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 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()
stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
# Once data is ready, run the tool and check the outputs - record API
# input, job info, tool run exception, as well as exceptions related to
# job output checking and register they with the test plugin so it can
# record structured information.
tool_inputs = None
job_stdio = None
job_output_exceptions = None
tool_execution_exception = None
try:
try:
tool_response = galaxy_interactor.run_tool( testdef, test_history )
data_list, jobs, tool_inputs = tool_response.outputs, tool_response.jobs, tool_response.inputs
data_collection_list = tool_response.output_collections
except RunToolException as e:
tool_inputs = e.inputs
tool_execution_exception = e
raise e
except Exception as e:
tool_execution_exception = e
raise e
self.assertTrue( data_list or data_collection_list )
try:
job_stdio = self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, data_collection_list, galaxy_interactor )
except JobOutputsError as e:
job_stdio = e.job_stdio
job_output_exceptions = e.output_exceptions
raise e
except Exception as e:
job_output_exceptions = [e]
raise e
finally:
job_data = {}
if tool_inputs is not None:
job_data["inputs"] = tool_inputs
if job_stdio is not None:
job_data["job"] = job_stdio
if job_output_exceptions:
job_data["output_problems"] = map(str, job_output_exceptions)
if tool_execution_exception:
job_data["execution_problem"] = str(tool_execution_exception)
register_job_data(job_data)
galaxy_interactor.delete_history( test_history )
def test_workflow( self, workflow_test_file=None ):
maxseconds = 120
workflow_test_file = workflow_test_file or WorkflowTestCase.workflow_test_file
assert workflow_test_file
workflow_test = parse_test_file( workflow_test_file )
galaxy_interactor = GalaxyWorkflowInteractor( self )
# Calling workflow https://github.com/jmchilton/blend4j/blob/master/src/test/java/com/github/jmchilton/blend4j/galaxy/WorkflowsTest.java
# Import workflow
workflow_id, step_id_map, output_defs = self.__import_workflow( galaxy_interactor, workflow_test.workflow )
# Stage data and history for workflow
test_history = galaxy_interactor.new_history()
stage_data_in_history( galaxy_interactor, workflow_test.test_data(), test_history )
# Build workflow parameters
uploads = galaxy_interactor.uploads
ds_map = {}
for step_index, input_dataset_label in workflow_test.input_datasets():
# Upload is {"src": "hda", "id": hid}
try:
upload = uploads[ workflow_test.upload_name( input_dataset_label ) ]
except KeyError:
raise AssertionError( "Failed to find upload with label %s in uploaded datasets %s" % ( input_dataset_label, uploads ) )
ds_map[ step_id_map[ step_index ] ] = upload
payload = {
"history": "hist_id=%s" % test_history,
"ds_map": dumps( ds_map ),
"workflow_id": workflow_id,
}
run_response = galaxy_interactor.run_workflow( payload ).json()
outputs = run_response[ 'outputs' ]
if not len( outputs ) == len( output_defs ):
msg_template = "Number of outputs [%d] created by workflow execution does not equal expected number from input file [%d]."
msg = msg_template % ( len( outputs ), len( output_defs ) )
raise AssertionError( msg )
galaxy_interactor.wait_for_ids( test_history, outputs )
for expected_output_def in workflow_test.outputs:
# Get the correct hid
name, outfile, attributes = expected_output_def
output_testdef = bunch.Bunch( name=name, outfile=outfile, attributes=attributes )
output_data = outputs[ int( name ) ]
try:
galaxy_interactor.verify_output( test_history, output_data, output_testdef=output_testdef, shed_tool_id=None, maxseconds=maxseconds )
except Exception:
for stream in ['stdout', 'stderr']:
stream_output = galaxy_interactor.get_job_stream( test_history, output_data, stream=stream )
print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True )
raise
def test_workflow( self, workflow_test_file=None ):
maxseconds = 120
workflow_test_file = workflow_test_file or WorkflowTestCase.workflow_test_file
assert workflow_test_file
workflow_test = parse_test_file( workflow_test_file )
galaxy_interactor = GalaxyWorkflowInteractor( self )
# Calling workflow https://github.com/jmchilton/blend4j/blob/master/src/test/java/com/github/jmchilton/blend4j/galaxy/WorkflowsTest.java
# Import workflow
workflow_id, step_id_map, output_defs = self.__import_workflow( galaxy_interactor, workflow_test.workflow )
# Stage data and history for workflow
test_history = galaxy_interactor.new_history()
stage_data_in_history( galaxy_interactor, workflow_test.test_data(), test_history )
# Build workflow parameters
uploads = galaxy_interactor.uploads
ds_map = {}
for step_index, input_dataset_label in workflow_test.input_datasets():
# Upload is {"src": "hda", "id": hid}
try:
upload = uploads[ workflow_test.upload_name( input_dataset_label ) ]
except KeyError:
raise AssertionError( "Failed to find upload with label %s in uploaded datasets %s" % ( input_dataset_label, uploads ) )
ds_map[ step_id_map[ step_index ] ] = upload
payload = {
"history": "hist_id=%s" % test_history,
"ds_map": dumps( ds_map ),
"workflow_id": workflow_id,
}
run_response = galaxy_interactor.run_workflow( payload ).json()
outputs = run_response[ 'outputs' ]
if not len( outputs ) == len( output_defs ):
msg_template = "Number of outputs [%d] created by workflow execution does not equal expected number from input file [%d]."
msg = msg_template % ( len( outputs ), len( output_defs ) )
raise AssertionError( msg )
galaxy_interactor.wait_for_ids( test_history, outputs )
for expected_output_def in workflow_test.outputs:
# Get the correct hid
name, outfile, attributes = expected_output_def
output_testdef = bunch.Bunch( name=name, outfile=outfile, attributes=attributes )
output_data = outputs[ int( name ) ]
try:
galaxy_interactor.verify_output( test_history, output_data, output_testdef=output_testdef, shed_tool_id=None, maxseconds=maxseconds )
except Exception:
for stream in ['stdout', 'stderr']:
stream_output = galaxy_interactor.get_job_stream( test_history, output_data, stream=stream )
print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True )
raise
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()
stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
data_list = galaxy_interactor.run_tool( testdef, test_history )
self.assertTrue( data_list )
self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor )
galaxy_interactor.delete_history( test_history )
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()
stage_data_in_history(galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id)
data_list = galaxy_interactor.run_tool(testdef, test_history)
self.assertTrue(data_list)
self._verify_outputs(testdef, test_history, shed_tool_id, data_list,
galaxy_interactor)
galaxy_interactor.delete_history(test_history)
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 do_it(self, testdef, resource_parameters={}):
"""
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()
stage_data_in_history(galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id)
# Once data is ready, run the tool and check the outputs - record API
# input, job info, tool run exception, as well as exceptions related to
# job output checking and register they with the test plugin so it can
# record structured information.
tool_inputs = None
job_stdio = None
job_output_exceptions = None
tool_execution_exception = None
expected_failure_occurred = False
try:
try:
tool_response = galaxy_interactor.run_tool(
testdef,
test_history,
resource_parameters=resource_parameters)
data_list, jobs, tool_inputs = tool_response.outputs, tool_response.jobs, tool_response.inputs
data_collection_list = tool_response.output_collections
except RunToolException as e:
tool_inputs = e.inputs
tool_execution_exception = e
if not testdef.expect_failure:
raise e
else:
expected_failure_occurred = True
except Exception as e:
tool_execution_exception = e
raise e
if not expected_failure_occurred:
self.assertTrue(data_list or data_collection_list)
try:
job_stdio = self._verify_outputs(testdef, test_history,
jobs, shed_tool_id,
data_list,
data_collection_list,
galaxy_interactor)
except JobOutputsError as e:
job_stdio = e.job_stdio
job_output_exceptions = e.output_exceptions
raise e
except Exception as e:
job_output_exceptions = [e]
raise e
finally:
job_data = {}
if tool_inputs is not None:
job_data["inputs"] = tool_inputs
if job_stdio is not None:
job_data["job"] = job_stdio
if job_output_exceptions:
job_data["output_problems"] = [
str(_) for _ in job_output_exceptions
]
if tool_execution_exception:
job_data["execution_problem"] = str(tool_execution_exception)
register_job_data(job_data)
galaxy_interactor.delete_history(test_history)
