mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
65083bd97b
... it has a PEP-8 detected bug (undefined reference) so it would fail even if it was used.
97 lines
4.7 KiB
Python
97 lines
4.7 KiB
Python
import logging
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import os
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import sys
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cwd = os.getcwd()
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if cwd not in sys.path:
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sys.path.append( cwd )
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new_path = [ os.path.join( cwd, "lib" ) ]
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if new_path not in sys.path:
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new_path.extend( sys.path )
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sys.path = new_path
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from galaxy.util import parse_xml
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log = logging.getLogger(__name__)
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# Set a 10 minute timeout for repository installation.
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repository_installation_timeout = 600
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def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ):
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"""
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Return the GALAXY_TEST_FILE_DIR, the containing repository name and the
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change set revision for the tool elem. This only happens when testing
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tools installed from the tool shed.
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"""
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tool_config_path = elem.get( 'file' )
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installed_tool_path_items = tool_config_path.split( '/repos/' )
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sans_shed = installed_tool_path_items[ 1 ]
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path_items = sans_shed.split( '/' )
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repository_owner = path_items[ 0 ]
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repository_name = path_items[ 1 ]
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changeset_revision = path_items[ 2 ]
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if repository_name != last_tested_repository_name or changeset_revision != last_tested_changeset_revision:
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# Locate the test-data directory.
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installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision )
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for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )):
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if '.' in dirs:
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dirs.remove( '.hg' )
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if 'test-data' in dirs:
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return os.path.join( root, 'test-data' ), repository_name, changeset_revision
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return None, repository_name, changeset_revision
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return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision
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def parse_tool_panel_config( config, shed_tools_dict ):
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"""
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Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed.
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"""
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last_galaxy_test_file_dir = None
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last_tested_repository_name = None
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last_tested_changeset_revision = None
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tool_path = None
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has_test_data = False
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tree = parse_xml( config )
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root = tree.getroot()
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tool_path = root.get('tool_path')
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for elem in root:
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if elem.tag == 'tool':
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galaxy_test_file_dir, \
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last_tested_repository_name, \
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last_tested_changeset_revision = get_installed_repository_info( elem,
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last_galaxy_test_file_dir,
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last_tested_repository_name,
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last_tested_changeset_revision,
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tool_path )
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if galaxy_test_file_dir:
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if not has_test_data:
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has_test_data = True
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if galaxy_test_file_dir != last_galaxy_test_file_dir:
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if not os.path.isabs( galaxy_test_file_dir ):
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galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
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guid = elem.get( 'guid' )
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shed_tools_dict[ guid ] = galaxy_test_file_dir
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last_galaxy_test_file_dir = galaxy_test_file_dir
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elif elem.tag == 'section':
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for section_elem in elem:
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if section_elem.tag == 'tool':
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galaxy_test_file_dir, \
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last_tested_repository_name, \
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last_tested_changeset_revision = get_installed_repository_info( section_elem,
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last_galaxy_test_file_dir,
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last_tested_repository_name,
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last_tested_changeset_revision,
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tool_path )
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if galaxy_test_file_dir:
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if not has_test_data:
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has_test_data = True
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if galaxy_test_file_dir != last_galaxy_test_file_dir:
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if not os.path.isabs( galaxy_test_file_dir ):
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galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
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guid = section_elem.get( 'guid' )
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shed_tools_dict[ guid ] = galaxy_test_file_dir
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last_galaxy_test_file_dir = galaxy_test_file_dir
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return has_test_data, shed_tools_dict
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