Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy
changeset 1:926847693e4d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2017 18:08:21 -0400 |
| parents | fafcd2f5db36 |
| children | 4af4e175db0d |
| files | data_manager/data_manager.py data_manager/ncbi_taxonomy_fetcher.xml |
| diffstat | 2 files changed, 29 insertions(+), 31 deletions(-) [+] |
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--- a/data_manager/data_manager.py Thu Oct 08 12:14:42 2015 -0400 +++ b/data_manager/data_manager.py Tue Apr 04 18:08:21 2017 -0400 @@ -3,17 +3,15 @@ import json import os import shutil -import sys import tarfile -import urllib2 import zipfile +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 -parser = argparse.ArgumentParser(description='Create data manager json.') -parser.add_argument('--out', dest='output', action='store', help='JSON filename') -parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID') -parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL') - -args = parser.parse_args() def url_download(url, workdir): file_path = os.path.join(workdir, 'download.dat') @@ -22,22 +20,18 @@ 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 - except Exception, e: - print >>sys.stderr, str(e) + 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() - if dst: - dst.close() if tarfile.is_tarfile(file_path): fh = tarfile.open(file_path, 'r:*') elif zipfile.is_zipfile(file_path): @@ -64,5 +58,12 @@ shutil.move(os.path.join(output_path, filename), target_directory) file(args.output, 'w').write(json.dumps(data_manager_json)) + if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Create data manager json.') + parser.add_argument('--out', dest='output', action='store', help='JSON filename') + parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID') + parser.add_argument('--url', dest='url', action='store', default='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz', help='Download URL') + args = parser.parse_args() + main(args)
--- a/data_manager/ncbi_taxonomy_fetcher.xml Thu Oct 08 12:14:42 2015 -0400 +++ b/data_manager/ncbi_taxonomy_fetcher.xml Tue Apr 04 18:08:21 2017 -0400 @@ -1,25 +1,22 @@ <?xml version="1.0"?> <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.0"> <description>taxonomy downloader</description> - <stdio> - <exit_code description="Error" level="fatal" range="1:" /> - </stdio> - <command interpreter="python"> + <command detect_errors="exit_code"> <![CDATA[ - data_manager.py --out "${out_file}" + python '$__tool_directory__/data_manager.py' --out '${out_file}' #if $taxonomy_url: - --url "${taxonomy_url}" + --url '${taxonomy_url}' #end if #if $database_name: - --name "${database_name}" + --name '${database_name}' #end if ]]> </command> <inputs> - <param help="Enter a unique identifier, or leave blank for today's date" label="Name for this database" name="database_name" type="text" optional="True" /> - <param label="Enter URL for taxonomy files" name="taxonomy_url" type="text" /> + <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" /> + <param name="taxonomy_url" type="text" label="Enter URL for taxonomy files" /> </inputs> <outputs> - <data format="data_manager_json" name="out_file" /> + <data name="out_file" format="data_manager_json" /> </outputs> </tool>