""" Test Tool execution and state handling logic.
"""
from unittest import TestCase
from paste import httpexceptions
import galaxy.model
import tools_support
from galaxy.tools.parameters import params_to_incoming
from galaxy.util.bunch import Bunch
from galaxy.util.odict import odict
BASE_REPEAT_TOOL_CONTENTS = '''
echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1
%s
'''
# Tool with a repeat parameter, to test state update.
REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % ''''''
REPEAT_COLLECTION_PARAM_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % ''''''
class ToolExecutionTestCase(TestCase, tools_support.UsesApp, tools_support.UsesTools):
def setUp(self):
self.setup_app()
self.history = galaxy.model.History()
self.trans = MockTrans(self.app, self.history)
self.app.dataset_collections_service = MockCollectionService()
self.tool_action = MockAction(self.trans)
def tearDown(self):
self.tear_down_app()
def test_state_new(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
vars = self.__handle_with_incoming(param1="moo")
state = self.__assert_rerenders_tool_without_errors(vars)
assert state["param1"] == "moo"
def test_execute(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
vars = self.__handle_with_incoming(param1="moo")
self.__assert_executed(vars)
# Didn't specify a rerun_remap_id so this should be None
assert self.tool_action.execution_call_args[0]["rerun_remap_job_id"] is None
def test_execute_exception(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
self.tool_action.raise_exception()
try:
self.__handle_with_incoming(param1="moo")
except Exception as e:
assert 'Error executing tool' in str(e)
def test_execute_errors(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
self.tool_action.return_error()
try:
self.__handle_with_incoming(param1="moo")
except Exception as e:
assert 'Test Error Message' in str(e)
def test_redirect(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
self.tool_action.expect_redirect = True
redirect_raised = False
try:
self.__handle_with_incoming(param1="moo")
except httpexceptions.HTTPFound:
redirect_raised = True
assert redirect_raised
def test_remap_job(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
vars = self.__handle_with_incoming(param1="moo", rerun_remap_job_id=self.app.security.encode_id(123))
self.__assert_executed(vars)
assert self.tool_action.execution_call_args[0]["rerun_remap_job_id"] == 123
def test_invalid_remap_job(self):
self._init_tool(tools_support.SIMPLE_TOOL_CONTENTS)
try:
self.__handle_with_incoming(param1="moo", rerun_remap_job_id='123')
except Exception as e:
assert 'invalid job' in str(e)
def test_data_param_execute(self):
self._init_tool(tools_support.SIMPLE_CAT_TOOL_CONTENTS)
hda = self.__add_dataset(1)
# Execute tool action
vars = self.__handle_with_incoming(param1=1)
self.__assert_executed(vars)
# Tool 'executed' once, with hda as param1
assert len(self.tool_action.execution_call_args) == 1
assert self.tool_action.execution_call_args[0]["incoming"]["param1"] == hda
def test_data_param_state_update(self):
self._init_tool(tools_support.SIMPLE_CAT_TOOL_CONTENTS)
hda = self.__add_dataset(1)
# Update state
vars = self.__handle_with_incoming(param1=1)
state = self.__assert_rerenders_tool_without_errors(vars)
assert hda == state["param1"]
def __handle_with_incoming(self, previous_state=None, **kwds):
""" Execute tool.handle_input with incoming specified by kwds
(optionally extending a previous state).
"""
if previous_state:
incoming = self.__to_incoming(previous_state, **kwds)
else:
incoming = kwds
return self.tool.handle_input(trans=self.trans, incoming=incoming)
def __to_incoming(self, state, **kwds):
new_incoming = {}
params_to_incoming(new_incoming, self.tool.inputs, state.inputs, self.app)
new_incoming["tool_state"] = self.__state_to_string(state)
new_incoming.update(kwds)
return new_incoming
def __add_dataset(self, id, state='ok'):
hda = galaxy.model.HistoryDatasetAssociation()
hda.id = id
hda.dataset = galaxy.model.Dataset()
hda.dataset.state = 'ok'
self.trans.sa_session.add(hda)
self.history.datasets.append(hda)
self.trans.sa_session.flush()
return hda
def __add_collection_dataset(self, id, collection_type="paired", *hdas):
hdca = galaxy.model.HistoryDatasetCollectionAssociation()
hdca.id = id
collection = galaxy.model.DatasetCollection()
hdca.collection = collection
collection.elements = [galaxy.model.DatasetCollectionElement(element=self.__add_dataset(1))]
collection.type = collection_type
self.trans.sa_session.model_objects[galaxy.model.HistoryDatasetCollectionAssociation][id] = hdca
self.history.dataset_collections.append(hdca)
return hdca
def __assert_rerenders_tool_without_errors(self, vars):
self.__assert_no_errors(vars)
return self.tool_action.execution_call_args[0]["incoming"]
def __assert_executed(self, vars):
self.__assert_no_errors(vars)
assert len(vars['jobs']) > 0
def __assert_no_errors(self, vars):
assert "job_errors" in vars
assert not vars["job_errors"]
class MockAction(object):
def __init__(self, expected_trans):
self.expected_trans = expected_trans
self.execution_call_args = []
self.expect_redirect = False
self.exception_after_exection = None
self.error_message_after_excution = None
def execute(self, tool, trans, **kwds):
assert self.expected_trans == trans
self.execution_call_args.append(kwds)
num_calls = len(self.execution_call_args)
if self.expect_redirect:
raise httpexceptions.HTTPFound("http://google.com")
if self.exception_after_exection is not None:
if num_calls > self.exception_after_exection:
raise Exception("Test Exception")
if self.error_message_after_excution is not None:
if num_calls > self.error_message_after_excution:
return None, "Test Error Message"
return galaxy.model.Job(), odict(dict(out1="1"))
def raise_exception(self, after_execution=0):
self.exception_after_exection = after_execution
def return_error(self, after_execution=0):
self.error_message_after_excution = after_execution
class MockTrans(object):
def __init__(self, app, history):
self.app = app
self.history = history
self.user = None
self.history._active_datasets_and_roles = [hda for hda in self.app.model.context.query(galaxy.model.HistoryDatasetAssociation).all() if hda.active and hda.history == history]
self.workflow_building_mode = False
self.webapp = Bunch(name="galaxy")
self.sa_session = self.app.model.context
def get_history(self, **kwargs):
return self.history
def get_current_user_roles(self):
return []
class MockCollectionService(object):
def __init__(self):
self.collection_info = object()
def match_collections(self, collections_to_match):
return self.collection_info