1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b34eaa5eaa31/ Changeset: b34eaa5eaa31 User: greg Date: 2014-04-29 21:11:46 Summary: Add a Tool Shed API script that can be used to retrieve the current set of categories from a Tool Shed (e.g. the test Tool Shed) and create each of them in a local development Tool Shed. This script can be used to streamline the process of creating a new development Tool Shed, populating it with categories expected in a public Tool Shed, and creating a new repository hierarchy that can be exported into a capsule and imported into the public Tool Shed. Affected #: 1 file
diff -r 87bf6a0324f3182ccf16ad18b662f80272f187bc -r b34eaa5eaa3176bc7498adcda597e7fa58996a2b lib/tool_shed/scripts/api/create_categories.py --- /dev/null +++ b/lib/tool_shed/scripts/api/create_categories.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python +""" +This script will retrieve a list of dictionaries (one for each category) from the Tool Shed defined +by the --from_tool_shed parameter, which should be a base Tool Shed URL. It will retrieve the category +name and description from each dictionary and create a new category with that name and description in +the Tool Shed defined by the --to_tool_shed parameter (a different base Tool Shed URL). Categories +that already exist with a specified name in the Tool Shed in which the categories are being created +will not be affected. + +This script is very useful for populating a new development Tool Shed with the set of categories that +currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building +new repository hierarchies in the development Tool Shed and exportin gthem into a capsule that can be +imported into one of the public Tool Sheds. + +Here is a working example of how to use this script to retrieve the current set of repositories that are +available in the test public Tool Shed and create each of them in a local development Tool Shed. + +./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009 +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import get +from common import submit + +def main( options ): + api_key = options.api + from_tool_shed = options.from_tool_shed.rstrip( '/' ) + to_tool_shed = options.to_tool_shed.rstrip( '/' ) + # Get the categories from the specified Tool Shed. + url = '%s/api/categories' % from_tool_shed + category_dicts = get( url ) + create_response_dicts = [] + for category_dict in category_dicts: + name = category_dict.get( 'name', None ) + description = category_dict.get( 'description', None ) + if name is not None and description is not None: + data = dict( name=name, + description=description ) + url = '%s/api/categories/new/create_category' % to_tool_shed + try: + response = submit( url, data, api_key ) + except Exception, e: + response = str( e ) + log.exception( str( e ) ) + create_response_dict = dict( response=response ) + create_response_dicts.append( create_response_dict ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Retrieve a list of categories from a Tool Shed and create them in another Tool Shed.' ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which categories will be created" ) + parser.add_argument( "-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the categories" ) + parser.add_argument( "-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the categories" ) + options = parser.parse_args() + main( options )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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