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Merge pull request #4387 from jmchilton/tool_unit_test_cleanup

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Cleanup of Unit Test Code for Loading Tools
This commit is contained in:
Björn Grüning
2017-08-16 14:55:14 +02:00
committed by GitHub
parent 8eb487e7c1 7de7f3f63a
commit b6f0600e98
8 changed files with 76 additions and 104 deletions
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lib/galaxy/tools/__init__.py
+23 -16
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@@ -191,6 +191,24 @@ class ToolNotFoundException( Exception ):
pass
def create_tool_from_source( app, tool_source, config_file=None, **kwds ):
# Allow specifying a different tool subclass to instantiate
tool_module = tool_source.parse_tool_module()
if tool_module is not None:
module, cls = tool_module
mod = __import__( module, globals(), locals(), [cls] )
ToolClass = getattr( mod, cls )
elif tool_source.parse_tool_type():
tool_type = tool_source.parse_tool_type()
ToolClass = tool_types.get( tool_type )
else:
# Normal tool
root = getattr( tool_source, 'root', None )
ToolClass = Tool
tool = ToolClass( config_file, tool_source, app, **kwds )
return tool
class ToolBox( BaseGalaxyToolBox ):
""" A derivative of AbstractToolBox with knowledge about Tool internals -
how to construct them, action types, dependency management, etc....
@@ -228,7 +246,7 @@ class ToolBox( BaseGalaxyToolBox ):
# Deprecated method, TODO - eliminate calls to this in test/.
return self._tools_by_id
def create_tool( self, config_file, repository_id=None, guid=None, **kwds ):
def create_tool( self, config_file, **kwds ):
try:
tool_source = get_tool_source(
config_file,
@@ -239,21 +257,10 @@ class ToolBox( BaseGalaxyToolBox ):
# capture and log parsing errors
global_tool_errors.add_error(config_file, "Tool XML parsing", e)
raise e
# Allow specifying a different tool subclass to instantiate
tool_module = tool_source.parse_tool_module()
if tool_module is not None:
module, cls = tool_module
mod = __import__( module, globals(), locals(), [cls] )
ToolClass = getattr( mod, cls )
elif tool_source.parse_tool_type():
tool_type = tool_source.parse_tool_type()
ToolClass = tool_types.get( tool_type )
else:
# Normal tool
root = getattr( tool_source, 'root', None )
ToolClass = Tool
tool = ToolClass( config_file, tool_source, self.app, guid=guid, repository_id=repository_id, **kwds )
return tool
return self._create_tool_from_source( tool_source, config_file=config_file, **kwds )
def _create_tool_from_source( self, tool_source, **kwds ):
return create_tool_from_source( self.app, tool_source, **kwds)
def get_tool_components( self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ):
"""