Medplum

// SPDX-FileCopyrightText: Copyright Orangebot, Inc. and Medplum contributors // SPDX-License-Identifier: Apache-2.0 import type { WithId } from '@medplum/core'; import { ContentType, SNOMED } from '@medplum/core'; import type { ConceptMap, OperationOutcome, Parameters } from '@medplum/fhirtypes'; import { randomUUID } from 'crypto'; import express from 'express'; import type { Pool } from 'pg'; import request from 'supertest'; import { initApp, shutdownApp } from '../../app'; import { loadTestConfig } from '../../config/loader'; import { DatabaseMode, getDatabasePool } from '../../database'; import { createTestProject } from '../../test.setup'; import type { Repository } from '../repo'; import { Column, Condition, SelectQuery } from '../sql'; import { importConceptMap } from './conceptmapimport'; const app = express(); const ICD10 = 'http://hl7.org/fhir/sid/icd-10-us'; describe('importConceptMap()', () => { beforeAll(async () => { const config = await loadTestConfig(); await initApp(app, config); }); afterAll(async () => { await shutdownApp(); }); test('Imports basic mappings from resource', async () => { const resource: WithId<ConceptMap> = { resourceType: 'ConceptMap', id: randomUUID(), version: '4.0.1', status: 'draft', experimental: true, group: [ { source: SNOMED, target: ICD10, element: [ { code: '263204007', target: [ { code: 'S52.209A', equivalence: 'narrower', comment: 'The target mapping to ICD-10-CM is narrower, since additional patient data on the encounter (initial vs. subsequent) and fracture type is required for a valid ICD-10-CM mapping.', }, { code: 'S52.209D', equivalence: 'narrower', comment: 'The target mapping to ICD-10-CM is narrower, since additional patient data on the encounter (initial vs. subsequent), fracture type and healing (for subsequent encounter) is required for a valid ICD-10-CM mapping.', }, ], }, ], }, ], }; const pool = getDatabasePool(DatabaseMode.WRITER); const db = await pool.connect(); await importConceptMap(db, resource); db.release(); const results = await getMappingRows(pool, resource); expect(results).toHaveLength(2); expect(results).toStrictEqual( expect.arrayContaining([ expect.objectContaining({ conceptMap: resource.id, sourceSystem: SNOMED, sourceCode: '263204007', targetSystem: ICD10, targetCode: 'S52.209A', relationship: 'narrower', comment: expect.stringContaining('subsequent'), }), expect.objectContaining({ conceptMap: resource.id, sourceSystem: SNOMED, sourceCode: '263204007', targetSystem: ICD10, targetCode: 'S52.209D', relationship: 'narrower', comment: expect.stringContaining('subsequent'), }), ]) ); }); test('Imports mapping metadata', async () => { const resource: WithId<ConceptMap> = { resourceType: 'ConceptMap', id: randomUUID(), version: '4.0.1', status: 'draft', experimental: true, group: [ { source: SNOMED, target: ICD10, element: [ { code: '1003470004', target: [ { code: 'Z12.9', equivalence: 'equivalent', }, { code: 'Z12.11', equivalence: 'equivalent', dependsOn: [{ property: 'context', system: SNOMED, value: '460591000124101' }], }, { code: 'Z12.72', equivalence: 'equivalent', dependsOn: [{ property: 'context', system: SNOMED, value: '146861000119102' }], product: [{ property: 'http://hl7.org/fhir/StructureDefinition/Patient#gender', value: 'female' }], }, ], }, ], }, ], }; const pool = getDatabasePool(DatabaseMode.WRITER); const db = await pool.connect(); await importConceptMap(db, resource); db.release(); const results = await getMappingRows(pool, resource); expect(results).toHaveLength(4); expect(results).toStrictEqual( expect.arrayContaining([ expect.objectContaining({ conceptMap: resource.id, sourceSystem: SNOMED, sourceCode: '1003470004', targetSystem: ICD10, targetCode: 'Z12.9', relationship: null, uri: null, type: null, value: null, kind: null, }), expect.objectContaining({ conceptMap: resource.id, sourceSystem: SNOMED, sourceCode: '1003470004', targetSystem: ICD10, targetCode: 'Z12.11', relationship: null, kind: 'dependsOn', uri: 'context', type: 'Coding', value: `{"system":"${SNOMED}","code":"460591000124101"}`, }), expect.objectContaining({ conceptMap: resource.id, sourceSystem: SNOMED, sourceCode: '1003470004', targetSystem: ICD10, targetCode: 'Z12.72', relationship: null, kind: 'dependsOn', uri: 'context', type: 'Coding', value: `{"system":"${SNOMED}","code":"146861000119102"}`, }), expect.objectContaining({ conceptMap: resource.id, sourceSystem: SNOMED, sourceCode: '1003470004', targetSystem: ICD10, targetCode: 'Z12.72', relationship: null, kind: 'product', uri: 'http://hl7.org/fhir/StructureDefinition/Patient#gender', type: 'code', value: `"female"`, }), ]) ); }); }); describe('ConceptMap/$import', () => { let accessToken: string; let repo: Repository; beforeAll(async () => { const config = await loadTestConfig(); await initApp(app, config); ({ accessToken, repo } = await createTestProject({ withAccessToken: true, withRepo: true, membership: { admin: true }, })); }); afterAll(async () => { await shutdownApp(); }); test('Imports concept mappings and attributes', async () => { const conceptMap = await repo.createResource<ConceptMap>({ resourceType: 'ConceptMap', status: 'draft', name: 'Test Imported ConceptMap', }); const res = await request(app) .post(`/fhir/R4/ConceptMap/${conceptMap.id}/$import`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Parameters', parameter: [ { name: 'mapping', part: [ { name: 'source', valueCoding: { system: 'http://snomed.info/sct', code: '10347006', display: 'Solar uticaria' }, }, { name: 'target', valueCoding: { system: 'http://hl7.org/fhir/sid/icd-10-cm', code: 'T50.905', display: 'Adverse effect of unspecified drugs, medicaments and biological substances, episode of care unspecified', }, }, { name: 'comment', valueString: 'CONSIDER ADDITIONAL CODE TO IDENTIFY SPECIFIC CONDITION OR DISEASE | EPISODE OF CARE INFORMATION NEEDED | MAP OF SOURCE CONCEPT IS CONTEXT DEPENDENT', }, { name: 'dependsOn', part: [ { name: 'code', valueCode: 'context' }, { name: 'value', valueCoding: { system: SNOMED, code: '403625006' } }, ], }, ], }, ], } satisfies Parameters); expect(res.status).toBe(200); const pool = getDatabasePool(DatabaseMode.READER); const results = await getMappingRows(pool, conceptMap); expect(results).toHaveLength(1); expect(results[0]).toStrictEqual({ conceptMap: conceptMap.id, sourceSystem: SNOMED, sourceCode: '10347006', sourceDisplay: 'Solar uticaria', targetSystem: 'http://hl7.org/fhir/sid/icd-10-cm', targetCode: 'T50.905', targetDisplay: expect.stringContaining('Adverse effect of unspecified drugs'), comment: expect.stringContaining('CONSIDER ADDITIONAL CODE'), relationship: null, kind: 'dependsOn', uri: 'context', type: 'Coding', value: `{"system":"http://snomed.info/sct","code":"403625006"}`, }); }); test('Requires admin privileges', async () => { const { accessToken, repo } = await createTestProject({ withAccessToken: true, withRepo: true, membership: { admin: false }, }); const conceptMap = await repo.createResource<ConceptMap>({ resourceType: 'ConceptMap', status: 'draft', name: 'Test Imported ConceptMap', }); const res = await request(app) .post(`/fhir/R4/ConceptMap/${conceptMap.id}/$import`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Parameters', parameter: [ { name: 'mapping', part: [ { name: 'source', valueCoding: { system: 'http://snomed.info/sct', code: '10347006' } }, { name: 'target', valueCoding: { system: 'http://hl7.org/fhir/sid/icd-10-cm', code: 'T50.905' } }, ], }, ], } satisfies Parameters); expect(res.status).toBe(403); }); test('Allows selecting ConceptMap by URL', async () => { const conceptMap = await repo.createResource<ConceptMap>({ resourceType: 'ConceptMap', status: 'draft', url: 'http://example.com/ConceptMap/' + randomUUID(), }); const res = await request(app) .post(`/fhir/R4/ConceptMap/$import`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Parameters', parameter: [ { name: 'url', valueUri: conceptMap.url }, { name: 'mapping', part: [ { name: 'source', valueCoding: { system: 'http://snomed.info/sct', code: '10347006' } }, { name: 'target', valueCoding: { system: 'http://hl7.org/fhir/sid/icd-10-cm', code: 'T50.905' } }, ], }, ], } satisfies Parameters); expect(res.status).toBe(200); }); test('Requires ConceptMap to be specified', async () => { const res = await request(app) .post(`/fhir/R4/ConceptMap/$import`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Parameters', parameter: [ { name: 'mapping', part: [ { name: 'source', valueCoding: { system: 'http://snomed.info/sct', code: '10347006' } }, { name: 'target', valueCoding: { system: 'http://hl7.org/fhir/sid/icd-10-cm', code: 'T50.905' } }, ], }, ], } satisfies Parameters); expect(res.status).toBe(400); expect(res.body).toMatchObject<OperationOutcome>({ resourceType: 'OperationOutcome', issue: [expect.objectContaining({ details: { text: 'ConceptMap to import into must be specified' } })], }); }); test('Cannot overspecify ConceptMap', async () => { const conceptMap = await repo.createResource<ConceptMap>({ resourceType: 'ConceptMap', status: 'draft', url: 'http://example.com/ConceptMap/' + randomUUID(), }); const res = await request(app) .post(`/fhir/R4/ConceptMap/${conceptMap.id}/$import`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Parameters', parameter: [ { name: 'url', valueUri: conceptMap.url }, { name: 'mapping', part: [ { name: 'source', valueCoding: { system: 'http://snomed.info/sct', code: '10347006' } }, { name: 'target', valueCoding: { system: 'http://hl7.org/fhir/sid/icd-10-cm', code: 'T50.905' } }, ], }, ], } satisfies Parameters); expect(res.status).toBe(400); expect(res.body).toMatchObject<OperationOutcome>({ resourceType: 'OperationOutcome', issue: [ expect.objectContaining({ details: { text: expect.stringContaining('not permitted for instance operation') } }), ], }); }); test('Requires source code to be specified', async () => { const conceptMap = await repo.createResource<ConceptMap>({ resourceType: 'ConceptMap', status: 'draft', url: 'http://example.com/ConceptMap/' + randomUUID(), }); const res = await request(app) .post(`/fhir/R4/ConceptMap/${conceptMap.id}/$import`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Parameters', parameter: [ { name: 'mapping', part: [ { name: 'source', valueCoding: { system: 'http://snomed.info/sct' } }, // Must specify code { name: 'target', valueCoding: { system: 'http://hl7.org/fhir/sid/icd-10-cm', code: 'T50.905' } }, ], }, ], } satisfies Parameters); expect(res.status).toBe(400); expect(res.body).toMatchObject<OperationOutcome>({ resourceType: 'OperationOutcome', issue: [expect.objectContaining({ details: { text: 'Source code for mapping is required' } })], }); }); test('Ignores unspecified source code in ConceptMap resource', async () => { const conceptMap = await repo.createResource<ConceptMap>({ resourceType: 'ConceptMap', status: 'draft', url: 'http://example.com/ConceptMap/' + randomUUID(), group: [ { source: SNOMED, element: [ { code: '364075005', target: [{ code: '8886-4', equivalence: 'equivalent' }], }, { target: [{ code: 'unmapped', equivalence: 'equal' }], }, ], }, ], }); const pool = getDatabasePool(DatabaseMode.READER); const results = await getMappingRows(pool, conceptMap); expect(results).toHaveLength(1); }); test('Handles ConceptMap with no valid mappings', async () => { const map: ConceptMap = await repo.createResource({ resourceType: 'ConceptMap', group: [ { target: 'urn:uuid:f2334818-8254-4c9f-95a4-335109e78c25', element: [{ target: [{ equivalence: 'disjoint' }] }], }, ], status: 'active', }); const pool = getDatabasePool(DatabaseMode.READER); const results = await getMappingRows(pool, map); expect(results).toHaveLength(0); }); }); async function getMappingRows(pool: Pool, conceptMap: ConceptMap): Promise<any[]> { const db = await pool.connect(); const query = new SelectQuery('ConceptMapping') .column('conceptMap') .column('sourceCode') .column('sourceDisplay') .column('targetCode') .column('targetDisplay') .column('relationship') .column('comment') .join( 'LEFT JOIN', 'ConceptMapping_Attribute', 'attr', new Condition(new Column('ConceptMapping', 'id'), '=', new Column('attr', 'mapping')) ) .column(new Column('attr', 'kind')) .column(new Column('attr', 'uri')) .column(new Column('attr', 'type')) .column(new Column('attr', 'value')) .join( 'INNER JOIN', 'CodingSystem', 'source', new Condition(new Column('source', 'id'), '=', new Column('ConceptMapping', 'sourceSystem')) ) .column(new Column('source', 'system', false, 'sourceSystem')) .join( 'INNER JOIN', 'CodingSystem', 'target', new Condition(new Column('target', 'id'), '=', new Column('ConceptMapping', 'targetSystem')) ) .column(new Column('target', 'system', false, 'targetSystem')) .where('conceptMap', '=', conceptMap.id); const results = await query.execute(db); db.release(); return results; }