class WorkflowFrameworkPerformanceTestCase(PerformanceTestCase):
framework_tool_and_types = True
def setUp(self):
super().setUp()
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
def test_run_simple(self):
self._run_performance_workflow("simple")
def test_run_wave(self):
self._run_performance_workflow("wave_simple")
def test_run_two_output(self):
self._run_performance_workflow("two_output")
def _run_performance_workflow(self, workflow_type):
workflow_yaml = self.workflow_populator.scaling_workflow_yaml(
workflow_type=workflow_type,
collection_size=GALAXY_TEST_PERFORMANCE_COLLECTION_SIZE,
workflow_depth=GALAXY_TEST_PERFORMANCE_WORKFLOW_DEPTH,
)
run_summary = self.workflow_populator.run_workflow(
workflow_yaml,
test_data={},
wait=False,
)
self.workflow_populator.wait_for_workflow(
run_summary.workflow_id,
run_summary.invocation_id,
run_summary.history_id,
assert_ok=True,
timeout=GALAXY_TEST_PERFORMANCE_TIMEOUT,
)
class MaximumWorkflowJobsPerSchedulingIterationTestCase(
integration_util.IntegrationTestCase):
framework_tool_and_types = True
def setUp(self):
super(MaximumWorkflowJobsPerSchedulingIterationTestCase, self).setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(
self.galaxy_interactor)
@classmethod
def handle_galaxy_config_kwds(cls, config):
config["maximum_workflow_jobs_per_scheduling_iteration"] = 1
def do_test(self):
workflow_id = self.workflow_populator.upload_yaml_workflow("""
class: GalaxyWorkflow
steps:
- type: input_collection
- tool_id: collection_creates_pair
state:
input1:
$link: 0
- tool_id: collection_paired_test
state:
f1:
$link: 1#paired_output
- tool_id: cat_list
state:
input1:
$link: 2#out1
""")
with self.dataset_populator.test_history() as history_id:
hdca1 = self.dataset_collection_populator.create_list_in_history(
history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]).json()
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
inputs = {
'0': {
"src": "hdca",
"id": hdca1["id"]
},
}
invocation_id = self.workflow_populator.invoke_workflow(
history_id, workflow_id, inputs)
self.workflow_populator.wait_for_workflow(history_id, workflow_id,
invocation_id)
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
self.assertEqual(
"a\nc\nb\nd\ne\ng\nf\nh\n",
self.dataset_populator.get_history_dataset_content(history_id,
hid=0))
class MaximumWorkflowJobsPerSchedulingIterationTestCase(
integration_util.IntegrationTestCase):
framework_tool_and_types = True
def setUp(self):
super().setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(
self.galaxy_interactor)
@classmethod
def handle_galaxy_config_kwds(cls, config):
config["maximum_workflow_jobs_per_scheduling_iteration"] = 1
def test_collection_explicit_and_implicit(self):
workflow_id = self.workflow_populator.upload_yaml_workflow("""
class: GalaxyWorkflow
steps:
- type: input_collection
- tool_id: collection_creates_pair
state:
input1:
$link: 0
- tool_id: collection_paired_test
state:
f1:
$link: 1/paired_output
- tool_id: cat_list
state:
input1:
$link: 2/out1
""")
with self.dataset_populator.test_history() as history_id:
hdca1 = self.dataset_collection_populator.create_list_in_history(
history_id, contents=["a\nb\nc\nd\n", "e\nf\ng\nh\n"]).json()
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
inputs = {
'0': {
"src": "hdca",
"id": hdca1["id"]
},
}
invocation_id = self.workflow_populator.invoke_workflow(
history_id, workflow_id, inputs)
self.workflow_populator.wait_for_workflow(history_id, workflow_id,
invocation_id)
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
self.assertEqual(
"a\nc\nb\nd\ne\ng\nf\nh\n",
self.dataset_populator.get_history_dataset_content(history_id,
hid=0))
def test_scheduling_rounds(self):
with self.dataset_populator.test_history() as history_id:
invocation_response = self.workflow_populator.run_workflow(
"""
class: GalaxyWorkflow
inputs:
input1: data
text_input: text
steps:
first_cat:
tool_id: cat1
in:
input1: input1
second_cat:
tool_id: cat1
in:
input1: first_cat/out_file1
collection_creates_dynamic_list_of_pairs:
tool_id: collection_creates_dynamic_list_of_pairs
in:
file: second_cat/out_file1
count_multi_file:
tool_id: count_multi_file
in:
input1: collection_creates_dynamic_list_of_pairs/list_output
outputs:
wf_output_1:
outputSource: collection_creates_dynamic_list_of_pairs/list_output
""",
test_data="""
input1:
value: 1.fasta
type: File
name: fasta1
text_input: foo
""",
history_id=history_id)
invocation = self._get("/invocations/{}".format(
invocation_response.invocation_id)).json()
assert 'wf_output_1' in invocation['output_collections']