.getValueSetsForDRCs(cqm_measure_basic);
+    const result: ValueSet[] =
+      terminologyService.getValueSetsForDRCs(cqm_measure_basic);
 
     expect(result.length).toBe(1);
 
@@ -171,6 +175,7 @@ describe("TerminologyServiceApi Tests", () => {
     );
     expect(result[0].concepts[0].code_system_name).toBe("LOINC");
     expect(result[0].concepts[0].display_name).toBe("Housing status");
+    expect(result[0].concepts[0].code_system_oid).toBe("2.16.840.1.113883.6.1");
   });
 
   it("test getValueSetsForDRCs no value sets", () => {

diff --git a/src/api/useCqlParsingService.ts b/src/api/useCqlParsingService.ts
@@ -0,0 +1,61 @@
+import axios from "axios";
+import useServiceConfig from "./useServiceConfig";
+import { ServiceConfig } from "./ServiceContext";
+import { useOktaTokens } from "@madie/madie-util";
+import { CqlDefinitionExpression } from "../util/GroupCoverageHelpers";
+import { CqlDefinitionCallstack } from "../components/editTestCase/groupCoverage/QiCoreGroupCoverage";
+
+export class CqlParsingService {
+  constructor(private baseUrl: string, private getAccessToken: () => string) {}
+
+  async getDefinitionCallstacks(cql: string): Promise<CqlDefinitionCallstack> {
+    try {
+      const response = await axios.put<string>(
+        `${this.baseUrl}/cql/callstacks`,
+        cql,
+        {
+          headers: {
+            Authorization: `Bearer ${this.getAccessToken()}`,
+            "Content-Type": "text/plain",
+          },
+        }
+      );
+      return response.data as unknown as CqlDefinitionCallstack;
+    } catch (err) {
+      const message = `Unable to retrieve used definition references`;
+      throw new Error(message);
+    }
+  }
+
+  async getAllDefinitionsAndFunctions(
+    cql: string
+  ): Promise<CqlDefinitionExpression[]> {
+    try {
+      const response = await axios.put<string>(
+        `${this.baseUrl}/cql/definitions`,
+        cql,
+        {
+          headers: {
+            Authorization: `Bearer ${this.getAccessToken()}`,
+            "Content-Type": "text/plain",
+          },
+        }
+      );
+      return response.data as unknown as CqlDefinitionExpression[];
+    } catch (err) {
+      const message = `Unable to retrieve definition and function references`;
+      throw new Error(message);
+    }
+  }
+}
+
+const useCqlParsingService = (): CqlParsingService => {
+  const serviceConfig: ServiceConfig = useServiceConfig();
+  const { getAccessToken } = useOktaTokens();
+  return new CqlParsingService(
+    serviceConfig?.elmTranslationService.baseUrl,
+    getAccessToken
+  );
+};
+
+export default useCqlParsingService;
diff --git a/src/api/useTerminologyServiceApi.ts b/src/api/useTerminologyServiceApi.ts
@@ -18,6 +18,11 @@ type ValueSetsSearchCriteria = {
   valueSetParams: ValueSetSearchParams[];
 };
 
+type CQLCodeWithCodeSystemOid = {
+  cqlCode: CQL.CQLCode;
+  codeSystemOid: string;
+};
+
 export class TerminologyServiceApi {
   constructor(private baseUrl: string, private getAccessToken: () => string) {}
 
@@ -173,9 +178,10 @@ export class TerminologyServiceApi {
 
   getValueSetsForDRCs(cqmMeasure: CqmMeasure): ValueSet[] {
     const drcValueSets = [];
-    const cqlCodes: CQL.CQLCode[] = this.getCqlCodesForDRCs(cqmMeasure);
-    if (cqlCodes) {
-      cqlCodes.forEach((cqlCode) => {
+    const cqlCodeWithCodeSystemOid: CQLCodeWithCodeSystemOid[] =
+      this.getCqlCodesForDRCs(cqmMeasure);
+    if (cqlCodeWithCodeSystemOid) {
+      cqlCodeWithCodeSystemOid.forEach(({ cqlCode, codeSystemOid }) => {
         const drcOid = this.getDrcOid(cqmMeasure, cqlCode.code);
         if (drcOid) {
           const valueSet = {
@@ -184,7 +190,7 @@ export class TerminologyServiceApi {
             concepts: [
               {
                 code: cqlCode.code,
-                code_system_oid: cqlCode.system,
+                code_system_oid: codeSystemOid,
                 code_system_name: cqlCode.system,
                 code_system_version: cqlCode.version,
                 display_name: cqlCode.display,
@@ -199,23 +205,31 @@ export class TerminologyServiceApi {
     return drcValueSets;
   }
 
-  getCqlCodesForDRCs(cqmMeasure: CqmMeasure): CQL.CQLCode[] {
-    const cqlCodes: CQL.CQLCode[] = [];
+  getCqlCodesForDRCs(cqmMeasure: CqmMeasure): CQLCodeWithCodeSystemOid[] {
+    const cqlCodeWithCodeSystemOid: CQLCodeWithCodeSystemOid[] = [];
     cqmMeasure?.cql_libraries?.forEach((library) => {
       const codeDefs = library?.elm?.library?.codes?.def;
+      const codeSystemDefs = library?.elm?.library?.codeSystems?.def;
       if (!_.isEmpty(codeDefs)) {
         codeDefs.forEach((def) => {
+          // find associated CodeSystem for this code, so that we can get codeSystem oid
+          const codeSystem = codeSystemDefs.find(
+            (cs) => cs.name === def.codeSystem.name
+          );
           const cqlCode = new CQL.Code(
             def?.id, //code
             def.codeSystem.name, //system
             "N/A", //version,
             def.display //display
           );
-          cqlCodes.push(cqlCode);
+          cqlCodeWithCodeSystemOid.push({
+            cqlCode: cqlCode,
+            codeSystemOid: codeSystem.id,
+          });
         });
       }
     });
-    return cqlCodes;
+    return cqlCodeWithCodeSystemOid;
   }
 
   getDrcOid(cqmMeasure: CqmMeasure, code: string): string {