feat: Compile IG StructureDefinitions (#219)

.npmignore

@@ -0,0 +1,40 @@
+# Don't include original .ts files when doing `npm pack`
+*.ts
+!*.template.ts
+!*.d.ts
+coverage
+.nyc_output
+*.tgz
+
+*.tsbuildinfo
+tsconfig.json
+.eslintrc.js
+.eslintignore
+.prettierrc.js
+.github
+.dockerignore
+serverless.yaml
+serverless_config.template.json
+CODE_OF_CONDUCT.md
+CONTRIBUTING.md
+CHANGELOG.md
+CODEOWNERS
+CUSTOMIZE.md
+DEVELOPMENT.md
+INSTALL.md
+LICENSE
+NOTICE
+README.md
+THIRD-PARTY
+
+auditLogMover/
+bulkExport/
+cloudformation/
+compiledImplementationGuides/
+implementationGuides/
+docker/
+integration-tests/
+postman/
+resources/
+scripts/
+src/

package.json

@@ -3,7 +3,8 @@
   "version": "2.4.0",
   "description": "FHIR Works on AWS deployment",
   "stackname": "fhir-works-on-aws-deployment",
-  "main": "src/index.ts",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
   "author": {
     "name": "Amazon Web Services",
     "email": "[email protected]",
@@ -68,10 +69,10 @@
     "serverless-plugin-typescript": "^1.1.9",
     "serverless-step-functions": "^2.27.1",
     "sinon": "^9.0.2",
+    "tmp-promise": "^3.0.2",
     "ts-jest": "^26.4.4",
     "typescript": "^4.1.3",
-    "wait-for-expect": "^3.0.2",
-    "tmp-promise": "^3.0.2"
+    "wait-for-expect": "^3.0.2"
   },
   "resolutions": {
     "dot-prop": "^5.1.1",

scripts/compile-igs.ts

@@ -1,24 +1,26 @@
-import { join, dirname } from 'path';
 import yargs from 'yargs';
-import { SearchImplementationGuides } from 'fhir-works-on-aws-search-es';
+import { join } from 'path';
 import { existsSync, mkdirSync } from 'fs';
+import { SearchImplementationGuides } from 'fhir-works-on-aws-search-es';
+import { StructureDefinitionImplementationGuides } from 'fhir-works-on-aws-routing/lib/implementationGuides';
 import { IGCompiler } from '../src/implementationGuides/IGCompiler';
+import { COMPILED_IGS_DIRECTORY } from "../src/implementationGuides/loadCompiledIGs";
 
 const PROJECT_DIR = join(__dirname, '..');
 
 function parseCmdOptions() {
     return yargs(process.argv.slice(2))
-        .usage('Usage: $0 [--ignoreVersion, -i ] [--igPath, -p IG pack directory] [--outputFile, -o output ]')
+        .usage('Usage: $0 [--ignoreVersion, -i ] [--igPath, -p IG pack directory] [--outputDir, -o output ]')
         .describe('ignoreVersion', "Don't care whether version of dependency lines up with version of installed IG")
         .boolean('ignoreVersion')
         .default('ignoreVersion', false)
         .alias('i', 'ignoreVersion')
         .describe('igPath', 'Path to folder with IG pack sub folders')
         .default('igPath', join(PROJECT_DIR, 'implementationGuides/'))
         .alias('p', 'igPath')
-        .describe('outputFile', 'Path to compiled output JSON file')
-        .alias('o', 'outputFile')
-        .default('outputFile', join(PROJECT_DIR, 'compiledImplementationGuides/fhir-works-on-aws-search-es.json')).argv;
+        .describe('outputDir', 'Path to compiled output JSON file')
+        .alias('o', 'outputDir')
+        .default('outputDir', join(PROJECT_DIR, COMPILED_IGS_DIRECTORY)).argv;
 }
 
 /**
@@ -34,14 +36,19 @@ async function compileIGs() {
         console.log(`IGs folder '${cmdArgs.igPath}' does not exist. No IGs found, exiting...`);
         return;
     }
-    const compiledIgsDir = dirname(cmdArgs.outputFile);
+    const compiledIgsDir = cmdArgs.outputDir.toString()
     if (!existsSync(compiledIgsDir)) {
         console.log(`folder for compiled IGs '${compiledIgsDir}' does not exist, creating it`);
         mkdirSync(compiledIgsDir, { recursive: true });
     }
 
     try {
-        await new IGCompiler(SearchImplementationGuides, options).compileIGs(cmdArgs.igPath, cmdArgs.outputFile);
+        await new IGCompiler(
+            SearchImplementationGuides,
+            new StructureDefinitionImplementationGuides,
+            options
+        )
+        .compileIGs(cmdArgs.igPath, cmdArgs.outputDir);
     } catch (ex) {
         console.error('Exception: ', ex.message, ex.stack);
     }

src/config.ts

@@ -24,7 +24,6 @@ const baseResources = fhirVersion === '4.0.1' ? BASE_R4_RESOURCES : BASE_STU3_RE
 const authService = IS_OFFLINE ? stubs.passThroughAuthz : new RBACHandler(RBACRules(baseResources), fhirVersion);
 const dynamoDbDataService = new DynamoDbDataService(DynamoDb);
 const dynamoDbBundleService = new DynamoDbBundleService(DynamoDb);
-
 const esSearch = new ElasticSearchService(
     [
         {
@@ -79,6 +78,7 @@ export const fhirConfig: FhirConfig = {
     profile: {
         systemOperations: ['transaction'],
         bundle: dynamoDbBundleService,
+        compiledImplementationGuides: loadImplementationGuides('fhir-works-on-aws-routing'),
         systemHistory: stubs.history,
         systemSearch: stubs.search,
         bulkDataAccess: dynamoDbDataService,

src/implementationGuides/IGCompiler.ts

@@ -59,14 +59,16 @@ export interface IGInfo {
 export class IGCompiler {
     private options: IGCompilerOptions;
 
-    private readonly implementationGuides: ImplementationGuides;
+    private readonly searchImplementationGuides: ImplementationGuides;
+    private readonly structureDefinitionImplementationGuides: ImplementationGuides;
 
-    constructor(implementationGuides: ImplementationGuides, options: IGCompilerOptions) {
+    constructor(searchImplementationGuides: ImplementationGuides, structureDefinitionImplementationGuides: ImplementationGuides, options: IGCompilerOptions) {
+        this.searchImplementationGuides = searchImplementationGuides;
+        this.structureDefinitionImplementationGuides = structureDefinitionImplementationGuides;
         this.options = options;
-        this.implementationGuides = implementationGuides;
     }
 
-    async collectResources(igDir: PathLike): Promise<any[]> {
+    async collectSearchParams(igDir: PathLike): Promise<any[]> {
         const indexJson = path.join(igDir.toString(), '.index.json');
         if (!existsSync(indexJson)) {
             throw new Error(`'.index.json' not found in ${igDir}`);
@@ -83,6 +85,23 @@ export class IGCompiler {
         return resources;
     }
 
+    async collectStructureDefinitions(igDir: PathLike): Promise<any[]> {
+        const indexJson = path.join(igDir.toString(), '.index.json');
+        if (!existsSync(indexJson)) {
+            throw new Error(`'.index.json' not found in ${igDir}`);
+        }
+        const index: any = await loadJson(indexJson);
+        const resources = [];
+        for (const file of index.files) {
+            if (file.resourceType === 'StructureDefinition') {
+                const filePath = path.join(igDir.toString(), file.filename);
+                console.log(`Compiling ${filePath}`);
+                resources.push(await loadJson(filePath));
+            }
+        }
+        return resources;
+    }
+
     /**
      * Main public function
      * @param igsDir
@@ -93,13 +112,19 @@ export class IGCompiler {
             throw new Error(`'${igsDir}' doesn't exist`);
         }
         const igInfos = await this.collectIGInfos(igsDir);
-        this.validateDependencies(igInfos);
-        const resources: any[] = [];
+        // this.validateDependencies(igInfos);
+
+        const searchParams: any[] = [];
+        const structureDefinitions: any[] = [];
         for (const igInfo of igInfos) {
-            resources.push(...(await this.collectResources(igInfo.path)));
+            searchParams.push(...(await this.collectSearchParams(igInfo.path)));
+            structureDefinitions.push(...(await this.collectStructureDefinitions(igInfo.path)));
         }
-        const compiledResources = await this.implementationGuides.compile(resources);
-        await storeJson(outputPath, compiledResources);
+        const compiledSearchParams = await this.searchImplementationGuides.compile(searchParams);
+        const compiledStructureDefinitions = await this.structureDefinitionImplementationGuides.compile(structureDefinitions);
+
+        await storeJson(path.join(outputPath.toString(), 'fhir-works-on-aws-search-es.json'), compiledSearchParams);
+        await storeJson(path.join(outputPath.toString(), 'fhir-works-on-aws-routing.json'), compiledStructureDefinitions);
     }
 
     createIGKey(name: string, version: string) {

src/implementationGuides/loadCompiledIGs.ts

@@ -4,17 +4,19 @@
  */
 
 import path from 'path';
-import { existsSync, readFileSync } from 'fs';
+import { existsSync, PathLike, readFileSync } from 'fs';
 
-const COMPILED_IGS_DIRECTORY = 'compiledImplementationGuides';
+export const COMPILED_IGS_DIRECTORY = 'compiledImplementationGuides';
 
 // eslint-disable-next-line import/prefer-default-export
-export const loadImplementationGuides = (moduleName: string): any[] | undefined => {
-    const implementationGuidesPath = path.join(__dirname, '..', '..', COMPILED_IGS_DIRECTORY);
-    const searchIgsPath = path.join(implementationGuidesPath, `${moduleName}.json`);
+export const loadImplementationGuides = (moduleName: string, implementationGuidesPath?: PathLike): any[] | undefined => {
+    if ( implementationGuidesPath === undefined) {
+        implementationGuidesPath = path.join(__dirname, '..', '..', COMPILED_IGS_DIRECTORY);
+    }
+    const igsPath = path.join(implementationGuidesPath.toString(), `${moduleName}.json`);
 
-    if (existsSync(searchIgsPath)) {
-        return JSON.parse(readFileSync(searchIgsPath, { encoding: 'utf8' }));
+    if (existsSync(igsPath)) {
+        return JSON.parse(readFileSync(igsPath, { encoding: 'utf8' }));
     }
     return undefined;
 };

tsconfig.json

@@ -6,6 +6,7 @@
     "esModuleInterop": true, // Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'.
     "forceConsistentCasingInFileNames": true, // Disallow inconsistently-cased references to the same file.
     "outDir": "dist",
+    "declaration": true,
     "sourceMap": true,
     "resolveJsonModule": true,
     "baseUrl": ".",