Merge pull request #717 from MeasureAuthoringTool/MAT-7529

MAT-7529 QI-Core Code Search/Apply - Apply Code to QI-Core Measures

package.json

@@ -93,7 +93,7 @@
     "@madie/madie-auth": "^0.0.1",
     "@madie/madie-design-system": "^1.2.41",
     "@madie/madie-editor": "^0.0.1",
-    "@madie/madie-models": "^1.4.23",
+    "@madie/madie-models": "^1.4.24",
     "@madie/madie-root": "^0.0.3",
     "@material-ui/core": "^4.12.4",
     "@mui/core": "^5.0.0-alpha.54",

src/components/__mocks__/bulkCreate.tsx

@@ -26,7 +26,7 @@ const bulkCreate = (count: number) => {
 
   const measureInput = {
     measureName: "",
-    model: "",
+    model: Model.QDM_5_6,
     cqlLibraryName: "",
   } as Measure;
 

src/components/editMeasure/editor/MeasureEditor.tsx

@@ -511,7 +511,7 @@ const MeasureEditor = () => {
   };
 
   const handleApplyCode = (code: Code) => {
-    const result = applyCode(editorVal, code);
+    const result = applyCode(editorVal, code, measure.model);
     if (result.status) {
       // if result status is true, we modified the CQL
       // let's store off the codeSystem/code/version

src/components/editMeasure/editor/codeApplier.test.ts

@@ -1,6 +1,6 @@
 import applyCode from "./codeApplier";
 import * as fs from "fs";
-import { Code } from "@madie/madie-models";
+import { Code, Model } from "@madie/madie-models";
 import { CqlApplyActionResult } from "./CqlApplyActionResult";
 
 const mockCode = {
@@ -86,7 +86,7 @@ describe("applyCode test cases", () => {
     expect(cql).not.toContain("281302008");
 
     const code = JSON.parse(codeJson);
-    let result: CqlApplyActionResult = applyCode(cql, code);
+    let result: CqlApplyActionResult = applyCode(cql, code, Model.QDM_5_6);
 
     expect(result.cql).toContain(
       `codesystem "SNOMEDCT": 'urn:oid:2.16.840.1.113883.6.96'`
@@ -109,7 +109,7 @@ describe("applyCode test cases", () => {
       `codesystem "SNOMEDCT": 'urn:oid:2.16.840.1.113883.6.96'`
     );
     expect(cql).not.toContain("281302008");
-    let result = applyCode(cql, mockCode);
+    let result = applyCode(cql, mockCode, Model.QDM_5_6);
     expect(result.cql).toContain(
       `codesystem "${mockCode.codeSystem}:${mockCode.svsVersion}": 'urn:oid:${mockCode.codeSystemOid}' version 'urn:hl7:version:${mockCode.svsVersion}'`
     );
@@ -123,7 +123,7 @@ describe("applyCode test cases", () => {
   });
 
   it("Should insert code if editor is blank", () => {
-    let result = applyCode("", mockCode);
+    let result = applyCode("", mockCode, Model.QDM_5_6);
     expect(result.message).toContain(
       `Code ${mockCode.name} has been successfully added to the CQL.`
     );
@@ -139,7 +139,7 @@ describe("applyCode test cases", () => {
 
   it("Should insert code if CQL has only library statement", () => {
     const libraryStatement = "library ABC version '0.0.000'";
-    let result = applyCode(libraryStatement, mockCode);
+    let result = applyCode(libraryStatement, mockCode, Model.QDM_5_6);
     const cqlArray = result.cql.split("\n");
     expect(cqlArray[0]).toEqual(libraryStatement);
     expect(cqlArray[1]).toEqual(
@@ -154,7 +154,7 @@ describe("applyCode test cases", () => {
     const usingStatement = "using QDM version '5.6'";
     const libraryStatement = "library ABC version '0.0.000'";
     const cql = `${libraryStatement}\n${usingStatement}`;
-    let result = applyCode(cql, mockCode);
+    let result = applyCode(cql, mockCode, Model.QDM_5_6);
     const cqlArray = result.cql.split("\n");
     expect(cqlArray[0]).toEqual(libraryStatement);
     expect(cqlArray[1]).toEqual(usingStatement);
@@ -172,7 +172,7 @@ describe("applyCode test cases", () => {
     const codeSystemStatement =
       "codesystem \"CPT\": 'urn:oid:2.16.840.1.113883.6.12'";
     const cql = `${libraryStatement}\n${usingStatement}\n${codeSystemStatement}`;
-    let result = applyCode(cql, mockCode);
+    let result = applyCode(cql, mockCode, Model.QDM_5_6);
     const cqlArray = result.cql.split("\n");
     expect(cqlArray[0]).toEqual(libraryStatement);
     expect(cqlArray[1]).toEqual(usingStatement);
@@ -184,4 +184,65 @@ describe("applyCode test cases", () => {
       `code "${mockCode.display} (${mockCode.suffix})": '${mockCode.name}' from "${mockCode.codeSystem}:${mockCode.svsVersion}" display '${mockCode.display}'`
     );
   });
+
+  describe("Apply code to QICore CQL", () => {
+    const code = {
+      name: "24353-5",
+      display:
+        "Glucose tolerance 2 hours gestational panel - Urine and Serum or Plasma",
+      version: "2.76",
+      codeSystem: "LOINC",
+      codeSystemOid: "2.16.840.1.113883.6.1",
+      status: "NA",
+      svsVersion: "2.78",
+      fhirVersion: "2.78",
+      codeSystemUrl: "http://loinc.org",
+      versionIncluded: false,
+    };
+    it("Should apply new code to QICore measure CQL", () => {
+      const cql =
+        "library MAT6197UCUMAnnotations version '0.0.000'\n" +
+        "using QICore version '4.1.1'";
+
+      let result: CqlApplyActionResult = applyCode(
+        cql,
+        code,
+        Model.QICORE_6_0_0
+      );
+      expect(result.cql).toContain("24353-5");
+      expect(result.status).toEqual("success");
+      expect(result.message).toEqual(
+        "Code 24353-5 has been successfully added to the CQL."
+      );
+
+      // include code system version
+      result = applyCode(
+        cql,
+        { ...code, versionIncluded: true },
+        Model.QICORE_6_0_0
+      );
+      expect(result.cql).toContain("LOINC:2.78");
+      expect(result.status).toEqual("success");
+      expect(result.message).toEqual(
+        "Code 24353-5 has been successfully added to the CQL."
+      );
+    });
+
+    it("Should update code for QICore measure CQL", () => {
+      const cql =
+        "library MAT6197UCUMAnnotations version '0.0.000'\n" +
+        "using QICore version '4.1.1'\n" +
+        "codesystem \"LOINC\": 'http://loinc.org'\n" +
+        "code \"Glucose tolerance 2 hours gestational panel - Urine and Serum or Plasma\": '24353-5' from \"LOINC:2.78\" display 'Glucose tolerance 2 hours gestational panel - Urine and Serum or Plasma'";
+
+      let result: CqlApplyActionResult = applyCode(
+        cql,
+        code,
+        Model.QICORE_6_0_0
+      );
+      expect(result.message).toEqual(
+        "Code 24353-5 has been updated successfully."
+      );
+    });
+  });
 });

src/components/editMeasure/editor/codeApplier.ts

@@ -1,8 +1,8 @@
 import { CqlAntlr, CqlResult } from "@madie/cql-antlr-parser/dist/src";
-import { Code } from "@madie/madie-models";
+import { Code, Model } from "@madie/madie-models";
 import { CqlApplyActionResult } from "./CqlApplyActionResult";
 
-const findCodeSystem = (code, codeSystems) => {
+const findCodeSystem = (code, codeSystems, measureModel) => {
   if (!code || !codeSystems) {
     return undefined;
   }
@@ -14,17 +14,21 @@ const findCodeSystem = (code, codeSystems) => {
     const oldCodeSystemVersion = codeSystem.version
       ?.replace(/["']/g, "")
       ?.replace(/urn:hl7:version:/g, "");
-
+    let updatedOid = code.codeSystemUrl;
+    let updatedVersion = code.fhirVersion;
+    if (measureModel === Model.QDM_5_6) {
+      updatedOid = code.codeSystemOid;
+      updatedVersion = code.svsVersion;
+    }
     if (code.versionIncluded) {
       return (
         oldCodeSystemName === `${code.codeSystem}:${code.svsVersion}` &&
-        oldCodeSystemOid === code.codeSystemOid &&
-        oldCodeSystemVersion === code.svsVersion
+        oldCodeSystemOid === updatedOid &&
+        oldCodeSystemVersion === updatedVersion
       );
     } else {
       return (
-        oldCodeSystemName === code.codeSystem &&
-        oldCodeSystemOid === code.codeSystemOid
+        oldCodeSystemName === code.codeSystem && oldCodeSystemOid === updatedOid
       );
     }
   });
@@ -57,25 +61,44 @@ const createCodeDeclaration = (code: Code) => {
   return newCode;
 };
 
-const createCodeSystemDeclaration = (code: Code) => {
+const createCodeSystemDeclaration = (code: Code, measureModel: Model) => {
+  let oid: string;
+  let codeSystemVersion: string;
+  let versionSuffix: string;
+  if (measureModel === Model.QDM_5_6) {
+    versionSuffix = code.svsVersion;
+    oid = `urn:oid:${code.codeSystemOid}`;
+    codeSystemVersion = `urn:hl7:version:${code.svsVersion}`;
+  } else {
+    versionSuffix = code.svsVersion; // TODO: confirm this
+    oid = code.codeSystemUrl;
+    codeSystemVersion = code.fhirVersion;
+  }
   if (code.versionIncluded) {
-    return `codesystem "${code.codeSystem}:${code.svsVersion}": 'urn:oid:${code.codeSystemOid}' version 'urn:hl7:version:${code.svsVersion}'`;
+    return `codesystem "${code.codeSystem}:${versionSuffix}": '${oid}' version '${codeSystemVersion}'`;
   } else {
-    return `codesystem "${code.codeSystem}": 'urn:oid:${code.codeSystemOid}'`;
+    return `codesystem "${code.codeSystem}": '${oid}'`;
   }
 };
 
-const applyCode = (cql: string, code: Code): CqlApplyActionResult => {
+const applyCode = (
+  cql: string,
+  code: Code,
+  measureModel?: Model
+): CqlApplyActionResult => {
   const cqlArr: string[] = cql.split("\n");
 
   // Parse CQL to get code and code systems
   const parseResults: CqlResult = new CqlAntlr(cql).parse();
-
   // Let's check if the code system is already in the CQL
-  const previousCodeSystem = findCodeSystem(code, parseResults.codeSystems);
+  const previousCodeSystem = findCodeSystem(
+    code,
+    parseResults.codeSystems,
+    measureModel
+  );
   // Add code system to CQL if it does not exist
   if (!previousCodeSystem) {
-    let newCodeSystem = createCodeSystemDeclaration(code);
+    let newCodeSystem = createCodeSystemDeclaration(code, measureModel);
     cqlArr.splice(findCodeSystemInsertPoint(parseResults), 0, newCodeSystem);
   }