1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/6498eb3e409a/ changeset: 6498eb3e409a user: greg date: 2012-06-14 21:46:36 summary: Fixes for recent changes to fix ToolDataTableManager to handle defined subdirectory locations in the Galaxy config. affected #: 6 files

diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -74,7 +74,7 @@ # Genomes self.genomes = Genomes( self ) # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path, self.config.tool_data_table_config_path ) # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs:

diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/jobs/deferred/genome_transfer.py --- a/lib/galaxy/jobs/deferred/genome_transfer.py +++ b/lib/galaxy/jobs/deferred/genome_transfer.py @@ -33,7 +33,7 @@ self.app = app self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__'] self.sa_session = app.model.context.current - tdtman = ToolDataTableManager() + tdtman = ToolDataTableManager( app.config.tool_data_path ) xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path ) for node in xmltree: table = node.get('name')

diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/jobs/deferred/liftover_transfer.py --- a/lib/galaxy/jobs/deferred/liftover_transfer.py +++ b/lib/galaxy/jobs/deferred/liftover_transfer.py @@ -14,7 +14,6 @@

from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.basic import DataToolParameter -from galaxy.tools.data import ToolDataTableManager

from galaxy.datatypes.checkers import *

diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -13,13 +13,14 @@

class ToolDataTableManager( object ): """Manages a collection of tool data tables""" - def __init__( self, config_filename=None ): + def __init__( self, tool_data_path, config_filename=None ): + self.tool_data_path = tool_data_path self.data_tables = {} # Store config elements for on-the-fly persistence. self.data_table_elems = [] self.data_table_elem_names = [] if config_filename: - self.load_from_config_file( config_filename ) + self.load_from_config_file( config_filename, self.tool_data_path ) def __getitem__( self, key ): return self.data_tables.__getitem__( key ) def __contains__( self, key ):

diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/tools/genome_index/__init__.py --- a/lib/galaxy/tools/genome_index/__init__.py +++ b/lib/galaxy/tools/genome_index/__init__.py @@ -66,7 +66,7 @@

if gitd: destination = None - tdtman = ToolDataTableManager() + tdtman = ToolDataTableManager( app.config.tool_data_path ) xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path ) for node in xmltree: table = node.get('name')

diff -r 19ed55acf0da8e8ed24f805035defab3009eec4f -r 6498eb3e409adb8ce71241f8e3b94bb23891f30f lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -37,7 +37,7 @@ # Tag handler self.tag_handler = CommunityTagHandler() # Tool data tables - never pass a config file here because the tool shed should always have an empty dictionary! - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager() + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) # The tool shed has no toolbox, but this attribute is still required. self.toolbox = None # Load security policy

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

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