Changes to CLI to support Axios Proxy, Large FHIR List Downloads, and Downloads of Layouts

csv_medadmin.json

@@ -0,0 +1,43 @@
+{
+	"header": true,
+	"fieldDelimiter": ",",
+	"valueDelimiter": "'",
+	"fieldMaps": [
+		{
+			"columnName": "id",
+			"jpath": "id"
+		},
+    {
+      "columnName": "medication_code",
+      "jpath": "medicationCodeableConcept.coding[0].code"
+    },
+    {
+      "columnName": "medication_display",
+      "jpath": "medicationCodeableConcept.coding[0].display"
+    },
+    {
+      "columnName": "medication_text",
+      "jpath": "medicationCodeableConcept.coding[0].text"
+    },
+    {
+      "columnName": "dose_text",
+      "jpath": "dosage.text"
+    },
+    {
+      "columnName": "dose",
+      "jpath": "dosage.dose.value"
+    },
+    {
+      "columnName": "dose_unit",
+      "jpath": "dosage.dose.unit"
+    },
+    {
+      "columnName": "subject",
+      "jpath": "subject.reference"
+    },
+    {
+      "columnName": "date",
+      "jpath": "effectiveDateTime"
+    }
+  ]
+}

csv_patient.json

@@ -0,0 +1,15 @@
+{
+	"header": true,
+	"fieldDelimiter": ",",
+	"valueDelimiter": "'",
+	"fieldMaps": [
+		{
+			"columnName": "id",
+			"jpath": "id"
+		},
+		{
+			"columnName": "dob",
+			"jpath": "birthDate"	
+		}
+	]
+}

lib/api.js

@@ -14,6 +14,7 @@ const { dirname } = require('path');
 const tokenProvider = require('./interceptor/tokenProvider');
 const debug = require('debug')('lo:api');
 const FileVerificationStream = require('./FileVerificationStream');
+const configureProxy = require('./proxy');
 
 axiosRetry(axios, {
   retries: 3
@@ -31,8 +32,11 @@ function request (options, condition = isNetworkOrIdempotentRequestError) {
     throw new Error(`Account needs to be set with 'lo defaults' or specified with the -a option.`);
   }
 
+  const proxy = configureProxy();
+
   const client = axios.create({
     baseURL: config.get(`${environment}.apiUrl`),
+    proxy: proxy,
     headers: {
       'LifeOmic-Account': account
     }
@@ -106,9 +110,12 @@ module.exports.download = async function (options, path, fileName) {
 
   const bar = progress(fileName);
 
+  const proxy = configureProxy();
+
   const res = await axios({
     method: 'get',
     url: response.data.downloadUrl,
+    proxy: proxy,
     responseType: 'stream'
   });
 
@@ -145,10 +152,12 @@ module.exports.getFileVerificationStream = async function (filePath, fileSize) {
 };
 
 module.exports.upload = async function (uploadUrl, fileSize, data, contentMD5) {
+  const proxy = configureProxy();
   await axios({
     method: 'put',
     url: uploadUrl,
     data,
+    proxy: proxy,
     headers: {
       'Content-Length': fileSize,
       'Content-MD5': contentMD5
@@ -214,10 +223,12 @@ module.exports.multipartUpload = async function (options, uploadId, fileName, fi
         try {
           debug(`Uploading part ${part}, size: ${size}`);
           const time = process.hrtime();
+          const proxy = configureProxy();
           await axios({
             method: 'put',
             url: response.data.uploadUrl,
             data: verifyStream.data,
+            proxy: proxy,
             headers: {
               'Content-Length': size,
               'Content-MD5': verifyStream.contentMD5

lib/apps.js

@@ -0,0 +1,53 @@
+'use strict';
+
+const axios = require('axios');
+const axiosRetry = require('axios-retry');
+// const tunnel = require('tunnel');
+const config = require('./config');
+const { name, version } = require('../package.json');
+const tokenProvider = require('./interceptor/tokenProvider');
+const configureProxy = require('./proxy');
+
+axiosRetry(axios, {
+  retries: 3
+});
+axios.defaults.headers.common['User-Agent'] = `${name}/${version}`;
+
+function request (options) {
+  const environment = config.getEnvironment();
+
+  const account = options.account || config.get(`${environment}.defaults.account`);
+  if (!account) {
+    throw new Error(`Account needs to be set with 'lo defaults' or specified with the -a option.`);
+  }
+
+  const proxy = configureProxy();
+  const baseURL = config.get(`${environment}.appsUrl`);
+
+  const client = axios.create({
+    baseURL: baseURL,
+    proxy: proxy,
+    headers: {
+      'LifeOmic-Account': account
+    }
+  });
+  client.interceptors.request.use(tokenProvider);
+  axiosRetry(client, { retries: 3 });
+  return client;
+}
+
+module.exports.get = function (options, path) {
+  return request(options).get(path);
+};
+
+module.exports.del = function (options, path) {
+  return request(options).delete(path);
+};
+
+module.exports.post = function (options, path, body) {
+  return request(options).post(path, body);
+};
+
+module.exports.put = function (options, path, body) {
+  return request(options).put(path, body);
+};

lib/cmds/fhir_cmds/list.js

@@ -5,6 +5,8 @@ const querystring = require('querystring');
 const { post, getAccount } = require('../../fhir');
 const print = require('../../print');
 const url = require('url');
+const jmespath = require('jmespath');
+const fs = require('fs');
 
 exports.command = 'list <type>';
 exports.desc = 'List FHIR resources by type <type>.';
@@ -22,14 +24,31 @@ exports.builder = yargs => {
     describe: 'Number of resources to return',
     type: 'integer',
     default: 1000
+  }).option('csv', {
+    describe: 'CSV Format Configuration file in json',
+    type: 'string'
   });
 };
 
 async function search (type, query, options) {
   const account = getAccount(options);
-  const result = [];
   const limit = options.limit;
 
+  const csvConfigFile = options.csv;
+
+  const csvConfig = csvConfigFile != null ? JSON.parse(fs.readFileSync(csvConfigFile, 'UTF-8')) : null;
+
+  if (csvConfig && csvConfig.header) {
+    let header = '';
+    csvConfig.fieldMaps.forEach(fieldMap => {
+      if (header.length > 0) {
+        header = header + ',';
+      }
+      header = header + fieldMap.columnName;
+    });
+    console.log(header);
+  }
+
   if (query) {
     query.pageSize = limit;
   } else {
@@ -46,22 +65,56 @@ async function search (type, query, options) {
     );
 
     const data = response.data;
-    result.push(...data.entry.map(x => x.resource));
+    const results = data.entry.map(x => x.resource);
 
-    if (result.length < limit && data.link) {
+    if (results.length > 0) {
+      if (csvConfig) {
+        const linesResult = formatResults(results, csvConfig, options);
+        linesResult.forEach(line => {
+          console.log(line);
+        });
+      } else {
+        results.forEach(result => print(result, options));
+      }
+    }
+
+    if (results.length < limit && data.link) {
       const next = data.link.find(x => x.relation === 'next');
       if (next) {
         const parsedUrl = url.parse(next.url, true);
         query = Object.assign(query, parsedUrl.query);
       } else {
-        return result;
+        return;
       }
     } else {
-      return result;
+      return;
     }
   }
 }
 
+function formatResults (results, csvConfig, options) {
+  const lines = [];
+  results.forEach(result => {
+    const fldD = csvConfig.fieldDelimiter;
+    const valueD = csvConfig.valueDelimiter;
+    const fields = [];
+    csvConfig.fieldMaps.forEach(fieldMap => {
+      const value = jmespath.search(result, fieldMap.jpath);
+      if (value && value.length > 0) {
+        fields.push(valueD + value + valueD);
+      } else {
+        fields.push('');
+      }
+    });
+    let line = '';
+    fields.forEach(field => {
+      line = line + field + fldD;
+    });
+    lines.push(line.substring(0, line.length - 1));
+  });
+  return lines;
+}
+
 exports.handler = async argv => {
   if (argv.query) {
     argv.query = querystring.parse(argv.query);
@@ -77,6 +130,5 @@ exports.handler = async argv => {
     }
   }
 
-  const result = await search(argv.type, argv.query, argv);
-  print(result, argv);
+  await search(argv.type, argv.query, argv);
 };

lib/cmds/layouts.js

@@ -0,0 +1,10 @@
+'use strict';
+
+const options = require('../common-yargs');
+
+exports.command = 'layouts <command>';
+exports.desc = 'Perform operations on layouts.';
+exports.builder = yargs => {
+  return options(yargs.commandDir('layouts_cmds'));
+};
+exports.handler = function (argv) {};

lib/cmds/layouts_cmds/get.js

@@ -0,0 +1,21 @@
+'use strict';
+
+const { get } = require('../../apps');
+const print = require('../../print');
+
+exports.command = 'get <projectId> <type>';
+exports.desc = 'Get Layouts information by <projectId> - <type> Patient|Insights';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The ID of the project which layouts to fetch.',
+    type: 'string'
+  }).positional('type', {
+    describe: 'The type of the layout of the project which layouts to fetch.',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await get(argv, `/configuration/layouts?project=${argv.projectId}&type=${argv.type}&format=json`);
+  print(response.data, argv);
+};

lib/cmds/setup.js

@@ -115,6 +115,26 @@ exports.handler = async argv => {
       mask: '*',
       default: a => config.get(`${a.environment}.defaults.clientSecret`),
       when: a => a.useClientCredentials && argv.apiKey === undefined && argv.authClientId === undefined && argv.clientId === undefined
+    },
+    {
+      type: 'confirm',
+      name: 'useHttpProxy',
+      message: 'Use an HTTP Proxy?',
+      default: a => config.get(`${a.environment}.defaults.useHttpProxy`) !== undefined
+    },
+    {
+      type: 'input',
+      name: 'httpProxyHost',
+      message: 'Http ProxyHost: ',
+      when: a => a.useHttpProxy,
+      default: a => config.get(`${a.environment}.defaults.httpProxyHost`)
+    },
+    {
+      type: 'input',
+      name: 'httpProxyPort',
+      message: 'Http ProxyPort: ',
+      when: a => a.useHttpProxy,
+      default: a => config.get(`${a.environment}.defaults.httpProxyPort`)
     }
   ];
 
@@ -147,5 +167,11 @@ exports.handler = async argv => {
   } else {
     config.delete(`${environment}.defaults.apiKey`);
   }
+
+  config.set(`${answers.environment}.defaults.useHttpProxy`, answers.useHttpProxy);
+  if (answers.useHttpProxy) {
+    config.set(`${answers.environment}.defaults.httpProxyHost`, answers.httpProxyHost);
+    config.set(`${answers.environment}.defaults.httpProxyPort`, answers.httpProxyPort);
+  }
   console.log(chalk.green(`Default settings have been saved.`));
 };

lib/common-yargs.js

@@ -5,6 +5,9 @@ module.exports = (yargs) => {
     .option('json', {
       describe: 'List output as JSON',
       type: 'boolean'
+    }).option('jsonLine', {
+      describe: 'List output as JSON LINE Format',
+      type: 'boolean'
     }).option('account', {
       describe: 'Override the account',
       type: 'string'

lib/config.js

@@ -7,8 +7,13 @@ const conf = new Configstore('lifeomic-cli', {
     userPooldId: 'us-east-2_ojOIXR4W7',
     clientId: '2qt93qphnctjbs9ftdpjhvgkl1',
     apiUrl: 'https://api.us.lifeomic.com',
+    appsUrl: 'https://apps.us.lifeomic.com/phc/api',
     fhirUrl: 'https://fhir.us.lifeomic.com',
-    ga4ghUrl: 'https://ga4gh.us.lifeomic.com'
+    ga4ghUrl: 'https://ga4gh.us.lifeomic.com',
+    useHttpProxy: false,
+    httpProxyHost: '',
+    httpProxyPort: '',
+    httpProxyHttps: false
   }
 });