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https://github.com/galaxyproject/galaxy.git
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Allow uninstalling multiple toolshed repositories at a time within the Galaxy UI, using checkboxes with grid multi-actions.
This commit is contained in:
Daniel Blankenberg
@@ -228,94 +228,104 @@ class AdminToolshed( AdminGalaxy ):
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but we may choose to do so in the future if it becomes necessary.
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"""
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message = escape( kwd.get( 'message', '' ) )
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statuses = [ None, '' 'info', 'done', 'warning', 'error' ]
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status = kwd.get( 'status', 'done' )
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if status in statuses:
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status = statuses.index( status )
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else:
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status = 1
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remove_from_disk = kwd.get( 'remove_from_disk', '' )
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remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk )
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tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] )
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shed_tool_conf, tool_path, relative_install_dir = \
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suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
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if relative_install_dir:
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if tool_path:
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relative_install_dir = os.path.join( tool_path, relative_install_dir )
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repository_install_dir = os.path.abspath( relative_install_dir )
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else:
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repository_install_dir = None
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errors = ''
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if kwd.get( 'deactivate_or_uninstall_repository_button', False ):
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if tool_shed_repository.includes_tools_for_display_in_tool_panel:
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# Handle tool panel alterations.
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tpm = tool_panel_manager.ToolPanelManager( trans.app )
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tpm.remove_repository_contents( tool_shed_repository,
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shed_tool_conf,
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uninstall=remove_from_disk_checked )
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if tool_shed_repository.includes_data_managers:
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dmh = data_manager.DataManagerHandler( trans.app )
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dmh.remove_from_data_manager( tool_shed_repository )
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if tool_shed_repository.includes_datatypes:
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# Deactivate proprietary datatypes.
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cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app )
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installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository,
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repository_install_dir,
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deactivate=True )
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if installed_repository_dict:
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converter_path = installed_repository_dict.get( 'converter_path' )
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if converter_path is not None:
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cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True )
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display_path = installed_repository_dict.get( 'display_path' )
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if display_path is not None:
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cdl.load_installed_display_applications( installed_repository_dict, deactivate=True )
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if remove_from_disk_checked:
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try:
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# Remove the repository from disk.
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shutil.rmtree( repository_install_dir )
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log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) )
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removed = True
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except Exception, e:
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log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) )
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if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ):
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tool_shed_repositories = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] )
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if not isinstance( tool_shed_repositories, list ):
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tool_shed_repositories = [tool_shed_repositories]
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for tool_shed_repository in tool_shed_repositories:
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shed_tool_conf, tool_path, relative_install_dir = \
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suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
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if relative_install_dir:
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if tool_path:
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relative_install_dir = os.path.join( tool_path, relative_install_dir )
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repository_install_dir = os.path.abspath( relative_install_dir )
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else:
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repository_install_dir = None
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errors = ''
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if kwd.get( 'deactivate_or_uninstall_repository_button', False ):
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if tool_shed_repository.includes_tools_for_display_in_tool_panel:
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# Handle tool panel alterations.
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tpm = tool_panel_manager.ToolPanelManager( trans.app )
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tpm.remove_repository_contents( tool_shed_repository,
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shed_tool_conf,
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uninstall=remove_from_disk_checked )
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if tool_shed_repository.includes_data_managers:
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dmh = data_manager.DataManagerHandler( trans.app )
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dmh.remove_from_data_manager( tool_shed_repository )
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if tool_shed_repository.includes_datatypes:
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# Deactivate proprietary datatypes.
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cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app )
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installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository,
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repository_install_dir,
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deactivate=True )
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if installed_repository_dict:
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converter_path = installed_repository_dict.get( 'converter_path' )
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if converter_path is not None:
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cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True )
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display_path = installed_repository_dict.get( 'display_path' )
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if display_path is not None:
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cdl.load_installed_display_applications( installed_repository_dict, deactivate=True )
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if remove_from_disk_checked:
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try:
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# Remove the repository from disk.
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shutil.rmtree( repository_install_dir )
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log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) )
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removed = True
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log.debug( "Repository directory does not exist on disk, marking as uninstalled." )
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else:
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removed = False
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if removed:
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tool_shed_repository.uninstalled = True
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# Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any
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# repository dependencies.
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tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error
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tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed )
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for tool_dependency in tool_dependencies_to_uninstall:
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uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency )
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if error_message:
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errors = '%s %s' % ( errors, error_message )
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tool_shed_repository.deleted = True
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if remove_from_disk_checked:
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tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED
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tool_shed_repository.error_message = None
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if trans.app.config.manage_dependency_relationships:
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# Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
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# installed_repository_manager.
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trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
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else:
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tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED
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trans.install_model.context.add( tool_shed_repository )
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trans.install_model.context.flush()
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if remove_from_disk_checked:
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message = 'The repository named <b>%s</b> has been uninstalled. ' % escape( tool_shed_repository.name )
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if errors:
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message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors
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status = 'error'
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except Exception, e:
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log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) )
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if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ):
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removed = True
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log.debug( "Repository directory does not exist on disk, marking as uninstalled." )
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else:
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removed = False
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if removed:
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tool_shed_repository.uninstalled = True
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# Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any
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# repository dependencies.
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tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error
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tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed )
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for tool_dependency in tool_dependencies_to_uninstall:
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uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency )
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if error_message:
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errors = '%s %s' % ( errors, error_message )
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tool_shed_repository.deleted = True
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if remove_from_disk_checked:
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tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED
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tool_shed_repository.error_message = None
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if trans.app.config.manage_dependency_relationships:
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# Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
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# installed_repository_manager.
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trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository )
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else:
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status = 'done'
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else:
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message = 'The repository named <b>%s</b> has been deactivated. ' % escape( tool_shed_repository.name )
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status = 'done'
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tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED
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trans.install_model.context.add( tool_shed_repository )
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trans.install_model.context.flush()
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if remove_from_disk_checked:
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message += 'The repository named <b>%s</b> has been uninstalled. ' % escape( tool_shed_repository.name )
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if errors:
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message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors
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status = max( status, statuses.index( 'error' ) )
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else:
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status = max( status, statuses.index( 'done' ) )
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else:
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message = 'The repository named <b>%s</b> has been deactivated. ' % escape( tool_shed_repository.name )
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status = max( status, statuses.index( 'done' ) )
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status = statuses[ status ]
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if kwd.get( 'deactivate_or_uninstall_repository_button', False ):
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return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
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action='browse_repositories',
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message=message,
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status=status ) )
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remove_from_disk_check_box = CheckboxField( 'remove_from_disk', checked=remove_from_disk_checked )
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return trans.fill_template( '/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako',
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repository=tool_shed_repository,
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repository=tool_shed_repositories,
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remove_from_disk_check_box=remove_from_disk_check_box,
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message=message,
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status=status )
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@@ -196,7 +196,7 @@ class InstalledRepositoryGrid( grids.Grid ):
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condition=( lambda item:
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not item.deleted and
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item.status != tool_shed_install.ToolShedRepository.installation_status.NEW ),
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allow_multiple=False,
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allow_multiple=True,
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url_args=dict( controller='admin_toolshed',
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action='browse_repositories',
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operation='deactivate or uninstall' ) ),
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@@ -275,8 +275,17 @@ def create_repository_admin_role( app, repository ):
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def get_installed_tool_shed_repository( app, id ):
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"""Get a tool shed repository record from the Galaxy database defined by the id."""
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return app.install_model.context.query( app.install_model.ToolShedRepository ) \
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.get( app.security.decode_id( id ) )
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rval = []
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if isinstance( id, list ):
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return_list = True
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else:
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id = [ id ]
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return_list = False
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for i in id:
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rval.append( app.install_model.context.query( app.install_model.ToolShedRepository ).get( app.security.decode_id( i ) ) )
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if return_list:
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return rval
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return rval[0]
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def get_repo_info_dict( app, user, repository_id, changeset_revision ):
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@@ -3,16 +3,28 @@
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<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
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<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
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${render_galaxy_repository_actions( repository )}
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<%
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repository = context.get( 'repository', None )
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if isinstance( repository, list ):
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repositories = repository
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else:
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repositories = [ repository ]
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%>
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%if len( repositories ) == 1:
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${render_galaxy_repository_actions( repositories[0] )}
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%endif
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%if message:
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${render_msg( message, status )}
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%endif
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<div class="toolForm">
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<form name="deactivate_or_uninstall_repository" id="deactivate_or_uninstall_repository" action="${ h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository' ) }" method="post" >
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%for repository in repositories:
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<input type="hidden" name="id" value="${ trans.security.encode_id( repository.id ) | h }" />
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<div class="toolFormTitle">${repository.name|h}</div>
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<div class="toolFormBody">
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<form name="deactivate_or_uninstall_repository" id="deactivate_or_uninstall_repository" action="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
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<div class="form-row">
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<label>Description:</label>
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${repository.description|h}
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@@ -169,10 +181,12 @@ ${render_galaxy_repository_actions( repository )}
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%endif
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%endif
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</div>
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</div>
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%endfor
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<div class="form-row">
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<%
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can_deactivate_repository = repository.can_deactivate
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can_uninstall_repository = repository.can_uninstall
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can_deactivate_repository = True in map( lambda x: x.can_deactivate, repositories )
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can_uninstall_repository = True in map( lambda x: x.can_uninstall, repositories )
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%>
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%if can_deactivate_repository and can_uninstall_repository:
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<% deactivate_uninstall_button_text = "Deactivate or Uninstall" %>
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