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Allow for an arbitrary number of tool_data_table_config_path files to be defined in ini file. Values are comma separated.

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This commit is contained in:
Daniel Blankenberg
2014-05-14 11:52:20 -04:00
parent 486dc41639
commit 3f87380dea
2 changed files with 16 additions and 13 deletions
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lib/galaxy/config.py
+1 -1
View File
@@ -102,7 +102,7 @@ class Configuration( object ):
self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root )
else:
self.shed_tool_data_path = self.tool_data_path
self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
self.tool_data_table_config_path = [ resolve_path( x, self.root ) for x in kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ).split( ',' ) ]
self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root )
self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) )
self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) )
lib/galaxy/tools/data/__init__.py
+15 -12
View File
@@ -56,19 +56,22 @@ class ToolDataTableManager( object ):
3. When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local
Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example:
"""
tree = util.parse_xml( config_filename )
root = tree.getroot()
table_elems = []
for table_elem in root.findall( 'table' ):
table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config )
table_elems.append( table_elem )
if table.name not in self.data_tables:
self.data_tables[ table.name ] = table
log.debug( "Loaded tool data table '%s'", table.name )
else:
log.debug( "Loading another instance of data table '%s', attempting to merge content.", table.name )
self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) #only merge content, do not persist to disk, do not allow duplicate rows when merging
# FIXME: This does not account for an entry with the same unique build ID, but a different path.
if not isinstance( config_filename, list ):
config_filename = [ config_filename ]
for filename in config_filename:
tree = util.parse_xml( filename )
root = tree.getroot()
for table_elem in root.findall( 'table' ):
table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config )
table_elems.append( table_elem )
if table.name not in self.data_tables:
self.data_tables[ table.name ] = table
log.debug( "Loaded tool data table '%s'", table.name )
else:
log.debug( "Loading another instance of data table '%s', attempting to merge content.", table.name )
self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) #only merge content, do not persist to disk, do not allow duplicate rows when merging
# FIXME: This does not account for an entry with the same unique build ID, but a different path.
return table_elems
def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False ):