First public commit

.editorconfig

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+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+# Matches multiple files with brace expansion notation
+# Set default charset
+[*.{js,json,yml}]
+charset = utf-8
+indent_style = space
+indent_size = 2

.gitignore

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+# Logs
+logs
+*.log
+npm-debug.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# dotenv environment variables file
+.env
+
+.vscode
+
+build/
+work/
+target/
+.git/
+node_modules/
+test/integration/data/output
+dist/
+*.log
+*.bak.js
+*.bak
+.DS_STORE
+dump.rdb
+test-results.xml
+
+deploy/.npmrc
+deploy/yarn.lock
+deploy/terraform/run.zip
+run.zip

.npmignore

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+test
+Jenkinsfile
+publish-private.sh

CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [3.1.0] - 2018-03-12
+
+### Added
+
+- Commands for task resources
+
+## [2.5.1] - 2018-01-19
+
+### Fixed
+
+- The `lo fhir` `--limit` option will not set pageSize when requesting resources
+
+## [2.5.0] - 2018-01-15
+
+### Added
+
+- Commands for FHIR resources
+
+## [2.4.2] - 2018-01-12
+
+### Fixed
+
+- `lo auth -c` now produces an error message if a clip board utility isn't installed
+- `lo auth` no longer hangs for 1 minute
+
+## [2.4.1] - 2018-01-04
+
+### Fixed
+
+- Changed `files-download` to work with new download response.
+
+## [2.4.0] - 2018-01-04
+
+### Added
+
+- Added support for GA4GH RNA Quantification sets.
+
+## [2.3.1] - 2018-01-03
+
+### Fixed
+
+- Throw a proper error when `setup` has not been performed.
+
+## [2.3.0] - 2018-01-02
+
+### Changed
+
+- The `auth` command was changed to perform authentication using the web login view.
+
+## [2.2.0] - 2017-12-21
+
+### Added
+
+- Commands for GA4GH resources
+
+## [2.1.0] - 2017-12-21
+
+### Added
+
+- Support to specify client credential settings in the `setup` command
+- Ability to automatically refresh access tokens on expiration
+
+## [2.0.0] - 2017-12-20
+
+### Added
+
+- Added a `--copy` option to the `auth` command to copy the access token to the
+  clipboard
+
+### Changed
+
+- Replaced the `defaults` command with a `setup` command

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2018 Phillip Gates-Idem
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# lifeomic-cli
+
+This project is a small CLI app that provides functionality around the LifeOmic
+API's.
+
+## Installation
+
+```bash
+yarn global add @lifeomic/lifeomic-cli
+```
+
+Run `lo setup` to configure the default environment and account you wish to use.
+You can later override the default account using the `-a` option for commands.
+If using client credentials, you will also be given the opportunity to store the
+client settings at this time.
+
+Use `lo auth` to obtain access credentials when using username / password
+authentication.  This command currently only supports LifeOmic users and not
+those that have been federated via social or SAML 2.0 identity providers.
+
+## Usage
+
+```bash
+lo <command> [options]
+```
+
+View available commands:
+
+```bash
+lo --help
+```
+
+Get help for a command:
+
+```bash
+lo <command> --help
+```

lib/api.js

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+'use strict';
+
+const axios = require('axios');
+const axiosRetry = require('axios-retry');
+const chalk = require('chalk');
+const { Bar } = require('cli-progress');
+const fs = require('fs');
+const config = require('./config');
+const mkdirp = require('mkdirp');
+const { name, version } = require('../package.json');
+const queue = require('queue');
+const { dirname } = require('path');
+const tokenProvider = require('./interceptor/tokenProvider');
+
+axiosRetry(axios, { retries: 3 });
+axios.defaults.headers.common['User-Agent'] = `${name}/${version}`;
+
+const FIVE_MB = 5 * 1024 * 1024;
+const MAX_PARTS = 10000;
+
+function request (options) {
+  const environment = config.getEnvironment();
+
+  const account = options.account || config.get(`${environment}.defaults.account`);
+  if (!account) {
+    throw new Error(`Account needs to be set with 'lo defaults' or specified with the -a option.`);
+  }
+
+  const client = axios.create({
+    baseURL: config.get(`${environment}.apiUrl`),
+    headers: {
+      'LifeOmic-Account': account
+    }
+  });
+  client.interceptors.request.use(tokenProvider);
+  axiosRetry(client, { retries: 3 });
+  return client;
+}
+
+function progress (name) {
+  return new Bar({
+    format: `${name} [{bar}] {percentage}% | ETA: {eta}s | {value}/{total} bytes`,
+    hideCursor: true,
+    clearOnComplete: true,
+    barsize: 30
+  });
+}
+
+module.exports.MULTIPART_MIN_SIZE = FIVE_MB;
+
+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.download = async function (options, path, fileName) {
+  mkdirp(dirname(fileName));
+
+  const response = await request(options).get(path);
+
+  const bar = progress(fileName);
+
+  const res = await axios({
+    method: 'get',
+    url: response.data.downloadUrl,
+    responseType: 'stream'
+  });
+
+  bar.start(res.headers['content-length'], 0);
+  res.data
+    .on('data', e => {
+      bar.increment(e.length);
+    })
+    .on('end', () => {
+      bar.stop();
+      console.log(chalk.green(`Downloaded: ${fileName}`));
+    })
+    // eslint-disable-next-line security/detect-non-literal-fs-filename
+    .pipe(fs.createWriteStream(fileName));
+};
+
+module.exports.upload = async function (uploadUrl, fileName, fileSize) {
+  const bar = progress(fileName);
+  bar.start(fileSize, 0);
+
+  // eslint-disable-next-line security/detect-non-literal-fs-filename
+  const stream = fs.createReadStream(fileName)
+    .on('data', e => {
+      bar.increment(e.length);
+    })
+    .on('end', () => {
+      bar.stop();
+    });
+
+  await axios({
+    method: 'put',
+    url: uploadUrl,
+    data: stream,
+    headers: {
+      'Content-Length': fileSize
+    }
+  });
+};
+
+function startQueue (q) {
+  return new Promise((resolve, reject) => {
+    q.start(error => {
+      if (error) {
+        reject(error);
+      } else {
+        resolve();
+      }
+    });
+  });
+}
+
+module.exports.multipartUpload = async function (options, uploadId, fileName, fileSize) {
+  const bar = progress(fileName);
+  bar.start(fileSize, 0);
+  const q = queue({
+    concurrency: options.parallel || 4
+  });
+
+  let partSize = Math.ceil(fileSize / MAX_PARTS);
+  partSize = Math.max(partSize, FIVE_MB);
+  const totalParts = Math.ceil(fileSize / partSize);
+
+  for (let part = 1; part <= totalParts; ++part) {
+    q.push(async () => {
+      const start = (part - 1) * (partSize);
+      const end = part === totalParts ? fileSize - 1 : start + partSize - 1;
+      const size = end - start + 1;
+      // eslint-disable-next-line security/detect-non-literal-fs-filename
+      const stream = fs.createReadStream(fileName, {
+        start: start,
+        end: end
+      });
+
+      const response = await request(options).get(`/v1/uploads/${uploadId}/parts/${part}`);
+
+      await axios({
+        method: 'put',
+        url: response.data.uploadUrl,
+        data: stream,
+        headers: {
+          'Content-Length': size
+        }
+      });
+      bar.increment(size);
+    });
+  }
+
+  await startQueue(q);
+
+  bar.stop();
+  await request(options).delete(`/v1/uploads/${uploadId}`);
+};

lib/cli.js

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+'use strict';
+
+const program = require('commander');
+const glob = require('glob');
+const path = require('path');
+const version = require('../package.json').version;
+
+exports.run = () => {
+  program
+    .version(version)
+    .arguments('<command>')
+    .usage('<command> [options]');
+
+  const commands = glob.sync(path.join(__dirname, 'commands/*.js'));
+  for (const command of commands) {
+    // eslint-disable-next-line security/detect-non-literal-require
+    require(command);
+  }
+
+  program.parse(process.argv);
+};