1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/ee4a47ed5371/ changeset: ee4a47ed5371 user: greg date: 2012-03-21 22:50:25 summary: Fix for checker for certain tools eliminated from the distribution. affected #: 1 file

diff -r e439813f0748dd615b2a7ad18b5de9cbd68b4f9d -r ee4a47ed53712fe87c5372f667c9058147415c04 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -9,7 +9,7 @@ from galaxy.tool_shed import install_manager from galaxy.tool_shed.migrate.common import *

-def check_for_missing_tools( tool_panel_config, latest_tool_migration_script_number ): +def check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ): # Get the 000x_tools.xml file associated with the current migrate_tools version number. tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. @@ -20,17 +20,18 @@ if elem.tag == 'repository': for tool_elem in elem.findall( 'tool' ): migrated_tool_configs.append( tool_elem.get( 'file' ) ) - # Parse the proprietary tool_panel_config (the default is tool_conf.xml) and generate the list of missing tool config file names. + # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. missing_tool_configs = [] - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ) - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs ) + for tool_panel_config in tool_panel_configs: + tree = util.parse_xml( tool_panel_config ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ) + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs ) return missing_tool_configs def check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ): file_path = elem.get( 'file', None )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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