1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ea869e917062/ Changeset: ea869e917062 User: jmchilton Date: 2014-05-07 07:24:00 Summary: Improve API test skipping when required tools are absent. Replace ad-hoc tools API test method for skipping tests with a more general purpose decorator. Use new decorator to specify required tools for workflow tests. Affected #: 3 files
diff -r 7eb53364de36c60654ee6e89207a63b280c74af1 -r ea869e917062e0d92da847e50f210dcb1e0cbfd2 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -1,3 +1,5 @@ +from operator import itemgetter + import time import json import StringIO @@ -12,6 +14,35 @@ DEFAULT_HISTORY_TIMEOUT = 5 # Secs to wait on history to turn ok
+def skip_without_tool( tool_id ): + """ Decorate an API test method as requiring a specific tool, + have nose skip the test case is the tool is unavailable. + """ + + def method_wrapper( method ): + + def get_tool_ids( api_test_case ): + index = api_test_case.galaxy_interactor.get( "tools", data=dict(in_panel=False) ) + tools = index.json() + # In panels by default, so flatten out sections... + tool_ids = map( itemgetter( "id" ), tools ) + return tool_ids + + def wrapped_method( api_test_case, *args, **kwargs ): + if tool_id not in get_tool_ids( api_test_case ): + from nose.plugins.skip import SkipTest + raise SkipTest( ) + + return method( api_test_case, *args, **kwargs ) + + # Must preserve method name so nose can detect and report tests by + # name. + wrapped_method.__name__ = method.__name__ + return wrapped_method + + return method_wrapper + + # Deprecated mixin, use dataset populator instead. # TODO: Rework existing tests to target DatasetPopulator in a setup method instead. class TestsDatasets:
diff -r 7eb53364de36c60654ee6e89207a63b280c74af1 -r ea869e917062e0d92da847e50f210dcb1e0cbfd2 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -3,6 +3,7 @@ from operator import itemgetter from .helpers import DatasetPopulator from .helpers import DatasetCollectionPopulator +from .helpers import skip_without_tool
class ToolsTestCase( api.ApiTestCase ): @@ -51,8 +52,8 @@ result_content = self._upload_and_get_content( table ) self.assertEquals( result_content, table )
+ @skip_without_tool( "cat1" ) def test_run_cat1( self ): - self.__skip_without_tool( "cat1" ) # Run simple non-upload tool with an input data parameter. history_id = self.dataset_populator.new_history() new_dataset = self.dataset_populator.new_dataset( history_id, content='Cat1Test' ) @@ -66,8 +67,8 @@ output1_content = self._get_content( history_id, dataset=output1 ) self.assertEqual( output1_content.strip(), "Cat1Test" )
+ @skip_without_tool( "cat1" ) def test_run_cat1_with_two_inputs( self ): - self.__skip_without_tool( "cat1" ) # Run tool with an multiple data parameter and grouping (repeat) history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='Cat1Test' ) @@ -83,8 +84,8 @@ output1_content = self._get_content( history_id, dataset=output1 ) self.assertEqual( output1_content.strip(), "Cat1Test\nCat2Test" )
+ @skip_without_tool( "cat1" ) def test_multirun_cat1( self ): - self.__skip_without_tool( "cat1" ) history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) @@ -104,8 +105,8 @@ self.assertEquals( output1_content.strip(), "123" ) self.assertEquals( output2_content.strip(), "456" )
+ @skip_without_tool( "cat1" ) def test_multirun_in_repeat( self ): - self.__skip_without_tool( "cat1" ) history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) @@ -127,8 +128,8 @@ self.assertEquals( output1_content.strip(), "Common\n123" ) self.assertEquals( output2_content.strip(), "Common\n456" )
+ @skip_without_tool( "cat1" ) def test_multirun_on_multiple_inputs( self ): - self.__skip_without_tool( "cat1" ) history_id = self.dataset_populator.new_history() new_dataset1 = self.dataset_populator.new_dataset( history_id, content='123' ) new_dataset2 = self.dataset_populator.new_dataset( history_id, content='456' ) @@ -153,8 +154,8 @@ assert "123\n0ab" in outputs_contents assert "456\n0ab" in outputs_contents
+ @skip_without_tool( "cat1" ) def test_map_over_collection( self ): - self.__skip_without_tool( "cat1" ) history_id = self.dataset_populator.new_history() hdca_id = self.__build_pair( history_id, [ "123", "456" ] ) inputs = { @@ -175,8 +176,8 @@ self.assertEquals( output1_content.strip(), "123" ) self.assertEquals( output2_content.strip(), "456" )
+ @skip_without_tool( "cat1" ) def test_map_over_nested_collections( self ): - self.__skip_without_tool( "cat1" ) history_id = self.dataset_populator.new_history() hdca_id = self.__build_nested_list( history_id ) inputs = { @@ -203,6 +204,7 @@ first_object_left_element = first_object[ "elements" ][ 0 ] self.assertEquals( outputs[ 0 ][ "id" ], first_object_left_element[ "object" ][ "id" ] )
+ @skip_without_tool( "cat1" ) def test_map_over_two_collections( self ): history_id = self.dataset_populator.new_history() hdca1_id = self.__build_pair( history_id, [ "123", "456" ] ) @@ -221,8 +223,8 @@ self.assertEquals( output1_content.strip(), "123\n789" ) self.assertEquals( output2_content.strip(), "456\n0ab" )
+ @skip_without_tool( "cat1" ) def test_cannot_map_over_incompatible_collections( self ): - self.__skip_without_tool( "cat1" ) history_id = self.dataset_populator.new_history() hdca1_id = self.__build_pair( history_id, [ "123", "456" ] ) hdca2_id = self.dataset_collection_populator.create_list_in_history( history_id ).json()[ "id" ] @@ -235,8 +237,8 @@ # on server. assert run_response.status_code >= 400
+ @skip_without_tool( "multi_data_param" ) def test_reduce_collections( self ): - self.__skip_without_tool( "multi_data_param" ) history_id = self.dataset_populator.new_history() hdca1_id = self.__build_pair( history_id, [ "123", "456" ] ) hdca2_id = self.dataset_collection_populator.create_list_in_history( history_id ).json()[ "id" ] @@ -257,8 +259,8 @@ assert output1_content.strip() == "123\n456" assert len( output2_content.strip().split("\n") ) == 3, output2_content
+ @skip_without_tool( "collection_paired_test" ) def test_subcollection_mapping( self ): - self.__skip_without_tool( "collection_paired_test" ) history_id = self.dataset_populator.new_history() hdca_list_id = self.__build_nested_list( history_id ) inputs = { @@ -334,11 +336,6 @@ tool_ids = map( itemgetter( "id" ), tools ) return tool_ids
- def __skip_without_tool( self, tool_id ): - from nose.plugins.skip import SkipTest - if tool_id not in self.__tool_ids( ): - raise SkipTest( ) - def __build_nested_list( self, history_id ): hdca1_id = self.__build_pair( history_id, [ "123", "456" ] ) hdca2_id = self.__build_pair( history_id, [ "789", "0ab" ] )
diff -r 7eb53364de36c60654ee6e89207a63b280c74af1 -r ea869e917062e0d92da847e50f210dcb1e0cbfd2 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -5,6 +5,7 @@ from .helpers import WorkflowPopulator from .helpers import DatasetPopulator from .helpers import DatasetCollectionPopulator +from .helpers import skip_without_tool
from base.interactor import delete_request # requests like delete
@@ -62,6 +63,7 @@ first_input = downloaded_workflow[ "steps" ][ "0" ][ "inputs" ][ 0 ] assert first_input[ "name" ] == "WorkflowInput1"
+ @skip_without_tool( "cat1" ) def test_run_workflow( self ): workflow = self.workflow_populator.load_workflow( name="test_for_run" ) workflow_request, history_id = self._setup_workflow_run( workflow ) @@ -71,6 +73,7 @@ self._assert_status_code_is( run_workflow_response, 200 ) self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ @skip_without_tool( "cat1" ) def test_extract_from_history( self ): workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) workflow_request, history_id = self._setup_workflow_run( workflow ) @@ -104,6 +107,7 @@ self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) assert len( downloaded_workflow[ "steps" ] ) == 3
+ @skip_without_tool( "collection_paired_test" ) def test_extract_workflows_with_dataset_collections( self ): history_id = self.dataset_populator.new_history() hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json() @@ -141,6 +145,7 @@ collection_step_state = loads( collection_step[ "tool_state" ] ) self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+ @skip_without_tool( "random_lines1" ) def test_run_replace_params_by_tool( self ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" ) workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) ) @@ -151,6 +156,7 @@ self.__assert_lines_hid_line_count_is( history_id, 2, 5 ) self.__assert_lines_hid_line_count_is( history_id, 3, 5 )
+ @skip_without_tool( "random_lines1" ) def test_run_replace_params_by_steps( self ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" ) workflow_summary_response = self._get( "workflows/%s" % workflow_request[ "workflow_id" ] ) @@ -177,6 +183,7 @@ pja = pjas[ 0 ] self._assert_has_keys( pja, "action_type", "output_name", "action_arguments" )
+ @skip_without_tool( "cat1" ) def test_invocation_usage( self ): workflow = self.workflow_populator.load_workflow( name="test_usage" ) workflow_request, history_id = self._setup_workflow_run( workflow ) @@ -200,6 +207,7 @@ for step in usage_details[ "steps" ].values(): self._assert_has_keys( step, "workflow_step_id", "order_index" )
+ @skip_without_tool( "cat1" ) def test_post_job_action( self ): """ Tests both import and execution of post job actions. """
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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