mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
Nicola Soranzo
949dcfdbc3
`logging.exception()` already adds the the exception information after the supplied message. Also: the `message` attribute of `Exception` class has been dropped in Python 3, always use `str(e)`. xref. https://github.com/galaxyproject/galaxy/issues/1715
94 lines
3.9 KiB
Python
94 lines
3.9 KiB
Python
#!/usr/bin/env python
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"""
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Script to reset metadata on certain repositories in the Tool Shed. If the received API key is associated
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with an admin user in the Tool Shed, setting the my_writable param value to True will restrict resetting
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metadata to only repositories that are writable by the user in addition to those repositories of type
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tool_dependency_definition. The my_writable param is ignored if the current user is not an admin user,
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in which case this same restriction is automatic.
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usage: reset_metadata_on_repositories.py key <my_writable>
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Here is a working example of how to use this script to reset metadata on certain repositories in a specified Tool Shed.
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python ./reset_metadata_on_repositories.py -a 22be3b -m True -u http://localhost:9009/
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"""
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from __future__ import print_function
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import argparse
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import logging
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import os
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import sys
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from common import get, submit
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log = logging.getLogger(__name__)
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def string_as_bool(string):
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if str(string).lower() in ['true']:
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return True
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else:
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return False
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def read_skip_file(skip_file):
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encoded_ids_to_skip = []
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if os.path.exists(skip_file):
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# Contents of file must be 1 encoded repository id per line.
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lines = open(skip_file, 'rb').readlines()
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for line in lines:
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if line.startswith('#'):
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# Skip comments.
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continue
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encoded_ids_to_skip.append(line.rstrip('\n'))
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return encoded_ids_to_skip
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def main(options):
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api_key = options.api
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base_tool_shed_url = options.tool_shed_url.rstrip('/')
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my_writable = options.my_writable
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one_per_request = options.one_per_request
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skip_file = options.skip_file
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if skip_file:
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encoded_ids_to_skip = read_skip_file(skip_file)
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else:
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encoded_ids_to_skip = []
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if string_as_bool(one_per_request):
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url = '%s/api/repositories/repository_ids_for_setting_metadata?key=%s&my_writable=%s' % (base_tool_shed_url, api_key, str(my_writable))
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repository_ids = get(url, api_key)
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for repository_id in repository_ids:
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if repository_id in encoded_ids_to_skip:
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print("--------")
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print("Skipping repository with id %s because it is in skip file %s" % (repository_id, skip_file))
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print("--------")
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else:
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data = dict(repository_id=repository_id)
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url = '%s/api/repositories/reset_metadata_on_repository' % base_tool_shed_url
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try:
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submit(url, data, options.api)
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except Exception:
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log.exception(">>>>>>>>>>>>>>>Blew up on data: %s", data)
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# An nginx timeout undoubtedly occurred.
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sys.exit(1)
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else:
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data = dict(encoded_ids_to_skip=encoded_ids_to_skip,
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my_writable=my_writable)
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url = '%s/api/repositories/reset_metadata_on_repositories' % base_tool_shed_url
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try:
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submit(url, data, options.api)
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except Exception:
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log.exception(">>>>>>>>>>>>>>>Blew up on data: %s", data)
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# An nginx timeout undoubtedly occurred.
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sys.exit(1)
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Reset metadata on certain repositories in the Tool Shed via the Tool Shed API.')
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parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
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parser.add_argument("-m", "--my_writable", dest="my_writable", required=False, default='False', help="Restrict to my writable repositories")
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parser.add_argument("-o", "--one_per_request", dest="one_per_request", required=False, default='True', help="One repository per request")
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parser.add_argument("-s", "--skip_file", dest="skip_file", required=False, help="Name of local file containing encoded repository ids to skip")
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parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
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options = parser.parse_args()
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main(options)
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