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Merge pull request #1517 from jmchilton/tool_cache_fixes

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[16.01] Tool cache fixes
This commit is contained in:
Dannon Baker
2016-01-15 10:14:56 -05:00
parent 3d1ad5ad8d c143d659d4
commit ae2ee4a443
1 changed files with 5 additions and 5 deletions
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lib/galaxy/tools/toolbox/base.py
+5 -5
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@@ -172,7 +172,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
if integrated_panel_dict is None:
integrated_panel_dict = self._integrated_tool_panel
if item_type == 'tool':
self._load_tool_tag_set( item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, tool_path=tool_path, load_panel_dict=load_panel_dict, guid=guid, index=index )
self._load_tool_tag_set( item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, tool_path=tool_path, load_panel_dict=load_panel_dict, guid=guid, index=index, internal=internal )
elif item_type == 'workflow':
self._load_workflow_tag_set( item, panel_dict=panel_dict, integrated_panel_dict=integrated_panel_dict, load_panel_dict=load_panel_dict, index=index )
elif item_type == 'section':
@@ -539,7 +539,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
else:
remove_from_dict( self._tool_panel, self._integrated_tool_panel )
def _load_tool_tag_set( self, item, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None ):
def _load_tool_tag_set( self, item, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None, internal=False ):
try:
path = item.get( "file" )
repository_id = None
@@ -581,7 +581,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
repository_id = self.app.security.encode_id( tool_shed_repository.id )
# Else there is not yet a tool_shed_repository record, we're in the process of installing
# a new repository, so any included tools can be loaded into the tool panel.
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id, use_cached=internal )
if string_as_bool(item.get( 'hidden', False )):
tool.hidden = True
key = 'tool_%s' % str( tool.id )
@@ -723,7 +723,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
if tool_loaded or force_watch:
self._tool_watcher.watch_directory( directory, quick_load )
def load_tool( self, config_file, guid=None, repository_id=None, use_cached=True, **kwds ):
def load_tool( self, config_file, guid=None, repository_id=None, use_cached=False, **kwds ):
"""Load a single tool from the file named by `config_file` and return an instance of `Tool`."""
# Parse XML configuration file and get the root element
tool_cache = getattr( self.app, 'tool_cache', None )
@@ -791,7 +791,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
status = 'error'
else:
old_tool = self._tools_by_id[ tool_id ]
new_tool = self.load_tool( old_tool.config_file )
new_tool = self.load_tool( old_tool.config_file, use_cached=False )
# The tool may have been installed from a tool shed, so set the tool shed attributes.
# Since the tool version may have changed, we don't override it here.
new_tool.id = old_tool.id