ecqm-bundler - npm Package Compare versions

Comparing version 0.0.1 to 0.0.2

dist/helpers/cql.js

@@ -5,3 +5,3 @@ "use strict";
 function getMainLibraryId(cql) {
-    const re = /library ([a-zA-Z0-9_]+)( version .*)?/g;
+    const re = /^library ([a-zA-Z0-9_]+)( version .*)?/gm;
     const matches = re.exec(cql);
@@ -8,0 +8,0 @@ if (matches) {

dist/helpers/translator.js

@@ -15,13 +15,43 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getELM = void 0;
+exports.getELM = exports.resolveDependencies = exports.getCQLInfo = void 0;
 const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
 const cql_translation_service_client_1 = require("cql-translation-service-client");
-function translateCQL(paths, client) {
+const cql_1 = require("./cql");
+function getCQLInfo(cqlFiles) {
+    const info = {};
+    cqlFiles.forEach(f => {
+        const cql = fs_1.default.readFileSync(f, 'utf8');
+        const libraryId = (0, cql_1.getMainLibraryId)(cql);
+        if (libraryId) {
+            info[libraryId] = { cql };
+        }
+    });
+    return info;
+}
+exports.getCQLInfo = getCQLInfo;
+function resolveDependencies(mainCqlContent, allCql) {
+    const res = [];
+    const re = /^include ([a-zA-Z0-9_]+)( version .*)?/gm;
+    let includes;
+    while ((includes = re.exec(mainCqlContent))) {
+        const libraryId = includes[1];
+        res.push(libraryId);
+        if (allCql[libraryId]) {
+            res.push(...resolveDependencies(allCql[libraryId].cql, allCql));
+        }
+    }
+    return res;
+}
+exports.resolveDependencies = resolveDependencies;
+function translateCQL(paths, client, mainLibraryId) {
     return __awaiter(this, void 0, void 0, function* () {
-        const cqlRequestBody = {};
-        paths.forEach(f => {
-            cqlRequestBody[path_1.default.basename(f, '.cql')] = {
-                cql: fs_1.default.readFileSync(f, 'utf8')
-            };
+        const cqlRequestBody = getCQLInfo(paths);
+        const usedDependencyIds = [
+            ...new Set(resolveDependencies(cqlRequestBody[mainLibraryId].cql, cqlRequestBody))
+        ];
+        // Only include cql files that are explicitly included by the dependency chain
+        Object.keys(cqlRequestBody).forEach(k => {
+            if (k !== mainLibraryId && !usedDependencyIds.includes(k)) {
+                delete cqlRequestBody[k];
+            }
         });
@@ -44,6 +74,6 @@ const elm = yield client.convertCQL(cqlRequestBody);
 }
-function getELM(cqlPaths, translatorUrl) {
+function getELM(cqlPaths, translatorUrl, mainLibraryId) {
     return __awaiter(this, void 0, void 0, function* () {
         const client = new cql_translation_service_client_1.Client(`${translatorUrl}?annotations=true&locators=true`);
-        const librariesOrError = yield translateCQL(cqlPaths, client);
+        const librariesOrError = yield translateCQL(cqlPaths, client, mainLibraryId);
         if (librariesOrError instanceof Error)
@@ -50,0 +80,0 @@ throw librariesOrError;

dist/index.js

@@ -26,5 +26,7 @@ #!/usr/bin/env node
 program
-    .requiredOption('-c, --cql-file <path>')
-    .addOption(new commander_1.Option('--deps <deps...>', 'List of CQL dependency files of the main file').default([]))
-    .option('--deps-directory <path>', 'Directory containing all dependent CQL files')
+    .option('-c, --cql-file <path>')
+    .option('-e,--elm-file <path>')
+    .option('--debug', 'Enable debug mode to write contents to a ./debug directory', false)
+    .addOption(new commander_1.Option('--deps <deps...>', 'List of CQL or ELM dependency files of the main file').default([]))
+    .option('--deps-directory <path>', 'Directory containing all dependent CQL or ELM files')
     .option('-n,--numer <expr>', 'Numerator expression name of measure', 'Numerator')
@@ -46,4 +48,12 @@ .option('-i,--ipop <expr>', 'Numerator expression name of measure', 'Initial Population')
 const opts = program.opts();
+if (opts.elmFile && opts.cqlFile) {
+    logger_1.default.error('ERROR: Cannot use both -c/--cql-file and -e/--elm-file\n');
+    program.help();
+}
+if (!(opts.elmFile || opts.cqlFile)) {
+    logger_1.default.error('ERROR: Must specify one of -c/--cql-file or -e/--elm-file\n');
+    program.help();
+}
 if (opts.deps.length !== 0 && opts.depsDirectory) {
-    console.error('ERROR: Must specify only one of -d/--deps and --deps-directory\n');
+    logger_1.default.error('ERROR: Must specify only one of -d/--deps and --deps-directory\n');
     program.help();
@@ -63,35 +73,62 @@ }
         .readdirSync(opts.depsDirectory)
-        .filter(f => path_1.default.extname(f) === '.cql' && f !== path_1.default.basename(opts.cqlFile))
+        .filter(f => {
+        if (opts.elmFile) {
+            return path_1.default.extname(f) === '.json' && f !== path_1.default.basename(opts.elmFile);
+        }
+        else {
+            return path_1.default.extname(f) === '.cql' && f !== path_1.default.basename(opts.cqlFile);
+        }
+    })
         .map(f => path_1.default.join(depsBasePath, f));
 }
 logger_1.default.info(`Successfully gathered ${deps.length} dependencies`);
-const mainCQLPath = path_1.default.resolve(opts.cqlFile);
-const allCQL = [mainCQLPath, ...deps];
-logger_1.default.info(`Using ${mainCQLPath} as main library`);
 function main() {
     var _a;
     return __awaiter(this, void 0, void 0, function* () {
-        const mainLibraryId = (0, cql_1.getMainLibraryId)(fs_1.default.readFileSync(mainCQLPath, 'utf8'));
         let elm;
-        try {
-            logger_1.default.info('Translating all CQL');
-            const [result, errors] = yield (0, translator_1.getELM)(allCQL, opts.translatorUrl);
-            if (result == null) {
-                logger_1.default.error('Error translating CQL:');
-                console.error(errors);
+        let mainLibraryId = null;
+        if (opts.elmFile) {
+            const mainELM = JSON.parse(fs_1.default.readFileSync(path_1.default.resolve(opts.elmFile), 'utf8'));
+            mainLibraryId = mainELM.library.identifier.id;
+            if (!mainLibraryId) {
+                logger_1.default.error(`Could not locate main library ID in ${opts.elmFile}`);
                 process.exit(1);
             }
-            elm = result;
+            elm = [mainELM, ...deps.map(d => JSON.parse(fs_1.default.readFileSync(path_1.default.resolve(d), 'utf8')))];
         }
-        catch (e) {
-            logger_1.default.error(`HTTP error translating CQL: ${e.message}`);
-            console.error(e.stack);
-            if ((_a = e.response) === null || _a === void 0 ? void 0 : _a.data) {
-                console.log(e.response.data);
+        else {
+            const mainCQLPath = path_1.default.resolve(opts.cqlFile);
+            const allCQL = [mainCQLPath, ...deps];
+            logger_1.default.info(`Using ${mainCQLPath} as main library`);
+            mainLibraryId = (0, cql_1.getMainLibraryId)(fs_1.default.readFileSync(mainCQLPath, 'utf8'));
+            if (!mainLibraryId) {
+                logger_1.default.error(`Could not locate main library ID in ${opts.cqlFile}`);
+                process.exit(1);
             }
-            process.exit(1);
+            try {
+                logger_1.default.info('Translating all CQL');
+                const [result, errors] = yield (0, translator_1.getELM)(allCQL, opts.translatorUrl, mainLibraryId);
+                if (result == null) {
+                    logger_1.default.error('Error translating CQL:');
+                    console.error(errors);
+                    process.exit(1);
+                }
+                elm = result;
+            }
+            catch (e) {
+                logger_1.default.error(`HTTP error translating CQL: ${e.message}`);
+                console.error(e.stack);
+                if ((_a = e.response) === null || _a === void 0 ? void 0 : _a.data) {
+                    console.log(e.response.data);
+                }
+                process.exit(1);
+            }
         }
-        if (!mainLibraryId) {
-            logger_1.default.error(`Could not locate main library ID in ${mainCQLPath}`);
-            process.exit(1);
+        if (opts.debug === true) {
+            if (!fs_1.default.existsSync('./debug')) {
+                fs_1.default.mkdirSync('./debug');
+            }
+            elm.forEach(e => {
+                fs_1.default.writeFileSync(`./debug/${e.library.identifier.id}.json`, JSON.stringify(e, null, 2), 'utf8');
+            });
         }
@@ -98,0 +135,0 @@ const mainLibELM = (0, elm_1.findELMByIdentifier)({

package.json

 {
   "name": "ecqm-bundler",
-  "version": "0.0.1",
+  "version": "0.0.2",
   "description": "CLI for bundling FHIR-based eCQMs",
@@ -5,0 +5,0 @@ "main": "dist/index.js",

README.md

@@ -15,4 +15,6 @@ # ecqm-bundler
 
-Must have an instance of the [cql-translation-service](https://github.com/cqframework/cql-translation-service) running somewhere.
+For bundling with CQL files as input, you must have an instance of the [cql-translation-service](https://github.com/cqframework/cql-translation-service) running somewhere.
 
+Bundling is also supported with JSON ELM content directly. See [Bundling from ELM Content](#bundling-from-elm-content)
+
 ## Basic Usage
@@ -32,2 +34,14 @@
 
+**NOTE**: It is okay for the dependency directory to include more CQL files that won't be used. The bundler will parse the CQL content to identify all of the libaries
+that need to be included with the translation request, and will omit any CQL files that aren't included somewhere in the dependency tree starting from the
+main CQL file
+
+### Bundling from ELM Content
+
+``` bash
+ecqm-bundler -e /path/to/main/elm/file.json --deps-directory /path/to/deps/directory -v /path/to/valueset/directory
+```
+
+This will forego the CQL translation and bundle the libraries with the ELM content provided.
+
 ## Advanced Usage/Features
@@ -70,2 +84,9 @@
 
+### Debugging
+
+Debug mode will write all of the ELM content to a file in the `./debug` directory, which it will create. This is useful for inspecting the contents of translated CQL before it gets
+base64 encoded onto a FHIR Library resource.
+
+To enable, use `--debug` as an option in the CLI amongst the other options
+
 ## Full List of Options
@@ -78,4 +99,6 @@
   -c, --cql-file <path>
-  --deps <deps...>                       List of CQL dependency files of the main file (default: [])
-  --deps-directory <path>                Directory containing all dependent CQL files
+  -e,--elm-file <path>
+  --debug                                Enable debug mode to write contents to a ./debug directory (default: false)
+  --deps <deps...>                       List of CQL or ELM dependency files of the main file (default: [])
+  --deps-directory <path>                Directory containing all dependent CQL or ELM files
   -n,--numer <expr>                      Numerator expression name of measure (default: "Numerator")
@@ -82,0 +105,0 @@ -i,--ipop <expr>                       Numerator expression name of measure (default: "Initial Population")

src/helpers/cql.ts

 export function getMainLibraryId(cql: string): string | null {
-  const re = /library ([a-zA-Z0-9_]+)( version .*)?/g;
+  const re = /^library ([a-zA-Z0-9_]+)( version .*)?/gm;
 
@@ -4,0 +4,0 @@ const matches = re.exec(cql);

src/helpers/translator.ts

 import fs from 'fs';
-import path from 'path';
 import translationService, { Client } from 'cql-translation-service-client';
+import { getMainLibraryId } from './cql';
 
-async function translateCQL(paths: string[], client: Client): Promise<any> {
-  const cqlRequestBody: translationService.CqlLibraries = {};
+export function getCQLInfo(cqlFiles: string[]): translationService.CqlLibraries {
+  const info: translationService.CqlLibraries = {};
 
-  paths.forEach(f => {
-    cqlRequestBody[path.basename(f, '.cql')] = {
-      cql: fs.readFileSync(f, 'utf8')
-    };
+  cqlFiles.forEach(f => {
+    const cql = fs.readFileSync(f, 'utf8');
+    const libraryId = getMainLibraryId(cql);
+
+    if (libraryId) {
+      info[libraryId] = { cql };
+    }
   });
 
+  return info;
+}
+
+export function resolveDependencies(
+  mainCqlContent: string,
+  allCql: translationService.CqlLibraries
+): string[] {
+  const res: string[] = [];
+  const re = /^include ([a-zA-Z0-9_]+)( version .*)?/gm;
+  let includes;
+  while ((includes = re.exec(mainCqlContent))) {
+    const libraryId = includes[1];
+
+    res.push(libraryId);
+    if (allCql[libraryId]) {
+      res.push(...resolveDependencies(allCql[libraryId].cql, allCql));
+    }
+  }
+
+  return res;
+}
+
+async function translateCQL(paths: string[], client: Client, mainLibraryId: string): Promise<any> {
+  const cqlRequestBody = getCQLInfo(paths);
+
+  const usedDependencyIds = [
+    ...new Set(resolveDependencies(cqlRequestBody[mainLibraryId].cql, cqlRequestBody))
+  ];
+
+  // Only include cql files that are explicitly included by the dependency chain
+  Object.keys(cqlRequestBody).forEach(k => {
+    if (k !== mainLibraryId && !usedDependencyIds.includes(k)) {
+      delete cqlRequestBody[k];
+    }
+  });
+
   const elm = await client.convertCQL(cqlRequestBody);
@@ -35,6 +74,7 @@ return elm;
   cqlPaths: string[],
-  translatorUrl: string
+  translatorUrl: string,
+  mainLibraryId: string
 ): Promise<[any[] | null, any[] | null]> {
   const client = new Client(`${translatorUrl}?annotations=true&locators=true`);
-  const librariesOrError = await translateCQL(cqlPaths, client);
+  const librariesOrError = await translateCQL(cqlPaths, client, mainLibraryId);
 
@@ -41,0 +81,0 @@ if (librariesOrError instanceof Error) throw librariesOrError;

src/index.ts

@@ -24,7 +24,11 @@ #!/usr/bin/env node
 program
-  .requiredOption('-c, --cql-file <path>')
+  .option('-c, --cql-file <path>')
+  .option('-e,--elm-file <path>')
+  .option('--debug', 'Enable debug mode to write contents to a ./debug directory', false)
   .addOption(
-    new Option('--deps <deps...>', 'List of CQL dependency files of the main file').default([])
+    new Option('--deps <deps...>', 'List of CQL or ELM dependency files of the main file').default(
+      []
+    )
   )
-  .option('--deps-directory <path>', 'Directory containing all dependent CQL files')
+  .option('--deps-directory <path>', 'Directory containing all dependent CQL or ELM files')
   .option('-n,--numer <expr>', 'Numerator expression name of measure', 'Numerator')
@@ -60,4 +64,14 @@ .option('-i,--ipop <expr>', 'Numerator expression name of measure', 'Initial Population')
 
+if (opts.elmFile && opts.cqlFile) {
+  logger.error('ERROR: Cannot use both -c/--cql-file and -e/--elm-file\n');
+  program.help();
+}
+
+if (!(opts.elmFile || opts.cqlFile)) {
+  logger.error('ERROR: Must specify one of -c/--cql-file or -e/--elm-file\n');
+  program.help();
+}
+
 if (opts.deps.length !== 0 && opts.depsDirectory) {
-  console.error('ERROR: Must specify only one of -d/--deps and --deps-directory\n');
+  logger.error('ERROR: Must specify only one of -d/--deps and --deps-directory\n');
   program.help();
@@ -82,3 +96,9 @@ }
     .readdirSync(opts.depsDirectory)
-    .filter(f => path.extname(f) === '.cql' && f !== path.basename(opts.cqlFile))
+    .filter(f => {
+      if (opts.elmFile) {
+        return path.extname(f) === '.json' && f !== path.basename(opts.elmFile);
+      } else {
+        return path.extname(f) === '.cql' && f !== path.basename(opts.cqlFile);
+      }
+    })
     .map(f => path.join(depsBasePath, f));
@@ -89,34 +109,62 @@ }
 
-const mainCQLPath = path.resolve(opts.cqlFile);
-const allCQL = [mainCQLPath, ...deps];
-
-logger.info(`Using ${mainCQLPath} as main library`);
-
 async function main(): Promise<fhir4.Bundle> {
-  const mainLibraryId = getMainLibraryId(fs.readFileSync(mainCQLPath, 'utf8'));
   let elm: any[];
-  try {
-    logger.info('Translating all CQL');
-    const [result, errors] = await getELM(allCQL, opts.translatorUrl);
+  let mainLibraryId: string | null = null;
+  if (opts.elmFile) {
+    const mainELM = JSON.parse(fs.readFileSync(path.resolve(opts.elmFile), 'utf8'));
 
-    if (result == null) {
-      logger.error('Error translating CQL:');
-      console.error(errors);
+    mainLibraryId = mainELM.library.identifier.id;
+
+    if (!mainLibraryId) {
+      logger.error(`Could not locate main library ID in ${opts.elmFile}`);
       process.exit(1);
     }
-    elm = result;
-  } catch (e: any) {
-    logger.error(`HTTP error translating CQL: ${e.message}`);
-    console.error(e.stack);
 
-    if (e.response?.data) {
-      console.log(e.response.data);
+    elm = [mainELM, ...deps.map(d => JSON.parse(fs.readFileSync(path.resolve(d), 'utf8')))];
+  } else {
+    const mainCQLPath = path.resolve(opts.cqlFile);
+    const allCQL = [mainCQLPath, ...deps];
+
+    logger.info(`Using ${mainCQLPath} as main library`);
+
+    mainLibraryId = getMainLibraryId(fs.readFileSync(mainCQLPath, 'utf8'));
+
+    if (!mainLibraryId) {
+      logger.error(`Could not locate main library ID in ${opts.cqlFile}`);
+      process.exit(1);
     }
 
-    process.exit(1);
+    try {
+      logger.info('Translating all CQL');
+      const [result, errors] = await getELM(allCQL, opts.translatorUrl, mainLibraryId);
+
+      if (result == null) {
+        logger.error('Error translating CQL:');
+        console.error(errors);
+        process.exit(1);
+      }
+      elm = result;
+    } catch (e: any) {
+      logger.error(`HTTP error translating CQL: ${e.message}`);
+      console.error(e.stack);
+
+      if (e.response?.data) {
+        console.log(e.response.data);
+      }
+
+      process.exit(1);
+    }
   }
 
-  if (!mainLibraryId) {
-    logger.error(`Could not locate main library ID in ${mainCQLPath}`);
-    process.exit(1);
+  if (opts.debug === true) {
+    if (!fs.existsSync('./debug')) {
+      fs.mkdirSync('./debug');
+    }
+    elm.forEach(e => {
+      fs.writeFileSync(
+        `./debug/${e.library.identifier.id}.json`,
+        JSON.stringify(e, null, 2),
+        'utf8'
+      );
+    });
   }
@@ -123,0 +171,0 @@

test/fixtures/genTestData.ts

@@ -10,3 +10,3 @@ import fs from 'fs';
 
-getELM([simpleLibraryCQL, simpleLibraryDependencyCQL], TRANSLATOR_URL)
+getELM([simpleLibraryCQL, simpleLibraryDependencyCQL], TRANSLATOR_URL, 'SimpleLibrary')
   .then(([elm, errors]) => {
@@ -13,0 +13,0 @@ if (elm == null || errors != null) {

test/helpers/cql.test.ts

@@ -14,3 +14,3 @@ import { getMainLibraryId } from '../../src/helpers/cql';
       using FHIR version 4.0.1
-    `;
+    `.trim();
 
@@ -26,3 +26,3 @@ expect(getMainLibraryId(cql)).toEqual(libraryId);
       using FHIR version 4.0.1
-    `;
+    `.trim();
 
@@ -29,0 +29,0 @@ expect(getMainLibraryId(cql)).toEqual(libraryId);

test/helpers/translator.test.ts

@@ -31,3 +31,4 @@ import path from 'path';
       [SIMPLE_LIBRARY_CQL_PATH, SIMPLE_LIBRARY_DEPENDENCY_CQL_PATH],
-      MOCK_URL
+      MOCK_URL,
+      simpleLibraryELM.library.identifier.id
     );
@@ -43,3 +44,7 @@
     await expect(() =>
-      getELM([SIMPLE_LIBRARY_CQL_PATH, SIMPLE_LIBRARY_DEPENDENCY_CQL_PATH], MOCK_URL)
+      getELM(
+        [SIMPLE_LIBRARY_CQL_PATH, SIMPLE_LIBRARY_DEPENDENCY_CQL_PATH],
+        MOCK_URL,
+        simpleLibraryELM.library.identifier.id
+      )
     ).rejects.toThrow();
@@ -63,3 +68,7 @@ });
 
-    const [elm, errors] = await getELM([SIMPLE_LIBRARY_CQL_PATH], MOCK_URL);
+    const [elm, errors] = await getELM(
+      [SIMPLE_LIBRARY_CQL_PATH],
+      MOCK_URL,
+      simpleLibraryELM.library.identifier.id
+    );
 
@@ -66,0 +75,0 @@ expect(elm).toBeNull();

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