swh:1:snp:68efb3baf28256c952b30ae9ecf5cb4fac86eafb
Tip revision: 5677c2ee4fce70c9898ea5e6cae125b6147ae36a authored by Nate Coraor on 24 February 2016, 20:29:14 UTC
Update version to 16.01
Update version to 16.01
Tip revision: 5677c2e
test_data_managers.py
import new
import tempfile
import os.path
import shutil
from test_toolbox import ToolTestCase
from base.interactor import stage_data_in_history
import logging
log = logging.getLogger( __name__ )
data_managers = None
class DataManagerToolTestCase( ToolTestCase ):
"""Test case that runs Data Manager tests based on a `galaxy.tools.test.ToolTest`"""
def do_it( self, testdef ):
"""
Run through a tool test case.
"""
shed_tool_id = self.shed_tool_id
self._handle_test_def_errors( testdef )
galaxy_interactor = self._galaxy_interactor( testdef )
test_history = galaxy_interactor.new_history() # history where inputs will be put, if any
stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
galaxy_interactor.run_tool( testdef, test_history ) # test_history will have inputs only, outputs are placed in the specialized data manager history
# FIXME: Move history determination and switching into the interactor
data_manager_history = None
for assoc in reversed( test_history.user.data_manager_histories ):
if not assoc.history.deleted:
data_manager_history = assoc.history
break
self.switch_history( id=self.security.encode_id( data_manager_history.id ) )
data_list = self.get_history_as_data_list()
# end
self.assertTrue( data_list )
self._verify_outputs( testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor )
self.switch_history( id=self.security.encode_id( test_history.id ) )
galaxy_interactor.delete_history( test_history )
def build_tests( tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None ):
"""
If the module level variable `data_managers` is set, generate `DataManagerToolTestCase`
classes for all of its tests and put them into this modules globals() so
they can be discovered by nose.
"""
if data_managers is None:
log.warning( 'data_managers was not set for Data Manager functional testing. Will not test.' )
return
# Push all the data_managers tests to module level
G = globals()
# Eliminate all previous tests from G.
for key, val in G.items():
if key.startswith( 'TestForDataManagerTool_' ):
del G[ key ]
# first we will loop through data table loc files and copy them to temporary location, then swap out filenames:
for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().iteritems():
for filename, value in list( data_table.filenames.items() ):
new_filename = tempfile.NamedTemporaryFile( prefix=os.path.basename( filename ), dir=tmp_dir ).name
try:
shutil.copy( filename, new_filename )
except IOError, e:
log.warning( "Failed to copy '%s' to '%s', will create empty file at '%s': %s", filename, new_filename, new_filename, e )
open( new_filename, 'wb' ).close()
if 'filename' in value:
value[ 'filename' ] = new_filename
del data_table.filenames[ filename ] # remove filename:value pair
data_table.filenames[ new_filename ] = value # add new value by
for i, ( data_manager_id, data_manager ) in enumerate( data_managers.data_managers.iteritems() ):
tool = data_manager.tool
if not tool:
log.warning( "No Tool has been specified for Data Manager: %s", data_manager_id )
if tool.tests:
# fixme data_manager.tool_shed_repository_info_dict should be filled when is toolshed based
shed_tool_id = None if not testing_shed_tools else tool.id
# Create a new subclass of ToolTestCase, dynamically adding methods
# named test_tool_XXX that run each test defined in the tool config.
name = "TestForDataManagerTool_" + data_manager_id.replace( ' ', '_' )
baseclasses = ( DataManagerToolTestCase, )
namespace = dict()
for j, testdef in enumerate( tool.tests ):
def make_test_method( td ):
def test_tool( self ):
self.do_it( td )
return test_tool
test_method = make_test_method( testdef )
test_method.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name )
namespace[ 'test_tool_%06d' % j ] = test_method
namespace[ 'shed_tool_id' ] = shed_tool_id
namespace[ 'master_api_key' ] = master_api_key
namespace[ 'user_api_key' ] = user_api_key
# The new.classobj function returns a new class object, with name name, derived
# from baseclasses (which should be a tuple of classes) and with namespace dict.
new_class_obj = new.classobj( name, baseclasses, namespace )
G[ name ] = new_class_obj