-
Notifications
You must be signed in to change notification settings - Fork 0
/
varvis-download.js
317 lines (288 loc) · 10 KB
/
varvis-download.js
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
#!/usr/bin/env node
const { CookieJar } = require('tough-cookie');
const { CookieClient } = require('http-cookie-agent/undici');
const yargs = require('yargs');
const fs = require('fs'); // Import the fs module
const path = require('path');
const readline = require('readline');
const { ProxyAgent, Agent } = require('undici');
const { version, name, author, license, repository } = require('./package.json');
const { loadConfig, loadLogo, getLastModifiedDate } = require('./js/configUtils');
const createLogger = require('./js/logger');
const AuthService = require('./js/authService');
const { fetchAnalysisIds, getDownloadLinks, listAvailableFiles, generateReport, metrics } = require('./js/fetchUtils');
const { downloadFile } = require('./js/fileUtils');
const { checkToolAvailability, ensureIndexFile, rangedDownloadBAM, indexBAM, generateOutputFileName } = require('./js/rangedUtils');
// Command line arguments setup
const argv = yargs
.usage('$0 <command> [args]')
.version(false)
.option('config', {
alias: 'c',
describe: 'Path to the configuration file',
type: 'string',
default: '.config.json'
})
.option('username', {
alias: 'u',
describe: 'Varvis API username',
type: 'string'
})
.option('password', {
alias: 'p',
describe: 'Varvis API password',
type: 'string'
})
.option('target', {
alias: 't',
describe: 'Target for the Varvis API',
type: 'string'
})
.option('analysisIds', {
alias: 'a',
describe: 'Analysis IDs to download files for (comma-separated)',
type: 'string'
})
.option('sampleIds', {
alias: 's',
describe: 'Sample IDs to filter analyses (comma-separated)',
type: 'string'
})
.option('limsIds', {
alias: 'l',
describe: 'LIMS IDs to filter analyses (comma-separated)',
type: 'string'
})
.option('list', {
alias: 'L',
describe: 'List available files for the specified analysis IDs',
type: 'boolean'
})
.option('destination', {
alias: 'd',
describe: 'Destination folder for the downloaded files',
type: 'string',
default: '.'
})
.option('proxy', {
alias: 'x',
describe: 'Proxy URL',
type: 'string'
})
.option('proxyUsername', {
alias: 'pxu',
describe: 'Proxy username',
type: 'string'
})
.option('proxyPassword', {
alias: 'pxp',
describe: 'Proxy password',
type: 'string'
})
.option('overwrite', {
alias: 'o',
describe: 'Overwrite existing files',
type: 'boolean',
default: false
})
.option('filetypes', {
alias: 'f',
describe: 'File types to download (comma-separated)',
type: 'string',
default: 'bam,bam.bai'
})
.option('loglevel', {
alias: 'll',
describe: 'Logging level (info, warn, error, debug)',
type: 'string',
default: 'info'
})
.option('logfile', {
alias: 'lf',
describe: 'Path to the log file',
type: 'string'
})
.option('reportfile', {
alias: 'r',
describe: 'Path to the report file',
type: 'string'
})
.option('filter', {
alias: 'F',
describe: 'Filter expressions (e.g., "analysisType=SNV", "sampleId>LB24-0001")',
type: 'array',
default: []
})
.option('range', {
alias: 'g',
describe: 'Genomic range for ranged download (e.g., chr1:1-100000)',
type: 'string',
})
.option('version', {
alias: 'v',
type: 'boolean',
description: 'Show version information',
default: false
})
.help()
.alias('help', 'h')
.argv;
// Create logger instance
const logger = createLogger(argv);
// Show version information if the --version flag is set
if (argv.version) {
const logo = loadLogo();
console.log(logo);
console.log(`${name} - Version ${version}`);
console.log(`Date Last Modified: ${getLastModifiedDate(__filename)}`);
console.log(`Author: ${author}`);
console.log(`Repository: ${repository.url}`);
console.log(`License: ${license}`);
process.exit(0);
}
// Load configuration file settings
const configFilePath = path.resolve(argv.config);
const config = loadConfig(configFilePath);
// Merge command line arguments with configuration file settings
const finalConfig = {
...config,
...argv,
filetypes: (argv.filetypes || config.filetypes || 'bam,bam.bai').split(',').map(ft => ft.trim()),
analysisIds: (argv.analysisIds || config.analysisIds || '').split(',').map(id => id.trim()).filter(id => id),
sampleIds: (argv.sampleIds || config.sampleIds || '').split(',').map(id => id.trim()).filter(id => id),
limsIds: (argv.limsIds || config.limsIds || '').split(',').map(id => id.trim()).filter(id => id),
filters: (argv.filter || config.filter || []).map(filter => filter.trim()),
destination: argv.destination !== '.' ? argv.destination : (config.destination || '.')
};
// Validate the final configuration
const requiredFields = ['username', 'password', 'target'];
for (const field of requiredFields) {
if (!finalConfig[field]) {
logger.error(`Error: Missing required argument --${field}`);
process.exit(1);
}
}
// Extract the final configuration values
const target = finalConfig.target;
const userName = finalConfig.username;
const password = finalConfig.password;
const analysisIds = finalConfig.analysisIds;
const sampleIds = finalConfig.sampleIds;
const limsIds = finalConfig.limsIds;
const destination = finalConfig.destination;
const proxy = finalConfig.proxy;
const proxyUsername = finalConfig.proxyUsername;
const proxyPassword = finalConfig.proxyPassword;
const overwrite = finalConfig.overwrite;
const filetypes = finalConfig.filetypes;
const reportfile = finalConfig.reportfile;
const filters = finalConfig.filters;
// Setup HTTP agent for proxy and cookie handling
const jar = new CookieJar();
const agentOptions = proxy ? { uri: proxy } : {};
if (proxyUsername && proxyPassword) {
agentOptions.auth = `${proxyUsername}:${proxyPassword}`;
}
const agent = proxy
? new ProxyAgent({
...agentOptions,
factory: (origin, opts) => new CookieClient(origin, {
...opts,
cookies: { jar },
}),
})
: new Agent({
factory: (origin, opts) => new CookieClient(origin, {
...opts,
cookies: { jar },
}),
});
// Initialize AuthService instance
const authService = new AuthService(logger, agent);
// Initialize readline interface for user prompts
const rl = readline.createInterface({
input: process.stdin,
output: process.stdout
});
// Main function to orchestrate the login and download process
async function main() {
try {
logger.debug('Starting main function');
// Ensure the destination directory exists
if (!fs.existsSync(destination)) {
logger.debug(`Creating destination directory: ${destination}`);
fs.mkdirSync(destination, { recursive: true });
}
logger.debug('Attempting to log in');
await authService.login({ username: userName, password: password }, target);
logger.debug('Login successful');
logger.debug('filters:', filters);
const ids = analysisIds.length > 0
? analysisIds
: await fetchAnalysisIds(target, authService.token, agent, sampleIds, limsIds, filters, logger);
if (argv.list) {
for (const analysisId of ids) {
await listAvailableFiles(analysisId, target, authService.token, agent, logger);
}
} else {
for (const analysisId of ids) {
const fileDict = await getDownloadLinks(analysisId, filetypes, target, authService.token, agent, logger);
logger.debug(`Fetched download links for analysis ID ${analysisId}`);
for (const [fileName, file] of Object.entries(fileDict)) {
const downloadLink = file.downloadLink;
logger.info(`Downloading ${fileName} file for analysis ID ${analysisId}...`);
const filePath = path.join(destination, fileName);
// Skip downloading .bai files in ranged download mode
if (fileName.endsWith('.bai') && argv.range) {
logger.info(`Skipping .bai file for ranged download: ${fileName}`);
continue;
}
if (fileName.endsWith('.bam') && argv.range) {
// Ensure BAM index file is downloaded before ranged download
const indexFileUrl = fileDict[`${fileName}.bai`]?.downloadLink;
const indexFilePath = path.join(destination, `${fileName}.bai`);
if (!indexFileUrl) {
logger.error(`Index file for BAM (${fileName}) not found.`);
continue;
}
// Check if the .bai file exists and skip downloading if not overwriting
if (!fs.existsSync(indexFilePath) || overwrite) {
await ensureIndexFile(downloadLink, indexFileUrl, indexFilePath, agent, rl, logger, metrics, overwrite);
} else {
logger.info(`Index file already exists: ${indexFilePath}`);
}
// Perform the ranged BAM download
logger.info(`Performing ranged download for BAM file: ${filePath}`);
logger.info(`Genomic range: ${argv.range}`);
const outputFile = path.join(destination, generateOutputFileName(fileName, argv.range, logger));
logger.info(`Output file: ${outputFile}`);
try {
await rangedDownloadBAM(downloadLink, argv.range, outputFile, indexFilePath, logger, overwrite);
await indexBAM(outputFile, logger, overwrite); // Optionally index the newly downloaded BAM file
} catch (error) {
logger.error(`Error during ranged download and indexing for BAM file: ${fileName}`);
logger.error(`Detailed error: ${error.message}`);
}
} else {
// Normal download for non-BAM or no-range files
await downloadFile(downloadLink, filePath, overwrite, agent, rl, logger, metrics);
}
}
}
logger.info('Download complete.');
generateReport(reportfile, logger);
}
} catch (error) {
logger.error('An error occurred:', error.message);
logger.debug(error.stack);
} finally {
rl.close();
process.exit(1);
}
}
main().catch(error => {
logger.error('An unexpected error occurred:', error.message);
logger.debug(error.stack);
rl.close();
process.exit(1);
});