mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
61 lines
3.0 KiB
Python
61 lines
3.0 KiB
Python
#!/usr/bin/env python
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"""
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Repair a specified repository revision previously installed into Galaxy.
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Here is a working example of how to use this script to repair a repository installed into Galaxy.
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./repair_tool_shed_repository.py --api <api key> --local <galaxy base url> --url http://testtoolshed.g2.bx.psu.edu --name gregs_filter --owner greg --revision f28d5018f9cb
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"""
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import argparse
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from common import display, submit
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def clean_url(url):
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if url.find('//') > 0:
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# We have an url that includes a protocol, something like: http://localhost:9009
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items = url.split('//')
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return items[1].rstrip('/')
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return url.rstrip('/')
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def main(options):
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"""Collect all user data and install the tools via the Galaxy API."""
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api_key = options.api
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base_galaxy_url = options.local_url.rstrip('/')
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base_tool_shed_url = options.tool_shed_url.rstrip('/')
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cleaned_tool_shed_url = clean_url(base_tool_shed_url)
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installed_tool_shed_repositories_url = '{}/api/{}'.format(base_galaxy_url, 'tool_shed_repositories')
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data = {}
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data['tool_shed_url'] = cleaned_tool_shed_url
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data['name'] = options.name
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data['owner'] = options.owner
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data['changeset_revision'] = options.changeset_revision
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tool_shed_repository_id = None
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installed_tool_shed_repositories = display(api_key, installed_tool_shed_repositories_url, return_formatted=False)
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for installed_tool_shed_repository in installed_tool_shed_repositories:
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tool_shed = str(installed_tool_shed_repository['tool_shed'])
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name = str(installed_tool_shed_repository['name'])
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owner = str(installed_tool_shed_repository['owner'])
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changeset_revision = str(installed_tool_shed_repository['changeset_revision'])
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if tool_shed == cleaned_tool_shed_url and name == options.name and owner == options.owner and changeset_revision == options.changeset_revision:
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tool_shed_repository_id = installed_tool_shed_repository['id']
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break
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if tool_shed_repository_id:
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url = '{}{}'.format(base_galaxy_url, '/api/tool_shed_repositories/%s/repair_repository_revision' % str(tool_shed_repository_id))
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submit(options.api, url, data)
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else:
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print("Invalid tool_shed / name / owner / changeset_revision.")
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Installation of tool shed repositories via the Galaxy API.')
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parser.add_argument("-u", "--url", dest="tool_shed_url", required=True, help="Tool Shed URL")
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parser.add_argument("-a", "--api", dest="api", required=True, help="API Key")
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parser.add_argument("-l", "--local", dest="local_url", required=True, help="URL of the galaxy instance.")
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parser.add_argument("-n", "--name", required=True, help="Repository name.")
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parser.add_argument("-o", "--owner", required=True, help="Repository owner.")
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parser.add_argument("-r", "--revision", dest="changeset_revision", required=True, help="Repository owner.")
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options = parser.parse_args()
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main(options)
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