Coverage 3.14.0 (#314)

* Update to handle coverage changes

Removes all localids that aren't in the annotation

* Add not null test and 3.15.0-translated fixtures

* Return string array from annotation search function

* Update comments and function name

README.md

@@ -49,6 +49,7 @@ Library for calculating Electronic Clinical Quality Measures (eCQMs) written in
 - [Recipes](#recipes)
   - [Displaying Highlighted HTML in a React App](#displaying-highlighted-html-in-a-react-app)
   - [Usage Within a FHIR Server](#usage-within-a-fhir-server)
+  - [Special Testing](#special-testing)
 - [Contributing](#contributing)
 - [License](#license)
 

src/calculation/ClauseResultsBuilder.ts

@@ -315,7 +315,7 @@ export function buildStatementAndClauseResults(
 
     if (includeClauseResults) {
       // create clause results for all localIds in this statement
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(elmLibrary, statementResult.statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(elmLibrary, statementResult.statementName);
       for (const localId in localIds) {
         const clause = localIds[localId];
         const rawClauseResult =

src/helpers/ClauseResultsHelpers.ts

@@ -3,13 +3,13 @@ import { ELMFunctionRef } from '../types/ELMTypes';
 import { ELM, ELMBinaryExpression, ELMStatement } from '../types/ELMTypes';
 
 /**
- * Finds all localIds in a statement by it's library and statement name.
+ * Finds all of the localIds that are needed for clause results for a single statement.
  * @public
  * @param {ELM} libraryElm - The library the statement belongs to.
  * @param {string} statementName - The statement name to search for.
- * @return {Hash} List of local ids in the statement.
+ * @return {Hash} List of result-relevant local ids in the statement.
  */
-export function findAllLocalIdsInStatementByName(libraryElm: ELM, statementName: string): any {
+export function findLocalIdsInStatementByName(libraryElm: ELM, statementName: string): any {
   // create place for aliases and their usages to be placed to be filled in later. Aliases and their usages (aka scope)
   // and returns do not have localIds in the elm but do in elm_annotations at a consistent calculable offset.
   // BE WARY of this calculable offset.
@@ -49,7 +49,37 @@ export function findAllLocalIdsInStatementByName(libraryElm: ELM, statementName:
       clause.isUnsupported = true;
     }
   }
-  return localIds;
+
+  // find all localids in the annotation
+  const allAnnotatedIds = findAnnotationLocalIds(statement?.annotation);
+  // filter out local ids that aren't in the annotation
+  const annotatedLocalIds: Record<string, any> = {};
+  for (const [key, value] of Object.entries(localIds)) {
+    if (allAnnotatedIds.includes(key)) {
+      annotatedLocalIds[key] = value;
+    }
+  }
+  return annotatedLocalIds;
+}
+
+/**
+ * Recursively finds localIds that are in an annotation structure by pulling out all "r:"-keyed values
+ * @public
+ * @param {object} annotation - all or a subset of the annotation structure to search
+ * @return {Array} List of local ids in the annotation.
+ */
+function findAnnotationLocalIds(annotation: any): string[] {
+  if (Array.isArray(annotation)) {
+    return annotation.flatMap(ent => findAnnotationLocalIds(ent));
+  } else if (typeof annotation === 'object') {
+    return Object.entries(annotation).flatMap(ent => {
+      // if key is r, return value, else recurse
+      if (ent[0] === 'r') return ent[1] as string;
+      return findAnnotationLocalIds(ent[1]);
+    });
+  }
+  // default empty
+  return [];
 }
 
 /**

test/unit/ClauseResultsHelper.test.ts

@@ -3,19 +3,19 @@ import { ELM } from '../../src/types/ELMTypes';
 import { getJSONFixture } from './helpers/testHelpers';
 
 describe('ClauseResultsHelpers', () => {
-  describe('findAllLocalIdsInStatementByName', () => {
+  describe('findLocalIdsInStatementByName', () => {
     test('finds localIds for an Equivalent comparison operator that is wrapped in a Not expression', () => {
       // ELM from test/unit/fixtures/cql/NotEquivalent.cql
       const libraryElm: ELM = getJSONFixture('elm/NotEquivalent.json');
 
       const statementName = 'Not Equivalent Clause';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the localId for the Equivalent statement
-      // is 23 and the localId for the Not expression is 24 but we want the Equivalent clause to take
-      // the result of the Not expression
-      expect(localIds[23]).toBeDefined();
-      expect(localIds[23]).toEqual({ localId: '23', sourceLocalId: '24' });
+      // is 23 and the localId for the Not expression is 24. We want 23 to not be included because 24 is
+      // the correct id from the annotation.
+      expect(localIds[23]).not.toBeDefined();
+      expect(localIds[24]).toBeDefined();
     });
 
     test('finds localIds for an Equal comparison operator that is wrapped in a Not expression', () => {
@@ -25,21 +25,35 @@ describe('ClauseResultsHelpers', () => {
       const libraryElm: ELM = getJSONFixture('elm/NotEqual.json');
 
       const statementName = 'Not Equal Clause';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the localId for the Equal statement
-      // is 100 and the localId for the Not expression is 23 but we want the Equal clause to take
-      // the result of the Not expression
-      expect(localIds[100]).toBeDefined();
-      expect(localIds[100]).toEqual({ localId: '100', sourceLocalId: '23' });
+      // is 100, and the localId for the Not expression is 23. We want 100 to not be included because 23 is
+      // the correct id from the annotation.
+      expect(localIds[23]).toBeDefined();
+      expect(localIds[100]).not.toBeDefined();
+    });
+
+    test('finds localIds for a not null operator', () => {
+      // ELM from test/unit/fixtures/cql/NotNull.cql, translated with 3.15.0 translator
+      const libraryElm: ELM = getJSONFixture('elm/3.15.0/NotNull.json');
+
+      const statementName = 'Not Null Clause';
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
+
+      // For the fixture loaded for this test it is known that the localId for the IsNull statement
+      // is 237, and the localId for the Not expression is 238. We want 237 to not be included because 238 is
+      // the correct id from the annotation.
+      expect(localIds[238]).toBeDefined();
+      expect(localIds[237]).not.toBeDefined();
     });
 
     test('finds localIds for an ELM Binary Expression with a comparison operator with a literal', () => {
       // ELM from test/unit/fixtures/cql/comparisonWithLiteral.cql
       const libraryElm: ELM = getJSONFixture('elm/ComparisonWithLiteral.json');
 
       const statementName = 'ipop';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the localId for the literal is 10 and
       // the localId for the comparison expression itself is 11 so the sourceLocalId for the literal
@@ -53,7 +67,7 @@ describe('ClauseResultsHelpers', () => {
       const libraryElm: ELM = getJSONFixture('elm/ComparisonWithoutLiteral.json');
 
       const statementName = 'ipop';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the ELM Binary Expression does not have a literal
       // so the localId for the right side of the comparison should just be 12 and not have a sourceLocalId
@@ -64,7 +78,7 @@ describe('ClauseResultsHelpers', () => {
     test('finds localIds for case statement items and properly finds sourceLocalId for them', () => {
       // ELM from test/unit/elm/queries/CaseStatement.cql
       const libraryElm: ELM = getJSONFixture('elm/queries/CaseStatement.json');
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, 'Case');
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, 'Case');
 
       expect(localIds[11]).toEqual({ localId: '11', sourceLocalId: '9' });
       expect(localIds[17]).toEqual({ localId: '17', sourceLocalId: '15' });
@@ -73,15 +87,15 @@ describe('ClauseResultsHelpers', () => {
     test('finds localIds for null literals and properly sets isFalsyLiteral to true', () => {
       // ELM from test/unit/elm/queries/CaseStatement.cql
       const libraryElm: ELM = getJSONFixture('elm/queries/CaseStatement.json');
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, 'Case');
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, 'Case');
 
       expect(localIds[18]).toEqual({ localId: '18', isFalsyLiteral: true });
     });
 
     test('finds localIds for false literals and properly sets isFalsyLiteral to true', () => {
       // ELM from test/unit/elm/queries/CaseStatement.cql
       const libraryElm: ELM = getJSONFixture('elm/queries/CaseStatement.json');
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, 'Case');
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, 'Case');
 
       expect(localIds[16]).toEqual({ localId: '16', isFalsyLiteral: true });
     });
@@ -94,7 +108,7 @@ describe('ClauseResultsHelpers', () => {
 
       // Find the localid for the specific statement with the global function ref.
       const statementName = 'Encounter with Principal Diagnosis and Age';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the library reference is 49 and the functionRef itself is 55.
       expect(localIds[49]).toBeDefined();
@@ -108,7 +122,7 @@ describe('ClauseResultsHelpers', () => {
 
       // Find the localid for the specific statement with the global function ref.
       const statementName = 'Initial Population';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the library reference is 109 and the functionRef itself is 110.
       expect(localIds[109]).toBeDefined();
@@ -122,7 +136,7 @@ describe('ClauseResultsHelpers', () => {
 
       // Find the localid for the specific statement with the global function ref.
       const statementName = 'Comfort Measures during Hospitalization';
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // For the fixture loaded for this test it is known that the library reference is 109 and the functionRef itself is 110.
       expect(localIds[42]).toBeDefined();
@@ -133,7 +147,7 @@ describe('ClauseResultsHelpers', () => {
       const libraryElm: ELM = getJSONFixture('elm/SimpleAliasUsage.json');
       const statementName = 'Some Encounter';
 
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // '8' is in the annotations but not in the ELM. We use '9' as the localId from the actual expression and subtract one from it
       expect(localIds['8']).toEqual({ localId: '8', sourceLocalId: '6' });
@@ -143,7 +157,7 @@ describe('ClauseResultsHelpers', () => {
       const libraryElm: ELM = getJSONFixture('elm/SimpleAliasFunctionRef.json');
       const statementName = 'Some Encounter';
 
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // '8' is in the annotations but not in the ELM. We use '9' as the localId from the actual expression and subtract one from it
       expect(localIds['8']).toEqual({ localId: '8', sourceLocalId: '6' });
@@ -153,7 +167,7 @@ describe('ClauseResultsHelpers', () => {
       const libraryElm: ELM = getJSONFixture('elm/queries/QICoreQuery.json');
       const statementName = 'Query';
 
-      const localIds = ClauseResultsHelpers.findAllLocalIdsInStatementByName(libraryElm, statementName);
+      const localIds = ClauseResultsHelpers.findLocalIdsInStatementByName(libraryElm, statementName);
 
       // '7' is in the annotations but not in the ELM. We use '8' as the localId from the actual expression and subtract one from it
       expect(localIds[7]).toBeDefined();

test/unit/fixtures/cql/NotNull.cql

@@ -0,0 +1,24 @@
+library Test
+
+using FHIR version '4.0.1'
+
+include FHIRHelpers version '4.0.1'
+include MATGlobalCommonFunctions version '5.0.000' called Global
+
+codesystem "EXAMPLE": 'http://example.com'
+codesystem "EXAMPLE-2": 'http://example.com/2'
+codesystem "ConditionClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-clinical'
+
+valueset "test-vs": 'http://example.com/test-vs'
+
+code "Active": 'active' from "ConditionClinicalStatusCodes"
+code "Recurrence": 'recurrence' from "ConditionClinicalStatusCodes"
+code "Relapse": 'relapse' from "ConditionClinicalStatusCodes"
+
+concept "Condition Active": { "Active", "Recurrence", "Relapse" } display 'Active'
+
+context Patient
+
+define "Not Null Clause":
+    [Condition: "test-vs"] C
+        where C.id is not null