Merge pull request #117 from lifeomic/LO-5734

LO-5734: Data Lake Query Commands

lib/cmds/data-lake.js

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

lib/cmds/data_lake_cmds/get-query.js

@@ -0,0 +1,18 @@
+'use strict';
+
+const { get } = require('../../api');
+const print = require('../../print');
+
+exports.command = 'get-query <queryId>';
+exports.desc = 'Fetch a single query execution.';
+exports.builder = yargs => {
+  yargs.positional('queryId', {
+    describe: 'Id of the query to fetch.',
+    type: 'string'
+  });
+};
+
+exports.handler = async argv => {
+  const response = await get(argv, `/v1/analytics/query/${argv.queryId}`);
+  print(response.data, argv);
+};

lib/cmds/data_lake_cmds/list-queries.js

@@ -0,0 +1,37 @@
+'use strict';
+
+const { list } = require('../../api');
+const print = require('../../print');
+const querystring = require('querystring');
+
+exports.command = 'list-queries <projectId>';
+exports.desc = 'List the query executions in the project.';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The ID of the project to fetch queries of.',
+    type: 'string'
+  }).option('page-size', {
+    alias: 'n',
+    type: 'number',
+    default: 25,
+    describe: 'Maximum number of queries to return.'
+  }).option('next-page-token', {
+    alias: 't',
+    type: 'string',
+    describe: 'Token to retrieve the next page of results'
+  });
+};
+
+exports.handler = async argv => {
+  const query = {
+    datasetId: argv.projectId,
+    pageSize: argv.pageSize
+  };
+
+  if (argv.nextPageToken) {
+    query.nextPageToken = argv.nextPageToken;
+  }
+
+  const response = await list(argv, `/v1/analytics/query?${querystring.stringify(query)}`);
+  print(response.data, argv);
+};

lib/cmds/data_lake_cmds/query.js

@@ -0,0 +1,39 @@
+'use strict';
+
+const { post } = require('../../api');
+const print = require('../../print');
+const read = require('../../read');
+
+exports.command = 'query <projectId>';
+exports.desc = 'Submits a query to the Lifeomic data-lake API. A SQL query string can also be read from stdin.';
+exports.builder = yargs => {
+  yargs.positional('projectId', {
+    describe: 'The ID of the project to search within.',
+    type: 'string'
+  }).option('query', {
+    alias: 'q',
+    type: 'string',
+    describe: 'The SQL query to run.'
+  }).option('output-file-name', {
+    alias: 'o',
+    type: 'string',
+    describe: 'Name of the results file.',
+    demandOption: true
+  });
+};
+
+exports.handler = async argv => {
+  const request = {
+    outputFileName: argv.outputFileName,
+    datasetId: argv.projectId
+  };
+
+  if (argv.query) {
+    request.query = argv.query;
+  } else {
+    request.query = await read(argv);
+  }
+
+  const response = await post(argv, '/v1/analytics/query', request);
+  print(response.data, argv);
+};

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@lifeomic/cli",
-  "version": "9.6.0",
+  "version": "9.7.0",
   "description": "CLI for interacting with the LifeOmic PHC API.",
   "main": "lo.js",
   "author": "LifeOmic <[email protected]>",
@@ -43,6 +43,7 @@
     "stream-chain": "^2.1.0",
     "stream-csv-as-json": "^1.0.1",
     "stream-json": "^1.2.1",
+    "uuid": "^3.3.2",
     "yargs": "^12.0.5"
   },
   "devDependencies": {

test/unit/commands/data-lake-test.js

@@ -0,0 +1,133 @@
+'use strict';
+
+const uuid = require('uuid');
+const yargs = require('yargs');
+const sinon = require('sinon');
+const test = require('ava');
+const proxyquire = require('proxyquire');
+
+const getStub = sinon.stub();
+const postStub = sinon.stub();
+const listStub = sinon.stub();
+const printSpy = sinon.spy();
+const readStub = sinon.stub();
+let callback;
+
+const queryCmd = proxyquire('../../../lib/cmds/data_lake_cmds/query', {
+  '../../api': {
+    post: postStub
+  },
+  '../../print': (data, opts) => {
+    printSpy(data, opts);
+    callback();
+  },
+  '../../read': async () => readStub()
+});
+
+const listCmd = proxyquire('../../../lib/cmds/data_lake_cmds/list-queries', {
+  '../../api': {
+    list: listStub
+  },
+  '../../print': (data, opts) => {
+    printSpy(data, opts);
+    callback();
+  }
+});
+
+const getCmd = proxyquire('../../../lib/cmds/data_lake_cmds/get-query', {
+  '../../api': {
+    get: getStub
+  },
+  '../../print': (data, opts) => {
+    printSpy(data, opts);
+    callback();
+  }
+});
+
+test.afterEach.always(t => {
+  getStub.resetHistory();
+  postStub.resetHistory();
+  listStub.resetHistory();
+  printSpy.resetHistory();
+  readStub.resetHistory();
+  callback = null;
+});
+
+test.serial.cb('The "data-lake-query" command should accept a query as an optional argument', t => {
+  const query = "SELECT sample_id, gene, impact, amino_acid_change, histology FROM variant WHERE tumor_site='breast'";
+  const datasetId = uuid();
+  const outputFileName = 'data-lake-test';
+
+  postStub.onFirstCall().returns({});
+
+  callback = () => {
+    t.is(postStub.callCount, 1);
+    t.is(postStub.getCall(0).args[1], '/v1/analytics/query');
+    t.deepEqual(postStub.getCall(0).args[2], {
+      query: query,
+      datasetId: datasetId,
+      outputFileName: outputFileName
+    });
+    t.is(printSpy.callCount, 1);
+    t.end();
+  };
+
+  yargs.command(queryCmd).parse(`query ${datasetId} -q "${query}" -o ${outputFileName}`);
+});
+
+test.serial.cb('The "data-lake-query" command should accept a query from stdin', t => {
+  const query = "SELECT sample_id, gene, impact, amino_acid_change, histology FROM variant WHERE tumor_site='breast'";
+  const datasetId = uuid();
+  const outputFileName = 'data-lake-test';
+
+  postStub.onFirstCall().returns({});
+  readStub.onFirstCall().returns(query);
+
+  callback = () => {
+    t.is(postStub.callCount, 1);
+    t.is(postStub.getCall(0).args[1], '/v1/analytics/query');
+    t.deepEqual(postStub.getCall(0).args[2], {
+      query: query,
+      datasetId: datasetId,
+      outputFileName: outputFileName
+    });
+    t.is(printSpy.callCount, 1);
+    t.end();
+  };
+
+  yargs.command(queryCmd).parse(`query ${datasetId} -o ${outputFileName}`);
+});
+
+test.serial.cb('The "data-lake-list-queries" should accept page-size and next-page-token', t => {
+  const datasetId = uuid();
+  const pageSize = 30;
+  const nextPageToken = uuid();
+
+  listStub.onFirstCall().returns({});
+  const expectedPath = `/v1/analytics/query?datasetId=${datasetId}&pageSize=${pageSize}&nextPageToken=${nextPageToken}`;
+
+  callback = () => {
+    t.is(listStub.callCount, 1);
+    t.is(listStub.getCall(0).args[1], expectedPath);
+    t.is(printSpy.callCount, 1);
+    t.end();
+  };
+
+  yargs.command(listCmd).parse(`list-queries ${datasetId} -n ${pageSize} -t ${nextPageToken}`);
+});
+
+test.serial.cb('The "data-lake-get-query" should add query-id to path', t => {
+  const queryId = uuid();
+
+  getStub.onFirstCall().returns({});
+  const expectedPath = `/v1/analytics/query/${queryId}`;
+
+  callback = () => {
+    t.is(getStub.callCount, 1);
+    t.is(getStub.getCall(0).args[1], expectedPath);
+    t.is(printSpy.callCount, 1);
+    t.end();
+  };
+
+  yargs.command(getCmd).parse(`get-query ${queryId}`);
+});