Mercurial > repos > iuc > data_manager_plant_tribes_scaffolds_downloader
diff data_manager/data_manager_plant_tribes_scaffolds_download.py @ 4:93253aebaf2e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
author | iuc |
---|---|
date | Fri, 17 Jul 2020 04:19:35 -0400 |
parents | 5833ef61c1f8 |
children | 1550b1741780 |
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--- a/data_manager/data_manager_plant_tribes_scaffolds_download.py Fri Aug 17 07:04:08 2018 -0400 +++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py Fri Jul 17 04:19:35 2020 -0400 @@ -7,9 +7,8 @@ import shutil import sys import tarfile -import urllib2 import zipfile - +from urllib.request import Request, urlopen DEFAULT_DATA_TABLE_NAMES = ["plant_tribes_scaffolds"] @@ -52,22 +51,20 @@ src = None dst = None try: - req = urllib2.Request(url) - src = urllib2.urlopen(req) - dst = open(file_path, 'wb') - while True: - chunk = src.read(2**10) - if chunk: - dst.write(chunk) - else: - break + 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 except Exception as e: - print >>sys.stderr, str(e) + sys.exit(str(e)) finally: if src: src.close() - if dst: - dst.close() return file_path @@ -117,9 +114,8 @@ args = parser.parse_args() -# Some magic happens with tools of type "manage_data" in that the output -# file contains some JSON data that allows us to define the target directory. -params = json.loads(open(args.out_file).read()) +with open(args.out_file) as fh: + params = json.loads(fh.read()) target_directory = params['output_data'][0]['extra_files_path'] make_directory(target_directory) @@ -131,6 +127,5 @@ # Get the scaffolds data. data_manager_dict = download(target_directory, args.web_url, args.config_web_url, description) # Write the JSON output dataset. -fh = open(args.out_file, 'wb') -fh.write(json.dumps(data_manager_dict)) -fh.close() +with open(args.out_file, 'w') as fh: + fh.write(json.dumps(data_manager_dict, sort_keys=True))