def test_serve_daemon(self):
port = network_util.get_free_port()
pid_file = os.path.join(self._home, "test.pid")
extra_args = ["--daemon", "--pid_file", pid_file]
serve = functools.partial(self._run, port, extra_args)
self._launch_thread_and_wait(serve, port)
admin_gi = api.gi(port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(port, user_api_key)
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
def test_serve_daemon(self):
port = network_util.get_free_port()
pid_file = os.path.join(self._home, "test.pid")
extra_args = ["--daemon", "--pid_file", pid_file]
serve = functools.partial(self._run, port, extra_args)
self._launch_thread_and_wait(serve, port)
admin_gi = api.gi(port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(port, user_api_key)
assert len(
user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
def _job_outputs_template_from_invocation(invocation_id, galaxy_url,
galaxy_api_key):
user_gi = gi(url=galaxy_url, key=galaxy_api_key)
invocation = user_gi.invocations.show_invocation(invocation_id)
outputs = {}
for label, output in invocation["outputs"].items():
ext = user_gi.datasets.show_dataset(output["id"])["extension"]
user_gi.datasets.download_dataset(output["id"],
use_default_filename=False,
file_path=f"test-data/{label}.{ext}")
outputs[label] = {'file': f"test-data/{label}.{ext}"}
for label, output in invocation["output_collections"].items():
collection = user_gi.dataset_collections.show_dataset_collection(
output['id'])
if ':' not in collection["collection_type"]:
user_gi.datasets.download_dataset(
collection["elements"][0]["object"]["id"],
use_default_filename=False,
file_path=
f"test-data/{label}.{collection['elements'][0].get('extension', 'txt')}"
)
outputs[label] = {
'element_tests': { # only check the first element
collection["elements"][0]["element_identifier"]:
f"test-data/{label}.{collection['elements'][0]['extension']}"
}
}
else:
outputs[label] = {'element_tests': 'nested_collection_todo'}
return outputs
def _job_inputs_template_from_invocation(invocation_id, galaxy_url,
galaxy_api_key):
def _template_from_collection(user_gi, collection_id):
collection = user_gi.dataset_collections.show_dataset_collection(
collection_id)
template = {
"class": "Collection",
"collection_type": collection["collection_type"],
"elements": []
}
for element in collection["elements"]:
if element["element_type"] == "hdca":
template['elements'].append(
_template_from_collection(element["object"]["id"]))
elif element["element_type"] == "hda":
user_gi.datasets.download_dataset(
element["object"]["id"],
use_default_filename=False,
file_path=
f"test-data/{input_step['label']}_{element['element_identifier']}.{ext}"
)
template['elements'].append({
"class":
"File",
"identifier":
element['element_identifier'],
"path":
f"test-data/{input_step['label']}_{element['element_identifier']}.{ext}",
})
return template
user_gi = gi(url=galaxy_url, key=galaxy_api_key)
invocation = user_gi.invocations.show_invocation(invocation_id)
template = {}
for input_step in invocation['inputs'].values():
if input_step["src"] == "hda":
ext = user_gi.datasets.show_dataset(input_step["id"])["extension"]
user_gi.datasets.download_dataset(
input_step["id"],
use_default_filename=False,
file_path=f"test-data/{input_step['label']}.{ext}")
template[input_step['label']] = {
"class": "File",
"path": f"test-data/{input_step['label']}.{ext}",
"filetype": ext
}
elif input_step["src"] == "hdca":
template[input_step['label']] = _template_from_collection(
user_gi, input_step["id"])
for param, param_step in invocation['input_step_parameters'].items():
template[param] = param_step["parameter_value"]
return template
def get_workflow_from_invocation_id(invocation_id, galaxy_url, galaxy_api_key):
user_gi = gi(url=galaxy_url, key=galaxy_api_key)
workflow_id = user_gi.invocations.show_invocation(
invocation_id)['workflow_id']
workflow = user_gi.workflows._get(workflow_id, params={'instance': 'true'})
workflow_name = '-'.join(workflow["name"].split())
user_gi.workflows.export_workflow_to_local_path(
use_default_filename=False,
file_local_path=f'./{workflow_name}.ga',
workflow_id=workflow["id"])
return workflow_name
def _user_gi(self):
admin_gi = api.gi(self._port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(self._port, key=user_api_key)
return user_gi
def _user_gi(self):
admin_gi = api.gi(self._port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(self._port, key=user_api_key)
return user_gi