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Fix for checker for certain tools eliminated from the distribution.

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Greg Von Kuster
2012-03-21 17:50:25 -04:00
parent 6dc657420f
commit af77721f3e
1 changed files with 12 additions and 11 deletions
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lib/galaxy/tool_shed/migrate/common.py
+12 -11
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@@ -9,7 +9,7 @@ import galaxy.tool_shed.tool_shed_registry
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 @@ def check_for_missing_tools( tool_panel_config, latest_tool_migration_script_num
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 )