Mercurial > repos > greg > data_manager_vsnp_excel
view data_manager/vsnp_excel_fetcher.py @ 0:84a356e0950a draft
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author | greg |
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date | Fri, 07 Feb 2020 13:02:25 -0500 |
parents | |
children | d1bf63483e33 |
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import argparse import json import os try: # For Python 3.0 and later from urllib.request import Request, urlopen except ImportError: # Fall back to Python 2 imports from urllib2 import Request, urlopen def url_download(url, target_directory): file_path = os.path.abspath(os.path.join(target_directory, os.path.basename(url))) src = None dst = None try: req = Request(url) src = urlopen(req) with open(file_path, 'wb') as dst: while True: chunk = src.read(2**10) if chunk: dst.write(chunk) else: break finally: if src: src.close() return file_path def download(dbkey, display_name, url, out_file): with open(out_file) as fh: params = json.loads(fh.read()) work_directory = params['output_data'][0]['extra_files_path'] target_directory = os.path.abspath(os.path.join(work_directory, "vsnp", dbkey)) os.mkdir(target_directory) file_path = url_download(url, target_directory) entry_name = "%s" % os.path.basename(file_path) data_manager_json = {"data_tables": {}} data_manager_entry = {} data_manager_entry['value'] = dbkey data_manager_entry['name'] = entry_name data_manager_entry['path'] = file_path data_manager_entry['description'] = "Excel file for %s" % display_name data_manager_json["data_tables"]["vsnp_excel"] = data_manager_entry with open(out_file, 'w') as fh: fh.write(json.dumps(data_manager_json, sort_keys=True)) parser = argparse.ArgumentParser() parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey') parser.add_argument('--display_name', dest='display_name', help='Reference display name') parser.add_argument('--url', dest='url', help='URL to download Excel file') parser.add_argument('--out_file', dest='out_file', help='JSON output file') args = parser.parse_args() download(args.dbkey, args.display_name, args.url, args.out_file)