Full linked Project ordering in CodeSystem lookup (#4522)

* Full linked Project ordering in CodeSystem lookup * Fully specify lookup order of Terminology Resources in linked projects
medplum · May 14, 2024 · 84b2ad7 · 84b2ad7
1 parent 20db8c7
commit 84b2ad7
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Showing 3 changed files with 104 additions and 23 deletions.
diff --git a/packages/server/src/fhir/operations/codesystemlookup.ts b/packages/server/src/fhir/operations/codesystemlookup.ts
@@ -25,9 +25,9 @@ export async function codeSystemLookupHandler(req: FhirRequest): Promise<FhirRes
   if (req.params.id) {
     codeSystem = await getAuthenticatedContext().repo.readResource<CodeSystem>('CodeSystem', req.params.id);
   } else if (params.system) {
-    codeSystem = await findTerminologyResource<CodeSystem>('CodeSystem', params.system, params.version);
+    codeSystem = await findTerminologyResource('CodeSystem', params.system, params.version);
   } else if (params.coding?.system) {
-    codeSystem = await findTerminologyResource<CodeSystem>('CodeSystem', params.coding.system, params.version);
+    codeSystem = await findTerminologyResource('CodeSystem', params.coding.system, params.version);
   } else {
     return [badRequest('No code system specified')];
   }

diff --git a/packages/server/src/fhir/operations/expand.test.ts b/packages/server/src/fhir/operations/expand.test.ts
@@ -1,4 +1,4 @@
-import { ContentType, HTTP_HL7_ORG, HTTP_TERMINOLOGY_HL7_ORG, LOINC, SNOMED } from '@medplum/core';
+import { ContentType, HTTP_HL7_ORG, HTTP_TERMINOLOGY_HL7_ORG, LOINC, SNOMED, createReference } from '@medplum/core';
 import {
   CodeSystem,
   OperationOutcome,
@@ -391,7 +391,6 @@ describe.each<Partial<Project>>([{ features: [] }, { features: ['terminology'] }
     const res2 = await request(app)
       .get(`/fhir/R4/ValueSet/$expand?url=${encodeURIComponent(url)}`)
       .set('Authorization', 'Bearer ' + accessToken);
-    console.log(JSON.stringify(res2.body, undefined, 2));
     expect(res2.status).toBe(200);
     expect(res2.body.expansion.contains).toEqual(
       expect.arrayContaining([
@@ -548,6 +547,69 @@ describe('Updated implementation', () => {
     expect(coding.display).toEqual('Test SNOMED override');
   });
 
+  test('Prefers CodeSystem from linked Projects in link order', async () => {
+    // Set up linked Projects and CodeSystem resources
+    const url = 'http://example.com/cs' + randomUUID();
+    const codeSystem: CodeSystem = {
+      resourceType: 'CodeSystem',
+      status: 'active',
+      content: 'complete',
+      url,
+    };
+
+    const { project: p2, accessToken: a2 } = await createTestProject({ withAccessToken: true });
+    const cs2 = await request(app)
+      .post(`/fhir/R4/CodeSystem`)
+      .set('Authorization', 'Bearer ' + a2)
+      .set('Content-Type', ContentType.FHIR_JSON)
+      .send({ ...codeSystem, concept: [{ code: '1', display: 'Incorrect coding' }] });
+    expect(cs2.status).toEqual(201);
+
+    const { project: p1, accessToken: a1 } = await createTestProject({ withAccessToken: true });
+    const cs1 = await request(app)
+      .post(`/fhir/R4/CodeSystem`)
+      .set('Authorization', 'Bearer ' + a1)
+      .set('Content-Type', ContentType.FHIR_JSON)
+      .send({ ...codeSystem, concept: [{ code: '1', display: 'Correct coding' }] });
+    expect(cs1.status).toEqual(201);
+
+    const { project: p3, accessToken: a3 } = await createTestProject({ withAccessToken: true });
+    const cs3 = await request(app)
+      .post(`/fhir/R4/CodeSystem`)
+      .set('Authorization', 'Bearer ' + a3)
+      .set('Content-Type', ContentType.FHIR_JSON)
+      .send({ ...codeSystem, concept: [{ code: '1', display: 'Another incorrect coding' }] });
+    expect(cs3.status).toEqual(201);
+
+    accessToken = await initTestAuth({
+      project: {
+        features: ['terminology'],
+        link: [{ project: createReference(p1) }, { project: createReference(p2) }, { project: createReference(p3) }],
+      },
+    });
+
+    const res2 = await request(app)
+      .post(`/fhir/R4/ValueSet`)
+      .set('Authorization', 'Bearer ' + accessToken)
+      .set('Content-Type', ContentType.FHIR_JSON)
+      .send({
+        resourceType: 'ValueSet',
+        status: 'active',
+        url: 'https://example.com/' + randomUUID(),
+        compose: { include: [{ system: url }] },
+      });
+    expect(res2.status).toBe(201);
+
+    const res3 = await request(app)
+      .get(`/fhir/R4/ValueSet/$expand?url=${encodeURIComponent(res2.body.url)}`)
+      .set('Authorization', 'Bearer ' + accessToken);
+    expect(res3.status).toBe(200);
+    const coding = res3.body.expansion.contains[0];
+    expect(coding.system).toBe(url);
+    expect(coding.code).toBe('1');
+    expect(coding.display).toEqual('Correct coding');
+  });
+
   test('Returns error when property filter is invalid for CodeSystem', async () => {
     const res1 = await request(app)
       .post(`/fhir/R4/CodeSystem`)

diff --git a/packages/server/src/fhir/operations/utils/terminology.ts b/packages/server/src/fhir/operations/utils/terminology.ts
@@ -1,8 +1,8 @@
-import { OperationOutcomeError, Operator, badRequest } from '@medplum/core';
+import { OperationOutcomeError, Operator, badRequest, createReference, resolveId } from '@medplum/core';
 import { getAuthenticatedContext } from '../../../context';
-import { r4ProjectId } from '../../../seed';
-import { CodeSystem, CodeSystemConceptProperty, ConceptMap, ValueSet } from '@medplum/fhirtypes';
+import { CodeSystem, CodeSystemConceptProperty, ConceptMap, Reference, ValueSet } from '@medplum/fhirtypes';
 import { SelectQuery, Conjunction, Condition, Column, Union } from '../../sql';
+import { getSystemRepo } from '../../repo';
 
 export const parentProperty = 'http://hl7.org/fhir/concept-properties#parent';
 export const childProperty = 'http://hl7.org/fhir/concept-properties#child';
@@ -15,12 +15,12 @@ export async function findTerminologyResource<T extends TerminologyResource>(
   url: string,
   version?: string
 ): Promise<T> {
-  const { repo } = getAuthenticatedContext();
+  const { repo, project } = getAuthenticatedContext();
   const filters = [{ code: 'url', operator: Operator.EQUALS, value: url }];
   if (version) {
     filters.push({ code: 'version', operator: Operator.EQUALS, value: version });
   }
-  const resources = await repo.searchResources<T>({
+  const results = await repo.searchResources<T>({
     resourceType,
     filters,
     sortRules: [
@@ -31,24 +31,43 @@ export async function findTerminologyResource<T extends TerminologyResource>(
     ],
   });
 
-  if (!resources.length) {
+  if (!results.length) {
     throw new OperationOutcomeError(badRequest(`${resourceType} ${url} not found`));
-  } else if (resources.length === 1) {
-    return resources[0];
+  } else if (results.length === 1 || !sameTerminologyResourceVersion(results[0], results[1])) {
+    return results[0];
   } else {
-    resources.sort((a: TerminologyResource, b: TerminologyResource) => {
-      // Select the non-base FHIR versions of resources before the base FHIR ones
-      // This is kind of a kludge, but is required to break ties because some CodeSystems (including SNOMED)
-      // don't have a version and the base spec version doesn't include a date (and so is always considered current)
-      if (a.meta?.project === r4ProjectId) {
-        return 1;
-      } else if (b.meta?.project === r4ProjectId) {
-        return -1;
+    const resourceReferences: Reference<T>[] = [];
+    for (const resource of results) {
+      resourceReferences.push(createReference(resource));
+    }
+    const resources = (await getSystemRepo().readReferences(resourceReferences)) as (T | Error)[];
+    const projectResource = resources.find((r) => r instanceof Error || r.meta?.project === project.id);
+    if (projectResource instanceof Error) {
+      throw projectResource;
+    } else if (projectResource) {
+      return projectResource;
+    }
+    if (project.link) {
+      for (const linkedProject of project.link) {
+        const linkedResource = resources.find(
+          (r) => !(r instanceof Error) && r.meta?.project === resolveId(linkedProject.project)
+        ) as T | undefined;
+        if (linkedResource) {
+          return linkedResource;
+        }
       }
-      return 0;
-    });
-    return resources[0];
+    }
+    throw new OperationOutcomeError(badRequest(`${resourceType} ${url} not found`));
+  }
+}
+
+function sameTerminologyResourceVersion(a: TerminologyResource, b: TerminologyResource): boolean {
+  if (a.version !== b.version) {
+    return false;
+  } else if (a.date !== b.date) {
+    return false;
   }
+  return true;
 }
 
 export function addPropertyFilter(query: SelectQuery, property: string, value: string, isEqual?: boolean): SelectQuery {