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111 lines
4.9 KiB
Python
111 lines
4.9 KiB
Python
import new
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import tempfile
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import os.path
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import shutil
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from test_toolbox import ToolTestCase
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from base.interactor import stage_data_in_history
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import logging
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log = logging.getLogger( __name__ )
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data_managers = None
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class DataManagerToolTestCase( ToolTestCase ):
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"""Test case that runs Data Manager tests based on a `galaxy.tools.test.ToolTest`"""
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def do_it( self, testdef ):
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"""
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Run through a tool test case.
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"""
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shed_tool_id = self.shed_tool_id
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self._handle_test_def_errors( testdef )
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galaxy_interactor = self._galaxy_interactor( testdef )
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test_history = galaxy_interactor.new_history() # history where inputs will be put, if any
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stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
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galaxy_interactor.run_tool( testdef, test_history ) # test_history will have inputs only, outputs are placed in the specialized data manager history
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# FIXME: Move history determination and switching into the interactor
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data_manager_history = None
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for assoc in reversed( test_history.user.data_manager_histories ):
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if not assoc.history.deleted:
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data_manager_history = assoc.history
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break
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self.switch_history( id=self.security.encode_id( data_manager_history.id ) )
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data_list = self.get_history_as_data_list()
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# end
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self.assertTrue( data_list )
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self._verify_outputs( testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor )
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self.switch_history( id=self.security.encode_id( test_history.id ) )
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galaxy_interactor.delete_history( test_history )
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def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None ):
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"""
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If the module level variable `data_managers` is set, generate `DataManagerToolTestCase`
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classes for all of its tests and put them into this modules globals() so
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they can be discovered by nose.
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"""
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if data_managers is None:
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log.warning( 'data_managers was not set for Data Manager functional testing. Will not test.' )
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return
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# Push all the data_managers tests to module level
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G = globals()
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# Eliminate all previous tests from G.
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for key, val in G.items():
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if key.startswith( 'TestForDataManagerTool_' ):
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del G[ key ]
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# first we will loop through data table loc files and copy them to temporary location, then swap out filenames:
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for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().iteritems():
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for filename, value in list( data_table.filenames.items() ):
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new_filename = tempfile.NamedTemporaryFile( prefix=os.path.basename( filename ), dir=tmp_dir ).name
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try:
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shutil.copy( filename, new_filename )
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except IOError, e:
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log.warning( "Failed to copy '%s' to '%s', will create empty file at '%s': %s", filename, new_filename, new_filename, e )
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open( new_filename, 'wb' ).close()
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if 'filename' in value:
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value[ 'filename' ] = new_filename
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del data_table.filenames[ filename ] # remove filename:value pair
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data_table.filenames[ new_filename ] = value # add new value by
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for i, ( data_manager_id, data_manager ) in enumerate( data_managers.data_managers.iteritems() ):
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tool = data_manager.tool
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if not tool:
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log.warning( "No Tool has been specified for Data Manager: %s", data_manager_id )
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if tool.tests:
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# fixme data_manager.tool_shed_repository_info_dict should be filled when is toolshed based
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shed_tool_id = None if not testing_shed_tools else tool.id
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# Create a new subclass of ToolTestCase, dynamically adding methods
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# named test_tool_XXX that run each test defined in the tool config.
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name = "TestForDataManagerTool_" + data_manager_id.replace( ' ', '_' )
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baseclasses = ( DataManagerToolTestCase, )
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namespace = dict()
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for j, testdef in enumerate( tool.tests ):
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def make_test_method( td ):
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def test_tool( self ):
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self.do_it( td )
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return test_tool
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test_method = make_test_method( testdef )
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test_method.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name )
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namespace[ 'test_tool_%06d' % j ] = test_method
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namespace[ 'shed_tool_id' ] = shed_tool_id
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namespace[ 'master_api_key' ] = master_api_key
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namespace[ 'user_api_key' ] = user_api_key
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# The new.classobj function returns a new class object, with name name, derived
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# from baseclasses (which should be a tuple of classes) and with namespace dict.
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new_class_obj = new.classobj( name, baseclasses, namespace )
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G[ name ] = new_class_obj
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