commit/galaxy-central: inithello: Handle errors when cloning a tool shed repository.
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0491c1081542/ changeset: 0491c1081542 user: inithello date: 2012-09-07 17:22:09 summary: Handle errors when cloning a tool shed repository. affected #: 2 files diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 0491c108154248cab0006533d30e462df3ade6f9 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -355,12 +355,16 @@ return tool_shed_url.rstrip( '/' ) def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" - commands.clone( get_configured_ui(), - str( repository_clone_url ), - dest=str( repository_file_dir ), - pull=True, - noupdate=False, - rev=util.listify( str( ctx_rev ) ) ) + try: + commands.clone( get_configured_ui(), + str( repository_clone_url ), + dest=str( repository_file_dir ), + pull=True, + noupdate=False, + rev=util.listify( str( ctx_rev ) ) ) + return True + except: + return False def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" if dest_path is None: diff -r 5c09dfcc62c27857e0653c3a95df24c6fb316baf -r 0491c108154248cab0006533d30e462df3ade6f9 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -64,7 +64,8 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ), + link=( lambda item: iff( item.status == model.ToolShedRepository.installation_status.ERROR, \ + None, dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -86,17 +87,29 @@ global_actions = [] operations = [ grids.GridOperation( "Get updates", allow_multiple=False, - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and item.status not in \ + [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='get updates' ) ), grids.GridOperation( "Deactivate or uninstall", allow_multiple=False, - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and item.status not in \ + [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ), + grids.GridOperation( "Uninstall", + allow_multiple=False, + condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='uninstall' ) ), + grids.GridOperation( "Reset to install", + allow_multiple=False, + condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='reset status to new' ) ), grids.GridOperation( "Activate or reinstall", allow_multiple=False, - condition=( lambda item: item.deleted ), + condition=( lambda item: ( item.deleted or item.uninstalled ) ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='activate or reinstall' ) ) ] standard_filters = [] @@ -342,6 +355,16 @@ return self.manage_repository( trans, **kwd ) if operation == "get updates": return self.check_for_updates( trans, **kwd ) + if operation == "uninstall": + kwd[ 'deactivate_or_uninstall_repository_button' ] = 'Deactivate or Uninstall' + kwd[ 'remove_from_disk' ] = [u'true', u'true'] + return self.deactivate_or_uninstall_repository( trans, **kwd ) + if operation == "reset status to new": + repository = get_repository( trans, kwd[ 'id' ] ) + repository.status = model.ToolShedRepository.installation_status.NEW + repository.deleted = False + repository.uninstalled = True + trans.app.model.context.current.flush() if operation == "activate or reinstall": repository = get_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: @@ -406,7 +429,7 @@ remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) tool_shed_repository = get_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) - repository_install_dir = os.path.abspath ( relative_install_dir ) + repository_install_dir = os.path.abspath ( relative_install_dir ) if relative_install_dir is not None else None errors = '' if params.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools: @@ -426,8 +449,12 @@ log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) ) removed = True except Exception, e: - log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - removed = False + if repository_install_dir is not None: + removed = False + log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) + else: + log.debug( "Repository installation directory does not exist." ) + removed = True if removed: tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. @@ -610,7 +637,12 @@ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + result = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + if not result: + update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.ERROR ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + tool_shed_repository_ids=[ trans.security.encode_id( tool_shed_repository.id ) ] ) ) if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) @@ -746,6 +778,12 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) + if repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: + message = "There was an error installing the repository '%s', please try again..." + status = 'warning' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + **kwd ) ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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