galaxy-commits January 2013

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commit/galaxy-central: dan: Enhance Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes issue where a server error would occur within workflows when parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input.
by Bitbucket 07 Jan '13

07 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb4dac39eed5/ changeset: eb4dac39eed5 user: dan date: 2013-01-07 17:07:52 summary: Enhance Tool.check_and_update_param_values_helper() to check that the type of value provided is valid for the input parameter currently declared. Fixes issue where a server error would occur within workflows when parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input. affected #: 1 file diff -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 -r eb4dac39eed53cc0ef1550ee63486358fd53ad59 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2181,7 +2181,12 @@ self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) else: # Regular tool parameter, no recursion needed - pass + try: + #this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input + input.value_from_basic( values[ input.name ], trans.app, ignore_errors=False ) + except: + messages[ input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, input.label ) + values[ input.name ] = input.get_initial_value( trans, context ) def handle_unvalidated_param_values( self, input_values, app ): """ Find any instances of `UnvalidatedValue` within input_values and Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f93f509ca0c2/ changeset: f93f509ca0c2 user: greg date: 2013-01-04 22:10:26 summary: Handle tool panel locations appropriately for tool shed repositories and repository dependencies being installed or reinstalled into Galaxy. affected #: 2 files diff -r 8fe64f73835cd19274dcac65c935187d426b18ba -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -5,6 +5,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.webapps.community.util import container_util import shed_util_common as suc +import galaxy.tools from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment from galaxy.tool_shed import encoding_util @@ -175,14 +176,17 @@ # Attempt to ensure we're copying an appropriate file. if is_data_index_sample_file( filename ): suc.copy_sample_file( app, filename, dest_path=dest_path ) -def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False ): +def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False, + no_changes_checked=False, tool_panel_section=None, new_tool_panel_section=None ): """ Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy instance and when uninstalled repositories are being reinstalled. """ message = '' + # There will be a one-to-one mapping between items in created_or_updated_tool_shed_repositories and tool_panel_section_keys. created_or_updated_tool_shed_repositories = [] + tool_panel_section_keys = [] # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. filtered_repo_info_dicts = [] if install_repository_dependencies: @@ -204,6 +208,11 @@ installed_tool_shed_repository, installed_changeset_revision = \ repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) if installed_tool_shed_repository: + tool_section, new_tool_panel_section, tool_panel_section_key = handle_tool_panel_selection( trans=trans, + metadata=installed_tool_shed_repository.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if reinstalling or install_repository_dependencies: if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: @@ -217,22 +226,23 @@ # There is a repository already installed which is a dependency of the repository being reinstalled. can_update = False else: - # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. - message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) - if installed_changeset_revision != changeset_revision: - message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision - else: - message += "was previously installed. " - if installed_tool_shed_repository.uninstalled: - message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " - elif installed_tool_shed_repository.deleted: - message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " - if installed_changeset_revision != changeset_revision: - message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " - message += "<b>Repository Actions</b> pop-up menu. " if len( all_repo_info_dicts ) == 1: + # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. + message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) + if installed_changeset_revision != changeset_revision: + message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision + else: + message += "was previously installed. " + if installed_tool_shed_repository.uninstalled: + message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. " + elif installed_tool_shed_repository.deleted: + message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. " + if installed_changeset_revision != changeset_revision: + message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's " + message += "<b>Repository Actions</b> pop-up menu. " created_or_updated_tool_shed_repositories.append( installed_tool_shed_repository ) - return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + tool_panel_section_keys.append( tool_panel_section_key ) + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message else: can_update = True else: @@ -243,6 +253,36 @@ metadata_dict={} dist_to_shed = False if can_update: + if reinstalling or install_repository_dependencies: + # Get the repository metadata to see where it was previously located in the tool panel. + installed_tool_shed_repository = suc.get_repository_for_dependency_relationship( app=trans.app, + tool_shed=tool_shed_url, + name=name, + owner=repository_owner, + changeset_revision=changeset_revision ) + if installed_tool_shed_repository: + tool_section, new_tool_panel_section, tool_panel_section_key = \ + handle_tool_panel_selection( trans=trans, + metadata=installed_tool_shed_repository.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) + else: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + else: + tool_panel_section_key = None + else: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + else: + tool_panel_section_key = None tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, name=name, description=description, @@ -255,8 +295,9 @@ owner=repository_owner, dist_to_shed=False ) created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + tool_panel_section_keys.append( tool_panel_section_key ) filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) - return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): return dict( tool_shed=tool_shed, repository_name=name, @@ -836,6 +877,60 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies +def handle_tool_panel_selection( trans, metadata, no_changes_checked, tool_panel_section, new_tool_panel_section ): + """Handle the selected tool panel location for loading tools included in tool shed repositories when installing or reinstalling them.""" + # Get the location in the tool panel in which each tool was originally loaded. + tool_section = None + tool_panel_section_key = None + if 'tools' in metadata: + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if not tool_panel_dict: + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + else: + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + # This forces everything to be loaded into the same section (or no section) in the tool panel. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_id = tool_section_dict[ 'id' ] + original_section_name = tool_section_dict[ 'name' ] + if no_changes_checked: + if original_section_id: + tool_panel_section_key = 'section_%s' % str( original_section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. + elem = Element( 'section' ) + elem.attrib[ 'name' ] = original_section_name + elem.attrib[ 'id' ] = original_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + else: + # The user elected to change the tool panel section to contain the tools. + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + tool_panel_section_key = 'section_%s' % str( section_id ) + if tool_panel_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + elif tool_panel_section: + tool_panel_section_key = 'section_%s' % tool_panel_section + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None + return tool_section, new_tool_panel_section, tool_panel_section_key def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ): """ Using the list of tool_version_dicts retrieved from the tool shed (one per changeset revison up to the currently installed changeset revision), diff -r 8fe64f73835cd19274dcac65c935187d426b18ba -r f93f509ca0c2a21acdf0ed17615d1caf839dcb98 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -396,7 +396,7 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: - if repository.includes_tools: + if repository.includes_tools or repository.has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', @@ -835,17 +835,19 @@ @web.require_admin def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ): """Install specified tool shed repositories.""" - repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) tool_path = kwd[ 'tool_path' ] includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) - tool_panel_section_key = kwd.get( 'tool_panel_section_key', None ) - if tool_panel_section_key: - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - tool_section = None - for tup in zip( tool_shed_repositories, repo_info_dicts ): - tool_shed_repository, repo_info_dict = tup + # There must be a one-to-one mapping between items in the 3 lists:tool_shed_repositories, tool_panel_section_keys, repo_info_dicts. + tool_panel_section_keys = util.listify( kwd[ 'tool_panel_section_keys' ] ) + repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] ) + for index, tool_shed_repository in enumerate( tool_shed_repositories ): + repo_info_dict = repo_info_dicts[ index ] + tool_panel_section_key = tool_panel_section_keys[ index ] + if tool_panel_section_key: + tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] + else: + tool_section = None if isinstance( repo_info_dict, basestring ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. @@ -1021,13 +1023,17 @@ encoded_kwd = kwd[ 'encoded_kwd' ] decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] + tool_panel_section_keys = decoded_kwd[ 'tool_panel_section_keys' ] + filtered_tool_panel_section_keys = [] repositories_for_installation = [] - for tsr_id in tsr_ids: + for index, tsr_id in enumerate( tsr_ids ): repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) + filtered_tool_panel_section_keys.append( tool_panel_section_keys[ index ] ) if repositories_for_installation: + decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' @@ -1154,6 +1160,7 @@ # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) + tool_panel_section_keys = [] # One or more repositories may include tools, but not necessarily all of them. includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) @@ -1191,13 +1198,16 @@ else: install_tool_dependencies = False tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) - created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, - install_repository_dependencies=install_repository_dependencies ) + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=False, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if message and len( repo_info_dicts ) == 1: installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ] message+= 'Click <a href="%s">here</a> to manage the repository. ' % \ @@ -1235,6 +1245,10 @@ tool_panel_section_key = None tool_section = None tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ] + # Create a one-to-one mapping of tool shed repository id and tool panel section key. All tools contained in the repositories + # being installed will be loaded into the same section in the tool panel. + for tsr in created_or_updated_tool_shed_repositories: + tool_panel_section_keys.append( tool_panel_section_key ) new_kwd = dict( includes_tools=includes_tools, includes_repository_dependencies=includes_repository_dependencies, install_repository_dependencies=install_repository_dependencies, @@ -1245,7 +1259,8 @@ shed_tool_conf=shed_tool_conf, status=status, tool_path=tool_path, - tool_panel_section_key=tool_panel_section_key, + + tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=tsrids_list, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) @@ -1369,66 +1384,25 @@ no_changes_checked = CheckboxField.is_checked( no_changes ) install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) - new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) - tool_panel_section = kwd.get( 'tool_panel_section', '' ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) clone_dir = os.path.join( tool_path, shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) tool_section = None + tool_panel_section = kwd.get( 'tool_panel_section', '' ) + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section_key = None + tool_panel_section_keys = [] metadata = tool_shed_repository.metadata if tool_shed_repository.includes_tools: - # Get the location in the tool panel in which each tool was originally loaded. - if 'tool_panel_section' in metadata: - tool_panel_dict = metadata[ 'tool_panel_section' ] - if not tool_panel_dict: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - else: - tool_panel_dict = shed_util.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - # Fix this to handle the case where the tools are distributed across in more than 1 ToolSection - this assumes everything was loaded into 1 - # section (or no section) in the tool panel. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] - original_section_id = tool_section_dict[ 'id' ] - original_section_name = tool_section_dict[ 'name' ] - if no_changes_checked: - if original_section_id: - tool_panel_section_key = 'section_%s' % str( original_section_id ) - if tool_panel_section_key in trans.app.toolbox.tool_panel: - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. - elem = Element( 'section' ) - elem.attrib[ 'name' ] = original_section_name - elem.attrib[ 'id' ] = original_section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - else: - # The user elected to change the tool panel section to contain the tools. - if new_tool_panel_section: - section_id = new_tool_panel_section.lower().replace( ' ', '_' ) - tool_panel_section_key = 'section_%s' % str( section_id ) - if tool_panel_section_key in trans.app.toolbox.tool_panel: - # Appending a tool to an existing section in trans.app.toolbox.tool_panel - log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - # Appending a new section to trans.app.toolbox.tool_panel - log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) - elem = Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section - elem.attrib[ 'id' ] = section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - elif tool_panel_section: - tool_panel_section_key = 'section_%s' % tool_panel_section - tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] - else: - tool_section = None + # Handle the selected tool panel location for loading tools included in the tool shed repository. + tool_section, new_tool_panel_section, tool_panel_section_key = \ + shed_util.handle_tool_panel_selection( trans=trans, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) # The repository's status must be updated from 'Uninstall' to 'New' when initiating reinstall so the repository_installation_updater will function. tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app, tool_shed_repository.name, @@ -1471,22 +1445,31 @@ repo_info_dict = encoding_util.tool_shed_encode( repo_info_dict ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. - created_or_updated_tool_shed_repositories = [ tool_shed_repository ] if install_repository_dependencies: # This is a bit screwy because filtered_repo_info_dicts in this block is a list of tool_shed_encoded dictionaries, but # in the associated else block, it is a list of unencoded dictionaries - not sure if this should be corrected... - created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=True, - install_repository_dependencies=install_repository_dependencies ) + install_repository_dependencies=install_repository_dependencies, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) if len( created_or_updated_tool_shed_repositories ) > 1: # Build repository dependency relationships. suc.build_repository_dependency_relationships( trans, repo_info_dicts, created_or_updated_tool_shed_repositories ) else: filtered_repo_info_dicts = [ repo_info_dict for repo_info_dict in repo_info_dicts ] + created_or_updated_tool_shed_repositories = [ tool_shed_repository ] + tool_panel_section_keys.append( tool_panel_section_key ) + # Defaulot the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location + # selected for the repository selected for reinstallation. + for index, tps_key in enumerate( tool_panel_section_keys ): + if tps_key is None: + tool_panel_section_keys[ index ] = tool_panel_section_key encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, @@ -1498,7 +1481,7 @@ status=status, tool_panel_section=tool_panel_section, tool_path=tool_path, - tool_panel_section_key=tool_panel_section_key, + tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=encoded_repository_ids, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) @@ -1530,6 +1513,7 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): + """Select or change the tool panel section to contain the tools included in the tool shed repositories being reinstalled.""" message = '' repository_id = kwd[ 'id' ] tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: james_taylor: remove trailing comma
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8fe64f73835c/ changeset: 8fe64f73835c user: james_taylor date: 2013-01-04 20:42:28 summary: remove trailing comma affected #: 1 file diff -r 312ba8a948a1c678bea807f4a0d3320af8363968 -r 8fe64f73835cd19274dcac65c935187d426b18ba templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -76,7 +76,7 @@ if( navigator.userAgent.match( /(iPhone|iPod|iPad)/i ) ) { $("iframe").parent().css( { "overflow": "scroll", - "-webkit-overflow-scrolling": "touch", + "-webkit-overflow-scrolling": "touch" }) } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: Fix for scrolling on iOS (thanks Carrie Ganote!)
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/312ba8a948a1/ changeset: 312ba8a948a1 user: james_taylor date: 2013-01-04 20:38:06 summary: Fix for scrolling on iOS (thanks Carrie Ganote!) affected #: 1 file diff -r 8676b55d191c6742e6e7b8864e47918719314f78 -r 312ba8a948a1c678bea807f4a0d3320af8363968 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -71,6 +71,15 @@ galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; } }); + + // Fix iFrame scrolling on iOS + if( navigator.userAgent.match( /(iPhone|iPod|iPad)/i ) ) { + $("iframe").parent().css( { + "overflow": "scroll", + "-webkit-overflow-scrolling": "touch", + }) + } + }); </script></%def> @@ -118,7 +127,9 @@ center_url = h.url_for( '/static/welcome.html' ) %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> + <div style="position: absolute; width: 100%; height: 100%"> + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> + </div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Improve wording for item sharing.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8676b55d191c/ changeset: 8676b55d191c user: jgoecks date: 2013-01-04 18:07:38 summary: Improve wording for item sharing. affected #: 1 file diff -r ad04a8d066e7092fb73d5469f1935196923b8ab3 -r 8676b55d191c6742e6e7b8864e47918719314f78 templates/sharing_base.mako --- a/templates/sharing_base.mako +++ b/templates/sharing_base.mako @@ -142,7 +142,7 @@ </form> %else: ## User has a public username, so private sharing and publishing options. - <h3>Making ${item_class_name} Accessible via Link and Publishing It</h3> + <h3>Make ${item_class_name} Accessible via Link and Publish It</h3><div> %if item.importable: @@ -214,7 +214,7 @@ ## ## Sharing with Galaxy users. ## - <h3>Sharing ${item_class_name} with Specific Users</h3> + <h3>Share ${item_class_name} with Individual Users</h3><div> %if item.users_shared_with: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Tool shed functional tests for repositories with invalid tools, functional test enhancement for repositories with workflows.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad04a8d066e7/ changeset: ad04a8d066e7 user: inithello date: 2013-01-04 17:30:11 summary: Tool shed functional tests for repositories with invalid tools, functional test enhancement for repositories with workflows. affected #: 9 files diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -97,7 +97,7 @@ Loop through each tool dictionary in the repository metadata associated with the received changeset_revision. For each of these, check for a tools attribute, and load the tool metadata page if it exists, then display that tool's page. ''' - repository_metadata = test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, changeset_revision ) + repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) metadata = repository_metadata.metadata if 'tools' not in metadata: raise AssertionError( 'No tools in %s revision %s.' % ( repository.name, changeset_revision ) ) @@ -118,10 +118,9 @@ strings_not_displayed=[] ) def check_repository_invalid_tools_for_changeset_revision( self, repository, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): '''Load the invalid tool page for each invalid tool associated with this changeset revision and verify the received error messages.''' - repository_metadata = test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, changeset_revision ) + repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) metadata = repository_metadata.metadata - if 'invalid_tools' not in metadata: - return + assert 'invalid_tools' in metadata, 'Metadata for changeset revision %s does not define invalid tools' % changeset_revision for tool_xml in metadata[ 'invalid_tools' ]: self.load_invalid_tool_page( repository, tool_xml=tool_xml, @@ -396,9 +395,11 @@ def get_repository_metadata( self, repository ): return [ metadata_revision for metadata_revision in repository.metadata_revisions ] def get_repository_metadata_by_changeset_revision( self, repository, changeset_revision ): - for metadata_revision in repository.metadata_revisions: + found = None + for metadata_revision in self.get_repository_metadata( repository ): if metadata_revision.changeset_revision == changeset_revision: - return metadata_revision + found = metadata_revision + return found def get_repository_metadata_revisions( self, repository ): return [ str( repository_metadata.changeset_revision ) for repository_metadata in repository.metadata_revisions ] def get_repository_tip( self, repository ): @@ -484,6 +485,8 @@ if not changeset_revision: changeset_revision = self.get_repository_tip( repository ) metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) + if not metadata: + raise AssertionError( 'Metadata not found for changeset revision %s.' % changeset_revision ) url = '/repository/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \ ( self.security.encode_id( metadata.id ), tool_shed_encode( workflow_name ) ) self.visit_url( url ) diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -2,8 +2,8 @@ import tool_shed.base.test_db_util as test_db_util repository_name = 'filtering_0000' -repository_description = "Galaxy's filtering tool" -repository_long_description = "Long description of Galaxy's filtering tool" +repository_description = "Galaxy's filtering tool for test 0000" +repository_long_description = "Long description of Galaxy's filtering tool for test 0000" class TestBasicRepositoryFeatures( ShedTwillTestCase ): diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -2,9 +2,8 @@ import tool_shed.base.test_db_util as test_db_util repository_name = 'filtering_0060' -repository_description = "Galaxy's filtering tool" -repository_long_description = "Long description of Galaxy's filtering tool" -workflow_repository_name = 'filtering_workflow_0060' +repository_description="Galaxy's filtering tool for test 0060" +repository_long_description="Long description of Galaxy's filtering tool for test 0060" workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' @@ -54,6 +53,7 @@ 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) +# raise Exception( self.get_repository_tip( repository ) ) self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] ) def test_0025_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_0070_invalid_tool.py --- a/test/tool_shed/functional/test_0070_invalid_tool.py +++ b/test/tool_shed/functional/test_0070_invalid_tool.py @@ -1,12 +1,13 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -repository_name = 'freebayes_0070' -repository_description = "Galaxy's freebayes tool" -repository_long_description = "Long description of Galaxy's freebayes tool" +repository_name = 'bismark_0070' +repository_description = "Galaxy's bismark wrapper" +repository_long_description = "Long description of Galaxy's bismark wrapper" +category_name = 'Test 0070 Invalid Tool Revisions' -class TestFreebayesRepository( ShedTwillTestCase ): - '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' +class TestBismarkRepository( ShedTwillTestCase ): + '''Testing bismark with valid and invalid tool entries.''' def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -19,14 +20,11 @@ admin_user = test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) - def test_0005_create_category( self ): - """Create a category for this test suite""" - self.create_category( name='Test 0070 Repository With Invalid Tool', description='Tests for a repository with an invalid tool.' ) - def test_0010_create_test_repository_and_upload_tool_xml( self ): - '''Create and populate a freebayes repository. After this test, it should contain one valid tool and one invalid tool.''' + def test_0005_create_category_and_repository( self ): + """Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool.""" + category = self.create_category( name=category_name, description='Tests for a repository with invalid tool revisions.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, @@ -34,20 +32,18 @@ category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, - 'freebayes/freebayes.xml', + 'bismark/bismark.tar', valid_tools_only=False, strings_displayed=[], - commit_message='Uploaded the tool xml.' ) + commit_message='Uploaded the tool tarball.' ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ] ) + invalid_revision = self.get_repository_tip( repository ) self.upload_file( repository, - 'filtering/filtering_1.1.0.tar', - valid_tools_only=False, + 'bismark/bismark_methylation_extractor.xml', + valid_tools_only=False, strings_displayed=[], - commit_message='Uploaded the tool xml.', - remove_repo_files_not_in_tar='No' ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Valid tools', 'Invalid tools' ] ) - changeset_revision = self.get_repository_tip( repository ) - self.check_repository_tools_for_changeset_revision( repository, changeset_revision ) - self.check_repository_invalid_tools_for_changeset_revision( repository, - changeset_revision, - strings_displayed=[ 'requires an entry' ], - strings_not_displayed=[] ) + remove_repo_files_not_in_tar='No', + commit_message='Uploaded an updated tool xml.' ) + valid_revision = self.get_repository_tip( repository ) + self.check_repository_tools_for_changeset_revision( repository, valid_revision ) + self.check_repository_invalid_tools_for_changeset_revision( repository, invalid_revision ) diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1060_install_repository_with_workflow.py --- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py +++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py @@ -2,8 +2,8 @@ import tool_shed.base.test_db_util as test_db_util repository_name = 'filtering_0060' -repository_description = "Galaxy's filtering tool" -repository_long_description = "Long description of Galaxy's filtering tool" +repository_description="Galaxy's filtering tool for test 0060", +repository_long_description="Long description of Galaxy's filtering tool for test 0060", workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1070_invalid_tool.py --- a/test/tool_shed/functional/test_1070_invalid_tool.py +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -1,9 +1,10 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util -repository_name = 'freebayes_0070' -repository_description = "Galaxy's freebayes tool" -repository_long_description = "Long description of Galaxy's freebayes tool" +repository_name = 'bismark_0070' +repository_description = "Galaxy's bismark wrapper" +repository_long_description = "Long description of Galaxy's bismark wrapper" +category_name = 'Test 0070 Invalid Tool Revisions' class TestFreebayesRepository( ShedTwillTestCase ): '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.''' @@ -26,11 +27,11 @@ admin_user_private_role = test_db_util.get_private_role( admin_user ) def test_0005_ensure_existence_of_repository_and_category( self ): '''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.''' - self.create_category( name='Test 0070 Repository With Invalid Tool', - description='Tests for a repository with an invalid tool.' ) + self.create_category( name=category_name, + description='Test 1070 for a repository with an invalid tool.' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + category = test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, @@ -39,27 +40,29 @@ strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, - 'freebayes/freebayes.xml', + 'bismark/bismark.tar', valid_tools_only=False, - commit_message='Uploaded the invalid tool xml.' ) + strings_displayed=[], + commit_message='Uploaded the tool tarball.' ) self.upload_file( repository, - 'filtering/filtering_1.1.0.tar', - valid_tools_only=False, - commit_message='Uploaded the valid tool xml.', - remove_repo_files_not_in_tar='No' ) + 'bismark/bismark_methylation_extractor.xml', + valid_tools_only=False, + strings_displayed=[], + remove_repo_files_not_in_tar='No', + commit_message='Uploaded an updated tool xml.' ) def test_0010_browse_tool_shed( self ): - """Browse the available tool sheds in this Galaxy instance and preview the freebayes repository.""" + """Browse the available tool sheds in this Galaxy instance and preview the bismark repository.""" self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) - self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0070 Repository With Invalid Tool' ] ) - category = test_db_util.get_category_by_name( 'Test 0070 Repository With Invalid Tool' ) + self.browse_tool_shed( url=self.url, strings_displayed=[ category_name ] ) + category = test_db_util.get_category_by_name( category_name ) self.browse_category( category, strings_displayed=[ repository_name ] ) self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[ repository_name ] ) def test_0015_install_freebayes_repository( self ): '''Install the test repository without installing tool dependencies.''' self.install_repository( repository_name, common.test_user_1_name, - 'Test 0070 Repository With Invalid Tool', + category_name, install_tool_dependencies=False, new_tool_panel_section='test_1070' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) @@ -70,11 +73,9 @@ installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'simple expressions', 'Invalid tools' ], - strings_not_displayed=[ 'variant detector' ] ) + strings_displayed=[ 'methylation extractor', 'Invalid tools' ], + strings_not_displayed=[ 'bisulfite mapper' ] ) self.verify_tool_metadata_for_installed_repository( installed_repository ) self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] ) - assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % installed_repository.name - def test_0020_verify_installed_repository_metadata( self ): - '''Verify that resetting the metadata on an installed repository does not change the metadata.''' - self.verify_installed_repository_metadata_unchanged( repository_name, common.test_user_1_name ) + assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % \ + installed_repository.name diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py --- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -27,8 +27,8 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name='filtering_0000', - description="Galaxy's filtering tool", - long_description="Long description of Galaxy's filtering tool", + description="Galaxy's filtering tool for test 0000", + long_description="Long description of Galaxy's filtering tool for test 0000", owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ) ) if self.repository_is_new( repository ): @@ -56,8 +56,8 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=True ) strings_not_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.installed_changeset_revision ] + installed_repository.description, + installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0020_reinstall_filtering_repository( self ): '''Reinstall the filtering repository.''' @@ -77,8 +77,8 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=False ) strings_not_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.installed_changeset_revision ] + installed_repository.description, + installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0030_reactivate_filtering_repository( self ): '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.''' diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/test_data/bismark/bismark.tar Binary file test/tool_shed/test_data/bismark/bismark.tar has changed diff -r eb67f0b3555df7e249c2d8715d75c598dc25055b -r ad04a8d066e7092fb73d5469f1935196923b8ab3 test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml --- /dev/null +++ b/test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml @@ -0,0 +1,306 @@ +<tool id="bismark_methylation_extractor" name="Bismark" version="0.7.7.3"> +  + <description>methylation extractor</description> +  + <requirements> + <requirement type="set_environment">SCRIPT_PATH</requirement> + <requirement type="package" version="0.12.8">bowtie</requirement> + <requirement type="package" version="2.0.0-beta7">bowtie2</requirement> + </requirements> + <parallelism method="basic"></parallelism> + <command interpreter="python"> + bismark_methylation_extractor.py + + --infile $input + + --bismark_path \$SCRIPT_PATH + + #if $singlePaired.sPaired == "single": + --single-end + #else: + --paired-end + $no_overlap + #end if + + #if str($ignore_bps) != "0": + --ignore $ignore_bps + #end if + + #if $report: + --report-file $o_report + #end if + + #if $comprehensive: + --comprehensive + #end if + + #if $merge_non_cpg: + --merge-non-cpg + #end if + + #if $compress: + --compress $compressed_output + #else: + #if $comprehensive == False and $merge_non_cpg == False: + ##twelfe files + --cpg_ot $cpg_ot + --chg_ot $chg_ot + --chh_ot $chh_ot + --cpg_ctot $cpg_ctot + --chg_ctot $chg_ctot + --chh_ctot $chh_ctot + --cpg_ob $cpg_ob + --chg_ob $chg_ob + --chh_ob $chh_ob + --cpg_ctob $cpg_ctob + --chg_ctob $chg_ctob + --chh_ctob $chh_ctob + #elif $merge_non_cpg and $comprehensive: + ## two files + --non_cpg_context $non_cpg_context + --cpg_context $cpg_context + #elif $comprehensive: + ## three files + --cpg_context $cpg_context + --chg_context $chg_context + --chh_context $chh_context + #elif $merge_non_cpg: + ## eight files + --non_cpg_context_ctot $non_cpg_context_ctot + --non_cpg_context_ot $non_cpg_context_ot + --non_cpg_context_ob $non_cpg_context_ob + --non_cpg_context_ctob $non_cpg_context_ctob + --cpg_ot $cpg_ot + --cpg_ctot $cpg_ctot + --cpg_ob $cpg_ob + --cpg_ctob $cpg_ctob + #end if + ## end compress + #end if + + </command> + <inputs> +  + <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" /> + <conditional name="singlePaired"> + <param name="sPaired" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single" /> + <when value="paired"> + <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" /> + </when> + </conditional> + + <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" /> + <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info +into context-dependent output files" help="" /> + <param name="merge_non_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all non-CpG contexts into one file" help="This will produce eight strand-specific output files, or two output files in comprehensive mode." /> + <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Short methylation summary output" /> + <param name="compress" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Compress all result files and output one single file" /> + + </inputs> + <outputs> +  + <data format="tabular" name="o_report" label="${tool.name} on ${on_string}: Report file"> + <filter> ( report is True ) </filter> + </data> + +  + <data format="tabular" name="cpg_ot" label="${tool.name} on ${on_string}: CpG original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ot" label="${tool.name} on ${on_string}: CHG original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ot" label="${tool.name} on ${on_string}: CHH original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="cpg_ctot" label="${tool.name} on ${on_string}: CpG complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ctot" label="${tool.name} on ${on_string}: CHG complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ctot" label="${tool.name} on ${on_string}: CHH complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + + <data format="tabular" name="cpg_ob" label="${tool.name} on ${on_string}: CpG original bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ob" label="${tool.name} on ${on_string}: CHG original bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ob" label="${tool.name} on ${on_string}: CHH original bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="cpg_ctob" label="${tool.name} on ${on_string}: CpG complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chg_ctob" label="${tool.name} on ${on_string}: CHG complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_ctob" label="${tool.name} on ${on_string}: CHH complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_CpG == False) </filter> + </data> + +  + <data format="tabular" name="cpg_context" label="${tool.name} on ${on_string}: CpG context dependent"> + <filter> ( compress == False and comprehensive) </filter> + </data> + <data format="tabular" name="chg_context" label="${tool.name} on ${on_string}: CHG context dependent"> + <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter> + </data> + <data format="tabular" name="chh_context" label="${tool.name} on ${on_string}: CHH context dependent"> + <filter> ( compress == False and comprehensive and merge_non_CpG == False) </filter> + </data> + + <data format="tabular" name="non_cpg_context" label="${tool.name} on ${on_string}: Non CpG context dependent"> + <filter> ( compress == False and comprehensive and merge_non_cpg) </filter> + </data> + + <data format="tabular" name="non_cpg_context_ot" label="${tool.name} on ${on_string}: Non CpG context dependent on original top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + <data format="tabular" name="non_cpg_context_ctot" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + <data format="tabular" name="non_cpg_context_ob" label="${tool.name} on ${on_string}: Non CpG context dependent on bottom top strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + <data format="tabular" name="non_cpg_context_ctob" label="${tool.name} on ${on_string}: Non CpG context dependent on complementary to bottom strand"> + <filter> ( compress == False and comprehensive == False and merge_non_cpg) </filter> + </data> + + <data format="gzipped" name="compressed_output" label="${tool.name} on ${on_string}: Result archive."> + <filter> ( compress ) </filter> + </data> + </outputs> + + <tests> + </tests> + + <help> + +**What it does** + +The following is a brief description of all options to control the Bismark_ +methylation extractor. The script reads in a bisulfite read alignment results file +produced by the Bismark bisulfite mapper and extracts the methylation information +for individual cytosines. This information is found in the methylation call field +which can contain the following characters: + + + - X = for methylated C in CHG context (was protected) + - x = for not methylated C CHG (was converted) + - H = for methylated C in CHH context (was protected) + - h = for not methylated C in CHH context (was converted) + - Z = for methylated C in CpG context (was protected) + - z = for not methylated C in CpG context (was converted) + - . = for any bases not involving cytosines + + +The methylation extractor outputs result files for cytosines in CpG, CHG and CHH +context (this distinction is actually already made in Bismark itself). As the methylation +information for every C analysed can produce files which easily have tens or even hundreds of +millions of lines, file sizes can become very large and more difficult to handle. The C +methylation info additionally splits cytosine methylation calls up into one of the four possible +strands a given bisulfite read aligned against: + + - OT = original top strand + - CTOT = complementary to original top strand + + - OB = original bottom strand + - CTOB = complementary to original bottom strand + +Thus, by default twelve individual output files are being generated per input file (unless +--comprehensive is specified, see below). The output files can be imported into a genome +viewer, such as SeqMonk, and re-combined into a single data group if desired (in fact +unless the bisulfite reads were generated preserving directionality it doesn't make any +sense to look at the data in a strand-specific manner). Strand-specific output files can +optionally be skipped, in which case only three output files for CpG, CHG or CHH context +will be generated. For both the strand-specific and comprehensive outputs there is also +the option to merge both non-CpG contexts (CHG and CHH) into one single non-CpG context. + + +.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ + + +It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2. + +------- + +**Bismark settings** + +All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin. + +------ + +**Outputs** + +The output files are in the following format (tab delimited):: + + + Column Description + -------- -------------------------------------------------------- + 1 seq-ID + 2 strand + 3 chromosome + 4 position + 5 methylation call + + + * Methylated cytosines receive a '+' orientation, + * Unmethylated cytosines receive a '-' orientation. + +------ + +**OPTIONS** + +Input:: + + -s/--single-end Input file(s) are Bismark result file(s) generated from single-end + read data. Specifying either --single-end or --paired-end is + mandatory. + + -p/--paired-end Input file(s) are Bismark result file(s) generated from paired-end + read data. Specifying either --paired-end or --single-end is + mandatory. + + --no_overlap For paired-end reads it is theoretically possible that read_1 and + read_2 overlap. This option avoids scoring overlapping methylation + calls twice. Whilst this removes a bias towards more methylation calls + towards the center of sequenced fragments it can de facto remove + a good proportion of the data. + + --ignore INT Ignore the first INT bp at the 5' end of each read when processing the + methylation call string. This can remove e.g. a restriction enzyme site + at the start of each read. + +Output:: + + --comprehensive Specifying this option will merge all four possible strand-specific + methylation info into context-dependent output files. The default + contexts are: + - CpG context + - CHG context + - CHH context + + --merge_non_CpG This will produce two output files (in --comprehensive mode) or eight + strand-specific output files (default) for Cs in + - CpG context + - non-CpG context + + --report Prints out a short methylation summary as well as the paramaters used to run + this script. + + + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: history panel: panel was not showing deleted datasets when a dataset was purged (even when set to 'include deleted datasets') - fix by using purge_async; history panel: fix history-options menu checkbox with new font awesome class format; pack scripts
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb67f0b3555d/ changeset: eb67f0b3555d user: carlfeberhard date: 2013-01-04 16:57:18 summary: history panel: panel was not showing deleted datasets when a dataset was purged (even when set to 'include deleted datasets') - fix by using purge_async; history panel: fix history-options menu checkbox with new font awesome class format; pack scripts affected #: 6 files diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -32,6 +32,38 @@ ]; }, + /** Set up js behaviors, event handlers for elements within the given container. + * Overridden from hda-base. + * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) + */ + _setUpBehaviors : function( $container ){ + //TODO: ideally this would be a DELETE call to the api + // using purge async for now + HDABaseView.prototype._setUpBehaviors.call( this, $container ); + + // use purge_async with an ajax call + var hdaView = this, + purge_url = this.urls.purge, + purge_link = $container.find( '#historyItemPurger-' + this.model.get( 'id' ) ); + if( purge_link ){ + //TODO: remove href from template + purge_link.attr( 'href', [ "javascript", "void(0)" ].join( ':' ) ); + purge_link.click( function( event ){ + //TODO??: confirm? + var ajaxPromise = jQuery.ajax( purge_url ); + ajaxPromise.success( function( message, status, responseObj ){ + hdaView.model.set( 'purged', true ); + }); + ajaxPromise.error( function( error, status, message ){ + //TODO: Exception messages are hidden within error page + //!NOTE: that includes the 'Removal of datasets by users is not allowed in this Galaxy instance.' + alert( '(' + error.status + ') Unable to purge this dataset:\n' + message ); + }); + }); + } + //TODO: same with undelete_async + }, + // ......................................................................... RENDER WARNINGS /** Render any hda warnings including: is deleted, is purged, is hidden. * Overrides _render_warnings to include links to further actions (undelete, etc.)). diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true)});f.error(function(h,g,i){alert("("+h.status+") Unable to purge this dataset:\n"+i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/packed/templates/compiled/template-popupmenu-menu.js --- a/static/scripts/packed/templates/compiled/template-popupmenu-menu.js +++ b/static/scripts/packed/templates/compiled/template-popupmenu-menu.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-popupmenu-menu"]=b(function(f,s,q,l,x){q=q||f.helpers;var r="",i,h,d="function",c=this.escapeExpression,p=this;function o(B,A){var y="",z;y+="\n ";z=B.options;z=q.each.call(B,z,{hash:{},inverse:p.noop,fn:p.program(2,n,A)});if(z||z===0){y+=z}y+="\n";return y}function n(B,A){var y="",z;y+="\n 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class="dropdown-menu">\n';i=s.options;i=i==null||i===false?i:i.length;i=q["if"].call(s,i,{hash:{},inverse:p.program(17,t,x),fn:p.program(1,o,x)});if(i||i===0){r+=i}r+="\n</ul>";return r})})(); \ No newline at end of file diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/templates/compiled/template-popupmenu-menu.js --- a/static/scripts/templates/compiled/template-popupmenu-menu.js +++ b/static/scripts/templates/compiled/template-popupmenu-menu.js @@ -96,7 +96,7 @@ function program15(depth0,data) { - return "<span class=\"ficon ok\"></span>";} + return "<span class=\"fa-icon-ok\"></span>";} function program17(depth0,data) { diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b static/scripts/templates/ui-templates.html --- a/static/scripts/templates/ui-templates.html +++ b/static/scripts/templates/ui-templates.html @@ -30,7 +30,7 @@ {{!NOTE: changed from # to void fn }} <li><a href="{{#if href }}{{ href }}{{else}}javascript:void(0);{{/if}}" {{#if href }}target="{{ target }}"{{/if}} class="popupmenu-option"> - {{#if checked }}<span class="ficon ok"></span>{{/if}} + {{#if checked }}<span class="fa-icon-ok"></span>{{/if}} {{{ html }}} </a></li> {{/if}} diff -r 564c49962741608b073e9c3fb87b57f7e8aa454b -r eb67f0b3555df7e249c2d8715d75c598dc25055b templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -124,7 +124,9 @@ url_dict = { # ................................................................ warning message links - 'purge' : h.url_for( controller='dataset', action='purge', + #'purge' : h.url_for( controller='dataset', action='purge', + # dataset_id=encoded_id_template ), + 'purge' : h.url_for( controller='dataset', action='purge_async', dataset_id=encoded_id_template ), #TODO: hide (via api) 'unhide' : h.url_for( controller='dataset', action='unhide', @@ -143,7 +145,6 @@ dataset_id=encoded_id_template ), #TODO: via api - #TODO: show deleted handled by history 'delete' : h.url_for( controller='dataset', action='delete_async', dataset_id=encoded_id_template ), # ................................................................ download links (and associated meta files), @@ -203,7 +204,6 @@ <%def name="get_hdas( history_id, hdas )"><% #BUG: one inaccessible dataset will error entire list - if not hdas: return '[]' # rather just use the history.id (wo the datasets), but... @@ -256,7 +256,6 @@ "mvc/dataset/hda-model", "mvc/dataset/hda-base", "mvc/dataset/hda-edit", - ##"mvc/dataset/hda-readonly", ##"mvc/tags", "mvc/annotations" @@ -302,9 +301,15 @@ $(function(){ galaxyPageSetUp(); - //Galaxy.historyFrame = window; - var debugging = ( new PersistantStorage( '__history_panel' ).get( 'debugging' ) || false ); + //NOTE: for debugging on non-local instances (main/test) + // 1. load history panel in own tab + // 2. from console: new PersistantStorage( '__history_panel' ).set( 'debugging', true ) + // -> history panel and hdas will display console logs in console + var debugging = false; + if( jQuery.jStorage.get( '__history_panel' ) ){ + debugging = new PersistantStorage( '__history_panel' ).get( 'debugging' ); + } // ostensibly, this is the App // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it... Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Make sure metata is set for repositories in the tool shed that contain only invalid tools.
by Bitbucket 04 Jan '13

04 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/564c49962741/ changeset: 564c49962741 user: greg date: 2013-01-04 15:17:47 summary: Make sure metata is set for repositories in the tool shed that contain only invalid tools. affected #: 1 file diff -r 8d7d70348e526c64168392501922aa56f45d0a84 -r 564c49962741608b073e9c3fb87b57f7e8aa454b lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1056,6 +1056,7 @@ tool, valid, error_message = load_tool_from_config( app, full_path ) if tool is None: if not valid: + invalid_tool_configs.append( name ) invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_copy_paths ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix bugs that prevented creating a Circster visualization from a dataset.
by Bitbucket 03 Jan '13

03 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d7d70348e52/ changeset: 8d7d70348e52 user: jgoecks date: 2013-01-04 04:07:55 summary: Fix bugs that prevented creating a Circster visualization from a dataset. affected #: 1 file diff -r d7475647cbb6a1c70218049fadc24ed1651d845a -r 8d7d70348e526c64168392501922aa56f45d0a84 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -725,12 +725,25 @@ Display a circster visualization. """ + # Get dataset to add. + if dataset_id: + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + # Get/create vis. if id: # Display existing viz. vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) else: # Create new viz. + if not dbkey: + # If dbkey not specified, use dataset's dbkey. + dbkey = dataset.dbkey + if not dbkey or dbkey == '?': + # Circster requires a valid dbkey. + return trans.show_error_message( "You must set the dataset's dbkey to view it. You can set " + "a dataset's dbkey by clicking on the pencil icon and editing " + "its attributes.", use_panels=True ) + vis = self.create_visualization( trans, type="genome", dbkey=dbkey, save=False ) # Get the vis config and work with it from here on out. Working with the @@ -739,12 +752,10 @@ viz_config = self.get_visualization_config( trans, vis ) # Add dataset if specified. - if dataset_id: - dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + if dataset: viz_config[ 'tracks' ].append( self.get_new_track_config( trans, dataset ) ) # Get genome info. - dbkey = viz_config[ 'dbkey' ] chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) genome = { 'dbkey': dbkey, 'chroms_info': chroms_info } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 12 new changesets
by Bitbucket 03 Jan '13

03 Jan '13

12 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de91f945a824/ changeset: de91f945a824 user: natefoo date: 2013-01-03 22:29:11 summary: Backed out 9ec94e5d6a28 affected #: 1 file <HgDiff de91f945a824:4c96179f6fe1 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/de8a5f5e064e/ changeset: de8a5f5e064e user: natefoo date: 2013-01-03 22:29:41 summary: backout 2f5544be71d1 affected #: 1 file <HgDiff de8a5f5e064e:de91f945a824 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/b78fc8715c33/ changeset: b78fc8715c33 user: natefoo date: 2013-01-03 22:30:07 summary: Backout 875ac898df00 affected #: 2 files <HgDiff b78fc8715c33:de8a5f5e064e ['lib/galaxy/jobs/runners/lwr.py']><HgDiff b78fc8715c33:de8a5f5e064e ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/09152e37a3e5/ changeset: 09152e37a3e5 user: natefoo date: 2013-01-03 22:30:21 summary: backout 6265bf3f27ad affected #: 1 file <HgDiff 09152e37a3e5:b78fc8715c33 ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/01ac1286291b/ changeset: 01ac1286291b user: natefoo date: 2013-01-03 22:30:32 summary: backout 5822038f8c96 affected #: 3 files <HgDiff 01ac1286291b:09152e37a3e5 ['lib/galaxy/jobs/runners/__init__.py']><HgDiff 01ac1286291b:09152e37a3e5 ['lib/galaxy/jobs/runners/lwr.py']><HgDiff 01ac1286291b:09152e37a3e5 ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/1e8a57a3004d/ changeset: 1e8a57a3004d user: natefoo date: 2013-01-03 22:30:42 summary: backout 50c1edba7fe0 affected #: 1 file <HgDiff 1e8a57a3004d:01ac1286291b ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/77e141b92b59/ changeset: 77e141b92b59 user: natefoo date: 2013-01-03 22:32:06 summary: backout 93dd6202175a affected #: 2 files <HgDiff 77e141b92b59:1e8a57a3004d ['lib/galaxy/jobs/runners/lwr.py']><HgDiff 77e141b92b59:1e8a57a3004d ['lib/galaxy/jobs/runners/lwr_client/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/f5477485ee0c/ changeset: f5477485ee0c user: natefoo date: 2013-01-03 22:32:17 summary: backout e4adc9ad0bb7 affected #: 1 file <HgDiff f5477485ee0c:77e141b92b59 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/9ca4a534c126/ changeset: 9ca4a534c126 user: natefoo date: 2013-01-03 22:32:29 summary: backout e6676636cfe7 affected #: 1 file <HgDiff 9ca4a534c126:f5477485ee0c ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/adb5231d1a5c/ changeset: adb5231d1a5c user: natefoo date: 2013-01-03 22:32:43 summary: backout 8c6cf637058a affected #: 1 file <HgDiff adb5231d1a5c:9ca4a534c126 ['lib/galaxy/jobs/runners/lwr.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/c382028a4f5b/ changeset: c382028a4f5b user: natefoo date: 2013-01-03 22:32:55 summary: backout ab827b2c7907 affected #: 1 file <HgDiff c382028a4f5b:adb5231d1a5c ['lib/galaxy/jobs/runners/__init__.py']> https://bitbucket.org/galaxy/galaxy-central/changeset/d7475647cbb6/ changeset: d7475647cbb6 user: natefoo date: 2013-01-03 22:34:40 summary: merge affected #: 1 file <HgDiff d7475647cbb6:c382028a4f5b ['templates/workflow/editor.mako']> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits January 2013