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Fix integrated_tool_panel dictionary before writing integrated_tool_panel.xml to keep tools/workflows in multiple sections

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Richard Burhans
2013-09-17 14:37:36 -04:00
parent 823634ab78
commit 29f96ebd3f
1 changed files with 16 additions and 0 deletions
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lib/galaxy/tools/__init__.py
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@@ -154,8 +154,24 @@ class ToolBox( object, Dictifiable ):
# This will cover cases where the Galaxy administrator manually edited one or more of the tool panel
# config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel
# will be False when things like functional tests are the caller.
self.fix_integrated_tool_panel_dict()
self.write_integrated_tool_panel_config_file()
def fix_integrated_tool_panel_dict( self ):
# HACK: instead of fixing after the fact, I suggest some combination of:
# 1) adjusting init_tools() and called methods to get this right
# 2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml
for key, value in self.integrated_tool_panel.iteritems():
if key.startswith( 'section_' ):
for section_key, section_value in value.elems.iteritems():
if section_value is None:
if section_key.startswith( 'tool_' ):
tool_id = section_key[5:]
value.elems[section_key] = self.tools_by_id.get( tool_id )
elif section_key.startswith( 'workflow_' ):
workflow_id = section_key[9:]
value.elems[section_key] = self.workflows_by_id.get( workflow_id )
def init_tools( self, config_filename ):
"""
Read the configuration file and load each tool. The following tags are currently supported: