Merge pull request #49 from mcode/update-fhir-types

Update FHIR type library, service library, and dependencies

package.json

@@ -23,32 +23,32 @@
   "license": "Apache-2.0",
   "dependencies": {
     "body-parser": "^1.19.0",
-    "clinical-trial-matching-service": "^0.0.3",
+    "clinical-trial-matching-service": "^0.0.7",
     "dotenv-flow": "^3.2.0",
     "express": "^4.17.1",
-    "fhirclient": "^2.3.11",
-    "fhirpath": "^2.7.4",
+    "fhirpath": "^3.3.0",
     "node-fetch": "^2.6.1"
   },
   "devDependencies": {
     "@istanbuljs/nyc-config-typescript": "^1.0.1",
     "@types/dotenv-flow": "^3.0.0",
     "@types/express": "^4.17.11",
-    "@types/jasmine": "^3.6.9",
-    "@types/node": "^14.14.41",
+    "@types/fhir": "^0.0.35",
+    "@types/jasmine": "^4.3.1",
+    "@types/node": "^18.11.17",
     "@types/supertest": "^2.0.11",
-    "@typescript-eslint/eslint-plugin": "^4.22.0",
-    "@typescript-eslint/parser": "^4.22.0",
-    "eslint": "^7.24.0",
-    "eslint-config-prettier": "^7.2.0",
-    "eslint-plugin-prettier": "^3.4.0",
+    "@typescript-eslint/eslint-plugin": "^5.47.0",
+    "@typescript-eslint/parser": "^5.47.0",
+    "eslint": "^8.30.0",
+    "eslint-config-prettier": "^8.5.0",
+    "eslint-plugin-prettier": "^4.2.1",
     "fhir": "^4.8.2",
-    "jasmine": "^3.7.0",
+    "jasmine": "^4.5.0",
     "nock": "^13.0.11",
     "nyc": "^15.1.0",
     "prettier": "^2.1.0",
     "supertest": "^6.1.3",
-    "ts-node": "^9.1.1",
+    "ts-node": "^10.9.1",
     "typescript": "^4.2.4"
   }
 }

spec/server.spec.ts

@@ -21,7 +21,7 @@ describe('TrailScopeService', () => {
       return request(server).get('/').set('Accept', 'application/json').expect(200);
     });
 
-    it('uses the query runner', (done) => {
+    it('uses the query runner', () => {
       const runQuery = spyOn(service.queryRunner, 'runQuery').and.callFake(() => {
         return Promise.resolve(new SearchSet([]));
       });
@@ -30,9 +30,8 @@ describe('TrailScopeService', () => {
         .send({ resourceType: 'Bundle', type: 'collection', entry: [] })
         .set('Accept', 'application/json')
         .expect(200)
-        .end(() => {
+        .then(() => {
           expect(runQuery).toHaveBeenCalled();
-          done();
         });
     });
   });

spec/trialscope.spec.ts

@@ -1,3 +1,8 @@
+import { ClinicalTrialsGovService, ResearchStudy } from 'clinical-trial-matching-service';
+import { Bundle, BundleEntry, FhirResource } from 'fhir/r4';
+// For spying purposes:
+import nock from 'nock';
+
 import {
   isTrialScopeResponse,
   isTrialScopeErrorResponse,
@@ -6,9 +11,6 @@ import {
   TrialScopeServerError,
   TrialScopeTrial
 } from '../src/trialscope';
-import { fhir, ClinicalTrialsGovService, ResearchStudy } from 'clinical-trial-matching-service';
-// For spying purposes:
-import nock from 'nock';
 
 describe('isTrialScopeResponse', () => {
   it('returns false with a non-object', () => {
@@ -45,12 +47,12 @@ describe('isTrialScopeErrorResponse', () => {
 describe('TrialScopeQuery', () => {
   it('ignores bad entries', () => {
     // This involves a bit of lying to TypeScript
-    const patientBundle: fhir.Bundle = {
+    const patientBundle: Bundle = {
       resourceType: 'Bundle',
       type: 'collection',
       entry: []
     };
-    patientBundle.entry.push(({ invalid: true } as unknown) as fhir.BundleEntry);
+    patientBundle.entry?.push({ invalid: true } as unknown as BundleEntry);
     new TrialScopeQuery(patientBundle);
     // Success is the object being created at all
   });
@@ -126,14 +128,15 @@ describe('TrialScopeQuery', () => {
     // TypeScript assumes extra fields are an error, although in this case the
     // FHIR types supplies are somewhat intentionally sparse as they're not a
     // full definition
-    const condition: fhir.Resource = {
+    const condition: FhirResource = {
       resourceType: 'Condition',
       meta: {
         profile: [
           'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-primary-cancer-condition',
           'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition'
         ]
       },
+      subject: {},
       clinicalStatus: {
         coding: [
           {
@@ -174,7 +177,7 @@ describe('TrialScopeQuery', () => {
           }
         }
       ]
-    } as fhir.Resource;
+    };
     const query = new TrialScopeQuery({
       resourceType: 'Bundle',
       type: 'collection',
@@ -203,15 +206,19 @@ describe('TrialScopeQuery', () => {
     // currently the case
     let m = /mcode:\s*{(.*?)}/.exec(graphQL);
     expect(m).toBeTruthy();
-    const mcodeFilters = m[1];
-    expect(mcodeFilters).toMatch(/primaryCancer:\s*BREAST_CANCER/);
+    if (m) {
+      const mcodeFilters = m[1];
+      expect(mcodeFilters).toMatch(/primaryCancer:\s*BREAST_CANCER/);
+    }
     m = /baseFilters:\s*{(.*?)}/.exec(graphQL);
     expect(m).toBeTruthy();
-    const baseFilters = m[1];
-    expect(baseFilters).toMatch(/zipCode:\s*"01234"/);
-    expect(baseFilters).toMatch(/travelRadius:\s*15\b/);
-    expect(baseFilters).toMatch(/phase:\s*PHASE_1\b/);
-    expect(baseFilters).toMatch(/recruitmentStatus:\s*RECRUITING\b/);
+    if (m) {
+      const baseFilters = m[1];
+      expect(baseFilters).toMatch(/zipCode:\s*"01234"/);
+      expect(baseFilters).toMatch(/travelRadius:\s*15\b/);
+      expect(baseFilters).toMatch(/phase:\s*PHASE_1\b/);
+      expect(baseFilters).toMatch(/recruitmentStatus:\s*RECRUITING\b/);
+    }
   });
 
   it("excludes parameters that weren't included", () => {
@@ -234,11 +241,13 @@ describe('TrialScopeQuery', () => {
     const graphQL = query.toQuery();
     const m = /baseFilters:\s*{(.*?)}/.exec(graphQL);
     expect(m).toBeTruthy();
-    const baseFilters = m[1];
-    expect(baseFilters).toMatch(/zipCode:\s*"98765"/);
-    expect(baseFilters).not.toMatch('travelRadius');
-    expect(baseFilters).not.toMatch('phase');
-    expect(baseFilters).not.toMatch('recruitmentStatus');
+    if (m) {
+      const baseFilters = m[1];
+      expect(baseFilters).toMatch(/zipCode:\s*"98765"/);
+      expect(baseFilters).not.toMatch('travelRadius');
+      expect(baseFilters).not.toMatch('phase');
+      expect(baseFilters).not.toMatch('recruitmentStatus');
+    }
   });
 });
 
@@ -256,8 +265,6 @@ describe('TrialScopeQueryRunner', () => {
   });
   afterEach(() => {
     expect(scope.isDone()).toBeTrue();
-    interceptor = null;
-    scope = null;
   });
 
   it('handles an empty response', () => {
@@ -308,7 +315,7 @@ describe('TrialScopeQueryRunner', () => {
   });
 
   describe('runQuery', () => {
-    let patientBundle: fhir.Bundle;
+    let patientBundle: Bundle;
     beforeEach(() => {
       // This is basically the minimum bundle required to run a query
       patientBundle = {
@@ -460,8 +467,9 @@ describe('TrialScopeQueryRunner', () => {
               expected.enrollment = [reference];
               // For the sake of this test, kill the createResourceId functions
               // (it shouldn't be enumerable anyway)
-              expected.createReferenceId = null;
-              (actual.entry[i].resource as ResearchStudy).createReferenceId = null;
+              // Note this involves lying to the TypeScript compiler
+              (expected as unknown as { createReferenceId: null }).createReferenceId = null;
+              (actual.entry[i].resource as unknown as { createReferenceId: null }).createReferenceId = null;
               expect(actual.entry[i].resource).toEqual(expected);
             }
             expect(actual.entry[0].search.score).toEqual(1);

src/mcode.ts

@@ -1,36 +1,16 @@
-import { fhirclient } from 'fhirclient/lib/types';
+import { Bundle, Coding, Quantity, Ratio, Resource } from 'fhir/r4';
 import * as fhirpath from 'fhirpath';
 
 import { CodeProfile, ProfileSystemCodes } from './profileSystemLogic';
 
 import profile_system_codes_json from '../data/profile-system-codes-json.json';
-import { fhir } from 'clinical-trial-matching-service';
 
 const profile_system_codes = profile_system_codes_json as ProfileSystemCodes;
 
 export type FHIRPath = string;
 // fhirpath now has official TypeScript types. Unfortunately, the result they use is "any"
 export type PathLookupResult = Record<string, unknown> | string | number;
 
-export interface Coding {
-  system?: string;
-  code?: string;
-  display?: string;
-}
-
-export interface Quantity {
-  value?: number | string;
-  comparator?: string;
-  unit?: string;
-  system?: string;
-  code?: string;
-}
-
-export interface Ratio {
-  numerator?: Quantity;
-  denominator?: Quantity;
-}
-
 export interface PrimaryCancerCondition {
   clinicalStatus?: Coding[];
   coding?: Coding[];
@@ -89,7 +69,7 @@ export class ExtractedMCODE {
   ecogPerformaceStatus: number;
   karnofskyPerformanceStatus: number;
 
-  constructor(patientBundle: fhir.Bundle) {
+  constructor(patientBundle: Bundle | null) {
     if (patientBundle != null) {
       for (const entry of patientBundle.entry) {
         if (!('resource' in entry)) {
@@ -319,12 +299,8 @@ export class ExtractedMCODE {
     }
   }
 
-  lookup(
-    resource: fhirclient.FHIR.Resource,
-    path: FHIRPath,
-    environment?: { [key: string]: string }
-  ): PathLookupResult[] {
-    return fhirpath.evaluate(resource, path, environment);
+  lookup(resource: Resource, path: FHIRPath, environment?: { [key: string]: string }): PathLookupResult[] {
+    return fhirpath.evaluate(resource, path, environment) as PathLookupResult[];
   }
   resourceProfile(profiles: PathLookupResult[], key: string): boolean {
     for (const profile of profiles) {
@@ -1299,13 +1275,10 @@ export class ExtractedMCODE {
     const system = this.normalizeCodeSystem(coding.system);
     for (const sheetName of sheetNames) {
       let codeProfile: CodeProfile = undefined;
-      try {
-        codeProfile = profile_system_codes[sheetName] as CodeProfile; // Pull the codes for the profile
-      } finally {
-        if (codeProfile == undefined) {
-          console.error('Code Profile ' + sheetName + ' is undefined.');
-          continue;
-        }
+      codeProfile = profile_system_codes[sheetName]; // Pull the codes for the profile
+      if (codeProfile == undefined) {
+        console.error('Code Profile ' + sheetName + ' is undefined.');
+        continue;
       }
 
       let codeSet: { code: string }[] = codeProfile[system] as { code: string }[]; // Pull the system codes from the codes

src/profileSystemLogic.ts

@@ -1,10 +1,10 @@
-import { Coding } from './mcode';
+import { Coding } from 'fhir/r4';
 
 export interface ProfileType {
   types: string[];
 }
 export interface ProfileSystemCodes {
-  [key: string] : CodeProfile;
+  [key: string]: CodeProfile;
   'Cancer-Skin'?: CodeProfile;
   'Treatment-Pertuzumab'?: CodeProfile;
   'Treatment-SRS-Brain'?: CodeProfile;
@@ -45,7 +45,7 @@ export interface ProfileSystemCodes {
   'Biomarker-ER'?: CodeProfile;
 }
 export interface CodeProfile {
-  [key: string] : { code: string }[];
+  [key: string]: { code: string }[];
   SNOMED?: { code: string }[];
   RxNorm?: { code: string }[];
   ICD10?: { code: string }[];

src/research-study-mapping.ts

@@ -1,6 +1,8 @@
-import { ResearchStudy, fhir, convertStringsToCodeableConcept } from 'clinical-trial-matching-service';
+import { ResearchStudy, convertStringsToCodeableConcept } from 'clinical-trial-matching-service';
 import { TrialScopeTrial } from './trialscope';
 
+type ResearchStudyStatus = ResearchStudy['status'];
+
 // Mappings between trialscope value sets and FHIR value sets
 const phaseCodeMap = new Map<string, string>([
   ['Early Phase 1', 'early-phase-1'],
@@ -13,7 +15,7 @@ const phaseCodeMap = new Map<string, string>([
   ['Phase 4', 'phase-4']
 ]);
 
-const statusMap = new Map<string, fhir.ResearchStudyStatus>([
+const statusMap = new Map<string, ResearchStudyStatus>([
   ['Active, not recruiting', 'closed-to-accrual'],
   ['Approved for marketing', 'approved'],
   ['Available', 'active'],
@@ -22,7 +24,7 @@ const statusMap = new Map<string, fhir.ResearchStudyStatus>([
   ['Recruiting', 'active']
 ]);
 
-function convertStatus(tsStatus: string): fhir.ResearchStudyStatus {
+function convertStatus(tsStatus: string): ResearchStudyStatus {
   return statusMap.get(tsStatus);
 }
 
@@ -55,7 +57,7 @@ export function convertTrialScopeToResearchStudy(trial: TrialScopeTrial, id: num
     };
   }
   if (trial.studyType) {
-    result.category = [{ text: "Study Type: " + trial.studyType }];
+    result.category = [{ text: 'Study Type: ' + trial.studyType }];
   }
   if (trial.conditions) {
     const conditions = convertStringsToCodeableConcept(trial.conditions);

src/server.ts

@@ -1,20 +1,16 @@
+import { ClinicalTrialsGovService, ClinicalTrialMatchingService, configFromEnv } from 'clinical-trial-matching-service';
+import * as dotenv from 'dotenv-flow';
 import express from 'express';
-import TrialScopeQueryRunner from './trialscope';
+import { Bundle } from 'fhir/r4';
 
-import {
-  fhir,
-  ClinicalTrialsGovService,
-  ClinicalTrialMatchingService,
-  configFromEnv
-} from 'clinical-trial-matching-service';
-import * as dotenv from 'dotenv-flow';
+import TrialScopeQueryRunner from './trialscope';
 
 export class TrialScopeService extends ClinicalTrialMatchingService {
   queryRunner: TrialScopeQueryRunner;
   backupService: ClinicalTrialsGovService;
 
   constructor(config: Record<string, string | number>) {
-    super((patientBundle: fhir.Bundle) => {
+    super((patientBundle: Bundle) => {
       return this.queryRunner.runQuery(patientBundle);
     }, config);