# HG changeset patch
# User devteam
# Date 1446837388 18000
# Node ID 078e803565cfb250f0c422a68b51ec6ba1a4f7c4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
diff -r 000000000000 -r 078e803565cf data_manager/data_manager.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py Fri Nov 06 14:16:28 2015 -0500
@@ -0,0 +1,68 @@
+import argparse
+import datetime
+import json
+import os
+import shutil
+import sys
+import tarfile
+import urllib2
+import zipfile
+
+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')
+ if not os.path.exists(workdir):
+ os.makedirs(workdir)
+ 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)
+ 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):
+ fh = zipfile.ZipFile(file_path, 'r')
+ else:
+ return
+ fh.extractall(workdir)
+ os.remove(file_path)
+
+
+def main(args):
+ workdir = os.path.join(os.getcwd(), 'taxonomy')
+ url_download(args.url, workdir)
+ data_manager_entry = {}
+ data_manager_entry['value'] = args.name.lower()
+ data_manager_entry['name'] = args.name
+ data_manager_entry['path'] = '.'
+ data_manager_json = dict(data_tables=dict(ncbi_taxonomy=data_manager_entry))
+ params = json.loads(open(args.output).read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ output_path = os.path.abspath(os.path.join(os.getcwd(), 'taxonomy'))
+ for filename in os.listdir(workdir):
+ shutil.move(os.path.join(output_path, filename), target_directory)
+ file(args.output, 'w').write(json.dumps(data_manager_json))
+
+if __name__ == '__main__':
+ main(args)
diff -r 000000000000 -r 078e803565cf data_manager/ncbi_taxonomy_fetcher.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/ncbi_taxonomy_fetcher.xml Fri Nov 06 14:16:28 2015 -0500
@@ -0,0 +1,25 @@
+
+
+ taxonomy downloader
+
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+
diff -r 000000000000 -r 078e803565cf data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Nov 06 14:16:28 2015 -0500
@@ -0,0 +1,18 @@
+
+
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+
diff -r 000000000000 -r 078e803565cf tool-data/ncbi_taxonomy.loc.sample
diff -r 000000000000 -r 078e803565cf tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 06 14:16:28 2015 -0500
@@ -0,0 +1,8 @@
+
+
+
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+