mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
d1bc98dfcb
Remove some debugging prints. Fix import order. Consolidate exception logging in ToolShed database migrations.
124 lines
6.1 KiB
Python
124 lines
6.1 KiB
Python
#!/usr/bin/env python
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"""
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Export a specified repository revision and optionally all of its defined repository
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dependencies from the tool shed into a compressed archive.
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Here is a working example of how to use this script to export a repository from the tool shed.
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./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
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"""
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from __future__ import print_function
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import argparse
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import os
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import sys
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import tempfile
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import requests
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sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
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from tool_shed.util import basic_util
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from common import display, submit # noqa: I100
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CAPSULE_FILENAME = 'capsule'
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CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies'
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CHUNK_SIZE = 2 ** 20 # 1Mb
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def generate_repository_archive_filename(tool_shed_url, name, owner, changeset_revision, file_type,
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export_repository_dependencies, use_tmp_archive_dir=False):
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tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url)
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file_type_str = basic_util.get_file_type_str(changeset_revision, file_type)
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if export_repository_dependencies:
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repositories_archive_filename = '%s_%s_%s_%s_%s' % (CAPSULE_WITH_DEPENDENCIES_FILENAME,
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tool_shed,
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name,
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owner,
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file_type_str)
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else:
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repositories_archive_filename = '%s_%s_%s_%s_%s' % (CAPSULE_FILENAME,
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tool_shed,
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name,
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owner,
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file_type_str)
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if use_tmp_archive_dir:
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tmp_archive_dir = tempfile.mkdtemp(prefix="tmp-toolshed-arcdir")
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repositories_archive_filename = os.path.join(tmp_archive_dir, repositories_archive_filename)
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return repositories_archive_filename
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def remove_protocol_from_tool_shed_url(tool_shed_url):
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protocol, base = tool_shed_url.split('://')
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base = base.replace(':', '_colon_')
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base = base.rstrip('/')
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return base
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def string_as_bool(string):
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if str(string).lower() in ('true', 'yes', 'on'):
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return True
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else:
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return False
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def main(options):
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"""Collect all user data and export the repository via the Tool Shed API."""
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base_tool_shed_url = options.tool_shed_url.rstrip('/')
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repositories_url = '%s/api/repositories' % base_tool_shed_url
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data = {}
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data['tool_shed_url'] = base_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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data['export_repository_dependencies'] = options.export_repository_dependencies
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repository_id = None
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repositories = display(repositories_url, api_key=None, return_formatted=False)
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for repository in repositories:
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name = str(repository['name'])
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owner = str(repository['owner'])
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if name == options.name and owner == options.owner:
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repository_id = repository['id']
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break
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if repository_id:
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# We'll currently support only gzip-compressed tar archives.
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file_type = 'gz'
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url = '%s%s' % (base_tool_shed_url, '/api/repository_revisions/%s/export' % str(repository_id))
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export_dict = submit(url, data, return_formatted=False)
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error_messages = export_dict['error_messages']
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if error_messages:
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print("Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages)
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else:
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export_repository_dependencies = string_as_bool(options.export_repository_dependencies)
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repositories_archive_filename = \
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generate_repository_archive_filename(base_tool_shed_url,
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options.name,
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options.owner,
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options.changeset_revision,
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file_type,
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export_repository_dependencies=export_repository_dependencies,
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use_tmp_archive_dir=False)
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download_url = export_dict['download_url']
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download_dir = os.path.abspath(options.download_dir)
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file_path = os.path.join(download_dir, repositories_archive_filename)
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src = requests.get(download_url, stream=True)
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with open(file_path, 'wb') as dst:
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for chunk in src.iter_content(chunk_size=CHUNK_SIZE):
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if chunk:
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dst.write(chunk)
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print("Successfully exported revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner)
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print("to location ", file_path)
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else:
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print("Invalid tool_shed / name / owner .")
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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("-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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parser.add_argument("-e", "--export_repository_dependencies", dest="export_repository_dependencies", required=False, default='False', help="Export repository dependencies.")
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parser.add_argument("-d", "--download_dir", dest="download_dir", required=False, default='/tmp', help="Download directory.")
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options = parser.parse_args()
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main(options)
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