feat: Implement 3.0 interface (#24)

awslabs · Nov 12, 2020 · 4c5c310 · 4c5c310
1 parent 9318894
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,14 @@
 
 All notable changes to this project will be documented in this file.
 
+## [2.0.0] - 2020-11-11
+
+### Added
+- Support for DB export by routing export requests to the corresponding BulkDataAccess interfaces as defined in `fhir-works-on-aws-interface` v3.0.0
+- Supporting capability statement configuration for OAuth as defined in `fhir-works-on-aws-interface` v3.0.0
+- Improved error handling to allow matching of same error objects across different `fhir-works-on-aws-interface` versions 
+- Support for configuring CORs header
+
 ## [1.1.0] - 2020-09-25
 - feat: Pass down allowed resource types to search service
 

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "fhir-works-on-aws-routing",
-  "version": "1.1.0",
+  "version": "2.0.0",
   "description": "FHIR Works on AWS routing implementation",
   "main": "lib/index.js",
   "types": "lib/index.d.ts",
@@ -33,7 +33,7 @@
     "cors": "^2.8.5",
     "errorhandler": "^1.5.1",
     "express": "^4.17.1",
-    "fhir-works-on-aws-interface": "^2.0.0",
+    "fhir-works-on-aws-interface": "^3.0.0",
     "flat": "^5.0.0",
     "http-errors": "^1.8.0",
     "lodash": "^4.17.15",
@@ -50,6 +50,7 @@
     "@types/jest": "^25.1.1",
     "@types/lodash": "^4.14.157",
     "@types/mime-types": "^2.1.0",
+    "@types/mock-req-res": "^1.1.2",
     "@types/node": "^12",
     "@types/uuid": "^3.4.7",
     "@typescript-eslint/eslint-plugin": "^2.18.0",
@@ -61,7 +62,9 @@
     "eslint-plugin-prettier": "^3.1.2",
     "jest": "^25.1.0",
     "jest-mock-extended": "^1.0.8",
+    "mock-req-res": "^1.2.0",
     "prettier": "^1.19.1",
+    "sinon": "^9.0.3",
     "ts-jest": "^25.1.0",
     "typescript": "^3.7.5"
   },

diff --git a/sampleData/r4FhirConfigWithExclusions.ts b/sampleData/r4FhirConfigWithExclusions.ts
@@ -5,7 +5,10 @@ const config: FhirConfig = {
     orgName: 'Organization Name',
     auth: {
         strategy: {
-            oauthUrl: 'http://example.com',
+            oauth: {
+                authorizationUrl: 'http://example.com/authorization',
+                tokenUrl: 'http://example.com/oauth2/token',
+            },
             service: 'SMART-on-FHIR',
         },
         authorization: stubs.passThroughAuthz,

diff --git a/sampleData/stu3FhirConfigWithExclusions.ts b/sampleData/stu3FhirConfigWithExclusions.ts
@@ -5,7 +5,10 @@ const config: FhirConfig = {
     orgName: 'Organization Name',
     auth: {
         strategy: {
-            oauthUrl: 'http://example.com',
+            oauth: {
+                authorizationUrl: 'http://example.com/authorization',
+                tokenUrl: 'http://example.com/oauth2/token',
+            },
             service: 'OAuth',
         },
         authorization: stubs.passThroughAuthz,

diff --git a/src/app.ts b/src/app.ts
@@ -18,6 +18,7 @@ import MetadataRoute from './router/routes/metadataRoute';
 import ResourceHandler from './router/handlers/resourceHandler';
 import RootRoute from './router/routes/rootRoute';
 import { applicationErrorMapper, httpErrorHandler, unknownErrorHandler } from './router/routes/errorHandling';
+import ExportRoute from './router/routes/exportRoute';
 
 const configVersionSupported: ConfigVersion = 1;
 
@@ -53,24 +54,31 @@ export function generateServerlessRouter(
         try {
             const requestInformation = getRequestInformation(req.method, req.path);
             const accessToken: string = cleanAuthHeader(req.headers.authorization);
-            const isAllowed: boolean = await fhirConfig.auth.authorization.isAuthorized({
+            await fhirConfig.auth.authorization.isAuthorized({
                 ...requestInformation,
                 accessToken,
             });
-            if (isAllowed) {
-                next();
-            } else {
-                res.status(403).json({ message: 'Forbidden' });
-            }
+            res.locals.requesterUserId = fhirConfig.auth.authorization.getRequesterUserId(accessToken);
+            next();
         } catch (e) {
-            res.status(403).json({ message: `Forbidden. ${e.message}` });
+            next(e);
         }
     });
 
     // Metadata
     const metadataRoute: MetadataRoute = new MetadataRoute(fhirVersion, configHandler, hasCORSEnabled);
     app.use('/metadata', metadataRoute.router);
 
+    // Export
+    if (fhirConfig.profile.bulkDataAccess) {
+        const exportRoute = new ExportRoute(
+            serverUrl,
+            fhirConfig.profile.bulkDataAccess,
+            fhirConfig.auth.authorization,
+        );
+        app.use('/', exportRoute.router);
+    }
+
     // Special Resources
     if (fhirConfig.profile.resources) {
         Object.entries(fhirConfig.profile.resources).forEach(async resourceEntry => {

diff --git a/src/regExpressions.test.ts b/src/regExpressions.test.ts
@@ -3,7 +3,7 @@
  *  SPDX-License-Identifier: Apache-2.0
  */
 
-import { captureFullUrlParts } from './regExpressions';
+import { captureFullUrlParts, dateTimeWithTimeZoneRegExp } from './regExpressions';
 
 describe('captureFullUrlParts', () => {
     test('Capture rootUrl, resourceType, id, versionId', () => {
@@ -52,4 +52,15 @@ describe('captureFullUrlParts', () => {
         // @ts-ignore
         expect([...actualMatch]).toEqual([...expectedMatch]);
     });
+    test('dateTimeWithTimeZoneRegExp', () => {
+        const utcTimeZone = '2020-09-02T00:00:00Z';
+        const estTimeZone = '2020-09-02T00:00:00-05:00';
+        const invalidUtcTimeZone = '2020-09-02T00:00:00R';
+        const timeWithoutTimeZone = '2020-09-02T00:00:00';
+
+        expect(dateTimeWithTimeZoneRegExp.test(utcTimeZone)).toBeTruthy();
+        expect(dateTimeWithTimeZoneRegExp.test(estTimeZone)).toBeTruthy();
+        expect(dateTimeWithTimeZoneRegExp.test(invalidUtcTimeZone)).toBeFalsy();
+        expect(dateTimeWithTimeZoneRegExp.test(timeWithoutTimeZone)).toBeFalsy();
+    });
 });
diff --git a/src/regExpressions.ts b/src/regExpressions.ts
@@ -6,7 +6,8 @@
 export const uuidRegExp = /\w{8}-\w{4}-\w{4}-\w{4}-\w{12}/;
 export const resourceTypeWithUuidRegExp = /\w+\/\w{8}-\w{4}-\w{4}-\w{4}-\w{12}/;
 
-export const utcTimeRegExp = /\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}.\d+Z/;
+export const utcTimeRegExp = /\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(.\d+)?Z/;
+export const dateTimeWithTimeZoneRegExp = /\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(.\d+)?(?:Z|[+-](?:2[0-3]|[01][0-9]):[0-5][0-9])/;
 export const timeFromEpochInMsRegExp = /\d{13}/;
 
 // Exp. Patient/de5b1d47-2780-4508-9273-4e0ec133ee3a

diff --git a/src/router/__mocks__/dynamoDbDataService.ts b/src/router/__mocks__/dynamoDbDataService.ts
@@ -12,6 +12,8 @@ import {
     generateMeta,
     GenericResponse,
     clone,
+    InitiateExportRequest,
+    GetExportStatusResponse,
 } from 'fhir-works-on-aws-interface';
 import validPatient from '../../../sampleData/validV4Patient.json';
 
@@ -104,5 +106,17 @@ const DynamoDbDataService: Persistence = class {
     ): Promise<GenericResponse> {
         throw new Error('Method not implemented.');
     }
+
+    static initiateExport(request: InitiateExportRequest): Promise<string> {
+        throw new Error('Method not implemented.');
+    }
+
+    static cancelExport(jobId: string): Promise<void> {
+        throw new Error('Method not implemented');
+    }
+
+    static getExportStatus(jobId: string): Promise<GetExportStatusResponse> {
+        throw new Error('Method not implemented');
+    }
 };
 export default DynamoDbDataService;
diff --git a/src/router/bundle/bundleHandler.ts b/src/router/bundle/bundleHandler.ts
@@ -48,10 +48,11 @@ export default class BundleHandler implements BundleHandlerInterface {
         this.bundleService = bundleService;
         this.serverUrl = serverUrl;
         this.authService = authService;
-        this.validator = new Validator(fhirVersion);
+        this.supportedGenericResources = supportedGenericResources;
         this.genericResource = genericResource;
         this.resources = resources;
-        this.supportedGenericResources = supportedGenericResources;
+
+        this.validator = new Validator(fhirVersion);
     }
 
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
@@ -124,13 +125,10 @@ export default class BundleHandler implements BundleHandlerInterface {
             throw new createError.BadRequest(e.message);
         }
 
-        const isAllowed: boolean = await this.authService.isBundleRequestAuthorized({
+        await this.authService.isBundleRequestAuthorized({
             accessToken,
             requests,
         });
-        if (!isAllowed) {
-            throw new createError.Forbidden('Forbidden');
-        }
 
         if (requests.length > MAX_BUNDLE_ENTRIES) {
             throw new createError.BadRequest(

diff --git a/src/router/handlers/exportHandler.ts b/src/router/handlers/exportHandler.ts
@@ -0,0 +1,52 @@
+/*
+ *  Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+ *  SPDX-License-Identifier: Apache-2.0
+ */
+
+import {
+    AccessBulkDataJobRequest,
+    Authorization,
+    BulkDataAccess,
+    GetExportStatusResponse,
+    InitiateExportRequest,
+} from 'fhir-works-on-aws-interface';
+import createError from 'http-errors';
+
+export default class ExportHandler {
+    private bulkDataAccess: BulkDataAccess;
+
+    private authService: Authorization;
+
+    constructor(bulkDataAccess: BulkDataAccess, authService: Authorization) {
+        this.bulkDataAccess = bulkDataAccess;
+        this.authService = authService;
+    }
+
+    async initiateExport(initiateExportRequest: InitiateExportRequest): Promise<string> {
+        return this.bulkDataAccess.initiateExport(initiateExportRequest);
+    }
+
+    async getExportJobStatus(jobId: string, requesterUserId: string): Promise<GetExportStatusResponse> {
+        const jobDetails = await this.bulkDataAccess.getExportStatus(jobId);
+        await this.checkIfRequesterHasAccessToJob(jobDetails, requesterUserId);
+        return jobDetails;
+    }
+
+    async cancelExport(jobId: string, requesterUserId: string): Promise<void> {
+        const jobDetails = await this.bulkDataAccess.getExportStatus(jobId);
+        await this.checkIfRequesterHasAccessToJob(jobDetails, requesterUserId);
+        if (['completed', 'failed'].includes(jobDetails.jobStatus)) {
+            throw new createError.BadRequest(
+                `Job cannot be canceled because job is already in ${jobDetails.jobStatus} state`,
+            );
+        }
+
+        await this.bulkDataAccess.cancelExport(jobId);
+    }
+
+    private async checkIfRequesterHasAccessToJob(jobDetails: GetExportStatusResponse, requesterUserId: string) {
+        const { jobOwnerId } = jobDetails;
+        const accessBulkDataJobRequest: AccessBulkDataJobRequest = { requesterUserId, jobOwnerId };
+        await this.authService.isAccessBulkDataJobAllowed(accessBulkDataJobRequest);
+    }
+}
diff --git a/src/router/handlers/resourceHandler.test.ts b/src/router/handlers/resourceHandler.test.ts
@@ -22,6 +22,8 @@ import {
     ResourceNotFoundError,
     ResourceVersionNotFoundError,
     InvalidResourceError,
+    InitiateExportRequest,
+    GetExportStatusResponse,
 } from 'fhir-works-on-aws-interface';
 import ResourceHandler from './resourceHandler';
 import invalidPatient from '../../../sampleData/invalidV4Patient.json';
@@ -200,6 +202,18 @@ describe('ERROR CASES: Testing create, read, update, delete of resources', () =>
             throw new Error('Method not implemented.');
         }
 
+        static initiateExport(request: InitiateExportRequest): Promise<string> {
+            throw new Error('Method not implemented.');
+        }
+
+        static cancelExport(jobId: string): Promise<void> {
+            throw new Error('Method not implemented');
+        }
+
+        static getExportStatus(jobId: string): Promise<GetExportStatusResponse> {
+            throw new Error('Method not implemented');
+        }
+
         static conditionalDeleteResource(
             request: ConditionalDeleteResourceRequest,
             queryParams: any,

diff --git a/src/router/metadata/cap.rest.security.template.ts b/src/router/metadata/cap.rest.security.template.ts
@@ -20,7 +20,7 @@ export default function makeSecurity(authConfig: Auth, hasCORSEnabled: boolean =
                 },
             ],
         };
-        if (authConfig.strategy.oauthUrl) {
+        if (authConfig.strategy.oauth) {
             security = {
                 ...security,
                 ...{
@@ -30,11 +30,11 @@ export default function makeSecurity(authConfig: Auth, hasCORSEnabled: boolean =
                             extension: [
                                 {
                                     url: 'token',
-                                    valueUri: `${authConfig.strategy.oauthUrl}/token`,
+                                    valueUri: authConfig.strategy.oauth.tokenUrl,
                                 },
                                 {
                                     url: 'authorize',
-                                    valueUri: `${authConfig.strategy.oauthUrl}/authorize`,
+                                    valueUri: authConfig.strategy.oauth.authorizationUrl,
                                 },
                             ],
                         },

diff --git a/src/router/metadata/cap.rest.template.ts b/src/router/metadata/cap.rest.template.ts
@@ -6,7 +6,12 @@
 import { SystemOperation } from 'fhir-works-on-aws-interface';
 import { makeOperation } from './cap.rest.resource.template';
 
-export default function makeRest(resource: any[], security: any, globalOperations: SystemOperation[]) {
+export default function makeRest(
+    resource: any[],
+    security: any,
+    globalOperations: SystemOperation[],
+    bulkDataAccessEnabled: boolean,
+) {
     const rest: any = {
         mode: 'server',
         documentation: 'Main FHIR endpoint',
@@ -24,5 +29,19 @@ export default function makeRest(resource: any[], security: any, globalOperation
             },
         ];
     }
+    if (bulkDataAccessEnabled) {
+        rest.operation = [
+            {
+                name: 'export',
+                definition:
+                    'This FHIR Operation initiates the asynchronous generation of data to which the client is authorized. Currently only system level export is supported. For more information please refer here: http://hl7.org/fhir/uv/bulkdata/export/index.html#bulk-data-kick-off-request',
+            },
+            {
+                name: 'export-poll-status',
+                definition:
+                    'After a bulk data request has been started, the client MAY poll the status URL provided in the Content-Location header. For more details please refer here: http://hl7.org/fhir/uv/bulkdata/export/index.html#bulk-data-status-request',
+            },
+        ];
+    }
     return rest;
 }
diff --git a/src/router/metadata/metadataHandler.test.ts b/src/router/metadata/metadataHandler.test.ts
@@ -3,6 +3,7 @@
  *  SPDX-License-Identifier: Apache-2.0
  */
 
+import { clone, stubs } from 'fhir-works-on-aws-interface';
 import MetadataHandler from './metadataHandler';
 import { makeOperation } from './cap.rest.resource.template';
 import r4FhirConfigGeneric from '../../../sampleData/r4FhirConfigGeneric';
@@ -470,3 +471,31 @@ test('R4: FHIR Config V4 no generic set-up & mix of STU3 & R4', async () => {
         message: 'Success',
     });
 });
+test('R4: FHIR Config V4 with bulkDataAccess', async () => {
+    const r4ConfigWithBulkDataAccess = clone(r4FhirConfigGeneric);
+    r4ConfigWithBulkDataAccess.profile.bulkDataAccess = stubs.bulkDataAccess;
+    const configHandler: ConfigHandler = new ConfigHandler(r4ConfigWithBulkDataAccess, SUPPORTED_R4_RESOURCES);
+    const metadataHandler: MetadataHandler = new MetadataHandler(configHandler);
+    const response = await metadataHandler.capabilities({ fhirVersion: '4.0.1', mode: 'full' });
+
+    expect(response.resource.rest[0].operation).toEqual([
+        {
+            name: 'export',
+            definition:
+                'This FHIR Operation initiates the asynchronous generation of data to which the client is authorized. Currently only system level export is supported. For more information please refer here: http://hl7.org/fhir/uv/bulkdata/export/index.html#bulk-data-kick-off-request',
+        },
+        {
+            name: 'export-poll-status',
+            definition:
+                'After a bulk data request has been started, the client MAY poll the status URL provided in the Content-Location header. For more details please refer here: http://hl7.org/fhir/uv/bulkdata/export/index.html#bulk-data-status-request',
+        },
+    ]);
+});
+
+test('R4: FHIR Config V4 without bulkDataAccess', async () => {
+    const configHandler: ConfigHandler = new ConfigHandler(r4FhirConfigGeneric, SUPPORTED_R4_RESOURCES);
+    const metadataHandler: MetadataHandler = new MetadataHandler(configHandler);
+    const response = await metadataHandler.capabilities({ fhirVersion: '4.0.1', mode: 'full' });
+
+    expect(response.resource.rest[0].operation).toBeUndefined();
+});
diff --git a/src/router/metadata/metadataHandler.ts b/src/router/metadata/metadataHandler.ts
@@ -51,7 +51,7 @@ export default class MetadataHandler implements Capabilities {
 
         const generatedResources = this.generateResources(request.fhirVersion);
         const security = makeSecurity(auth, this.hasCORSEnabled);
-        const rest = makeRest(generatedResources, security, profile.systemOperations);
+        const rest = makeRest(generatedResources, security, profile.systemOperations, !!profile.bulkDataAccess);
         const capStatement = makeStatement(rest, orgName, server.url, request.fhirVersion);
 
         return {