def test_prepare_workflow_manifest_raises_an_error_for_dependencies_file_with_filepath_not_pointing_to_zip(
self
):
with self.assertRaises(ValueError):
utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path, dependencies="data/fake_test_deps.wdl"
)
def test_prepare_workflow_manifest_works_for_wdl_file_with_filepath(self):
manifest = utils.prepare_workflow_manifest(wdl_file=self.wdl_file_path)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'workflowOnHold': 'false',
}
assert (manifest['workflowSource'].getvalue() ==
expected_manifest['workflowSource'].getvalue())
def test_prepare_workflow_manifest_works_for_label_file_with_BytesIO(self):
manifest = utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path, label_file=self.label_file_BytesIO)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'labels': self.label_file_BytesIO,
'workflowOnHold': 'false',
}
assert manifest['labels'].getvalue(
) == expected_manifest['labels'].getvalue()
def test_prepare_workflow_manifest_works_for_on_hold(self):
manifest = utils.prepare_workflow_manifest(wdl_file=self.wdl_file_path,
on_hold=True)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'workflowOnHold': 'true',
}
assert (manifest['workflowSource'].getvalue() ==
expected_manifest['workflowSource'].getvalue())
assert manifest['workflowOnHold'] == expected_manifest[
'workflowOnHold']
def test_prepare_workflow_manifest_works_for_one_inputs_file_with_BytesIO(
self):
manifest = utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path, inputs_files=self.inputs_file_BytesIO)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'workflowInputs': self.inputs_file_BytesIO,
'workflowOnHold': 'false',
}
assert (manifest['workflowInputs'].getvalue() ==
expected_manifest['workflowInputs'].getvalue())
def test_prepare_workflow_manifest_works_for_collection_name(self):
manifest = utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path, collection_name='test_collection')
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'collectionName': 'test_collection',
'workflowOnHold': 'false',
}
assert (manifest['workflowSource'].getvalue() ==
expected_manifest['workflowSource'].getvalue())
assert manifest['collectionName'] == expected_manifest[
'collectionName']
def test_prepare_workflow_manifest_works_for_dependencies_file_with_BytesIO(
self):
manifest = utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path,
dependencies=self.deps_zip_file_BytesIO)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'workflowDependencies': self.deps_zip_file_BytesIO,
'workflowOnHold': 'false',
}
assert (manifest['workflowDependencies'].getvalue() ==
expected_manifest['workflowDependencies'].getvalue())
def test_prepare_workflow_manifest_works_for_multiple_inputs_files_with_filepath(
self, ):
manifest = utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path,
inputs_files=self.inputs_file_path_list)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'workflowInputs': self.inputs_file_BytesIO_list[0],
'workflowInputs_2': self.inputs_file_BytesIO_list[1],
'workflowOnHold': 'false',
}
assert (manifest['workflowInputs'].getvalue() ==
expected_manifest['workflowInputs'].getvalue())
assert (manifest['workflowInputs_2'].getvalue() ==
expected_manifest['workflowInputs_2'].getvalue())
def test_prepare_workflow_manifest_works_for_dependencies_file_with_list_of_files(
self, ):
manifest = utils.prepare_workflow_manifest(
wdl_file=self.wdl_file_path,
dependencies=self.deps_files_paths_list)
expected_manifest = {
'workflowSource': self.wdl_file_BytesIO,
'workflowDependencies': self.deps_zip_file_BytesIO,
'workflowOnHold': 'false',
}
with zipfile.ZipFile(manifest['workflowDependencies'], 'r') as zf:
with zf.open('test_task.wdl') as dep_file:
contents = io.BytesIO(dep_file.read())
with zipfile.ZipFile(expected_manifest['workflowDependencies'],
'r') as zf:
with zf.open('test_task.wdl') as dep_file:
expected_contents = io.BytesIO(dep_file.read())
# we have to unzip both of them to get the proper comparison during the test
assert contents.getvalue() == expected_contents.getvalue()
def submit(
cls: 'CromwellAPI',
auth: CromwellAuth,
wdl_file: Union[str, io.BytesIO],
inputs_files: Union[List[Union[str, io.BytesIO]], str,
io.BytesIO] = None,
options_file: Union[str, io.BytesIO] = None,
dependencies: Union[str, List[str], io.BytesIO] = None,
label_file: Union[str, io.BytesIO] = None,
collection_name: str = None,
on_hold: bool = False,
validate_labels: bool = False,
raise_for_status: bool = False,
) -> requests.Response:
""" Submits a workflow to Cromwell.
Args:
auth: authentication class holding auth information to a
Cromwell server.
wdl_file: The workflow source file to submit for execution. Could be either the
path to the file (str) or the file content in io.BytesIO.
inputs_files: The input data in JSON
format. Could be either the path to the file (str) or the file content in io.BytesIO. This could also
be a list of unlimited input file paths/contents, each of them should have a type of
Union[str, io.BytesIO].
options_file: The Cromwell options file for workflows. Could be either
the path to the file (str) or the file content in io.BytesIO.
dependencies: Workflow dependency files. Could be the path to
the zipped file (str) containing dependencies, a list of paths(List[str]) to all dependency files to be
zipped or a zipped file in io.BytesIO.
label_file: A collection of key/value pairs for workflow labels in JSON
format, could be either the path to the JSON file (str) or the file content in io.BytesIO.
collection_name: Collection in SAM that the workflow should belong to, if use CaaS.
on_hold: Whether to submit the workflow in "On Hold" status.
validate_labels: If True, validate cromwell labels.
raise_for_status: Whether to check and raise for status based on the response.
Raises:
requests.exceptions.HTTPError: This will be raised when raise_for_status is True and Cromwell returns
a response that satisfies 400 <= response.status_code < 600.
Returns:
HTTP response from Cromwell.
"""
submission_manifest = utilities.prepare_workflow_manifest(
wdl_file=wdl_file,
inputs_files=inputs_files,
options_file=options_file,
dependencies=dependencies,
label_file=label_file,
collection_name=collection_name,
on_hold=on_hold,
)
if auth.service_key_content:
submission_manifest[
'workflowOptions'] = utilities.compose_oauth_options_for_jes_backend_cromwell(
auth, submission_manifest.get('workflowOptions'))
if validate_labels and label_file is not None:
validate_cromwell_label(submission_manifest['labels'])
response = requests.post(
auth.url + cls._submit_endpoint,
files=submission_manifest,
auth=auth.auth,
headers=auth.header,
)
if raise_for_status:
cls._check_and_raise_status(response)
return response
