def test_transform_workflow_for_output_with_unfinished_workflow(self):
workflow = {
"Id": 3167,
"Status": 1000,
"CreatedDate": "2017-02-08T00:57:16.3403168+00:00",
"EndDate": None,
"FailureCode": 0,
"Message": None,
"Description": None,
"Process": "snapgatk-20170207_1"
}
args = testargs.get_test_args()
workflow_executor = malibuworkflow.WorkflowExecutor(args)
transformed = workflow_executor.transform_workflow_for_output(workflow)
self.assertIsNotNone(transformed)
self.assertEquals(transformed["Workflow ID"], "3167")
self.assertEquals(transformed["Status"], "Queued")
self.assertEquals(transformed["Message"], "")
self.assertEquals(transformed["Description"], "")
self.assertEquals(transformed["Process"], "snapgatk-20170207_1")
self.assertEquals(transformed["Created Date"],
"Wed, 08 Feb 2017 00:57:16 GMT")
self.assertEquals(transformed["End Date"], "")
self.assertTrue(
transformed["Wall Clock Time"]) # not None and not an empty string
def test_transform_workflow_formats_gbases_correctly(self):
workflow = {
"Id": 3167,
"Status": 20000,
"CreatedDate": "2017-02-08T00:57:16.3403168+00:00",
"EndDate": "2017-02-08T01:23:37.0531197+00:00",
"FailureCode": 0,
"Message": None,
"Description": "process_args",
"Process": "snapgatk-20170207_1",
"BasesProcessed": "127434222576"
}
expected = OrderedDict()
expected["Workflow ID"] = "3167"
expected["Status"] = "Completed successfully"
expected["Message"] = ""
expected["Process"] = "snapgatk-20170207_1"
expected["Description"] = "process_args"
expected["Created Date"] = "Wed, 08 Feb 2017 00:57:16 GMT"
expected["End Date"] = "Wed, 08 Feb 2017 01:23:37 GMT"
expected["Wall Clock Time"] = "0h 26m 21s"
expected["Bases Processed"] = "127,434,222,576 (127 GBase)"
args = testargs.get_test_args()
workflow_executor = malibuworkflow.WorkflowExecutor(args)
transformed = workflow_executor.transform_workflow_for_output(workflow)
self.assertDictEqual(transformed, expected)
def test_display_status_workflow_long(self):
"""
display_status prints lines like the following:
[01/18/2017 17:58:35 - Workflow ID: 1]: Message: Queued
Process: snapgatk
Description: Tru la la
"""
args = testargs.get_test_args()
workflow = malibuworkflow.WorkflowExecutor(args)
response_workflow = {
"Id": 1,
"Status": 1000,
"Process": "snapgatk",
"Description": "Tru la la"
}
real_stdout = sys.stdout
try:
string_stdout = StringIO()
sys.stdout = string_stdout
workflow.display_status(response_workflow, short=False)
printed = string_stdout.getvalue()
self.assertTrue("Workflow ID: 1" in printed)
self.assertTrue("Message: Queued" in printed)
self.assertTrue("snapgatk" in printed)
self.assertTrue("Tru la la" in printed)
finally:
sys.stdout = real_stdout
def test_get_input_output_dict_handles_two_files_with_sas(self):
args = testargs.get_test_args()
workflow = malibuworkflow.WorkflowExecutor(args)
workflow.datatransfer = FakeDataTransfer(None)
inputs, outputs = workflow.get_input_and_output_dict()
self.assertEquals(inputs["BLOBNAMES"],
"chr21-10k_1.fq.gz,chr21-10k_2.fq.gz,")
def test_lists(self):
"""Lists workflow items"""
args = testargs.get_test_args()
workflow = malibuworkflow.WorkflowExecutor(args)
workflow.list_workflows()
self.assertTrue(workflow.current_exit_status == 0)
def test_construct_optional_args_returns_empty_dictionary_without_args(
self):
args = testargs.get_test_args()
args.bqsr_enabled = None
workflow = malibuworkflow.WorkflowExecutor(args)
workflow.datatransfer = FakeDataTransfer(None)
optional_args = workflow.construct_optional_args()
self.assertDictEqual(optional_args, {})
def test_get_input_output_dict_handles_one_file_with_sas(self):
args = testargs.get_test_args()
args.input_blob_name_1 = ["file.bam?sas"]
args.input_blob_name_2 = []
workflow = malibuworkflow.WorkflowExecutor(args)
workflow.datatransfer = FakeDataTransfer(None)
inputs, outputs = workflow.get_input_and_output_dict()
self.assertEquals(inputs["BLOBNAMES"], "file.bam,")
def test_submit_and_status(self):
"""Submits a workflow item, assuming storage inputs
no download"""
args = testargs.get_test_args()
workflow = malibuworkflow.WorkflowExecutor(args)
workflow_id = workflow.post_workflow_blocking()
self.assertTrue(workflow_id > 0)
workflow.get_workflow_status()
self.assertTrue(workflow.current_exit_status > 1)
def test_construct_optional_args_returns_nonempty_dictionary(self):
args = testargs.get_test_args()
args.bqsr_enabled = True
workflow = malibuworkflow.WorkflowExecutor(args)
workflow.datatransfer = FakeDataTransfer(None)
optional_args = workflow.construct_optional_args()
self.assertDictEqual(optional_args, {"BQSR": True})
args.bqsr_enabled = False
optional_args = workflow.construct_optional_args()
self.assertDictEqual(optional_args, {"BQSR": False})
def test_get_input_output_dict_handles_multiple_files(self):
args = testargs.get_test_args()
args.input_blob_name_1 = ["chr21-10k_1.fq.gz", "chr22-10k_1.fq.gz"]
args.input_blob_name_2 = ["chr21-10k_2.fq.gz", "chr22-10k_2.fq.gz"]
workflow = malibuworkflow.WorkflowExecutor(args)
workflow.datatransfer = FakeDataTransfer(None)
inputs, outputs = workflow.get_input_and_output_dict()
self.assertEquals(
inputs["BLOBNAMES"],
"chr21-10k_1.fq.gz,chr21-10k_2.fq.gz,chr22-10k_1.fq.gz,chr22-10k_2.fq.gz,"
)
def test_submit_and_cancel_np(self):
"""Submits a workflow item, assuming storage inputs
no download"""
args = testargs.get_test_args()
args.poll = False
workflow = malibuworkflow.WorkflowExecutor(args)
workflow_id = workflow.post_workflow_blocking()
workflow.cancel_workflow()
self.assertTrue(workflow_id > 0)
def setUp(self):
args = testargs.get_test_args()
url = malibucommon.get_api_url_from_base(args.api_url_base)
self.service = malibuservice.MalibuService(
url, args.access_key)
#create an instace of the worflow to set the dictionaries
workflow = malibuworkflow.WorkflowExecutor(args)
self.input_dic, self.output_dic = workflow.get_input_and_output_dict()
self.process_name = args.process_name
self.process_args = args.process_args
self.storage_account_type = "AZURE_BLOCK_BLOB"
self.description = None
self.workflow_class = None
def test_display_status_with_message_and_response(self):
"""
display_status prints a line like the following:
[01/18/2017 17:56:28] - Message: This is unacceptable Status Code: None Response Code: 400
"""
args = testargs.get_test_args()
workflow = malibuworkflow.WorkflowExecutor(args)
real_stdout = sys.stdout
try:
string_stdout = StringIO()
sys.stdout = string_stdout
workflow.display_status({"Message": "This is unacceptable"},
response_code=400)
printed = string_stdout.getvalue()
self.assertTrue("This is unacceptable" in printed)
self.assertTrue("400" in printed)
finally:
sys.stdout = real_stdout
def test_exit_status_states(self):
"""test exit status by result, response code and
workflow status"""
args = testargs.get_test_args()
result = 1
response = 200
status = 1000
workflow = malibuworkflow.WorkflowExecutor(args)
#when only result is set, all other parameters are not considered
result = 1
workflow.set_exit_code(result, response, status)
self.assertTrue(workflow.current_exit_status == result)
#response code not in the mapping dict, default to error"
response = 500
self.assertTrue(response not in workflow.exit_status_by_response)
workflow.set_exit_code(None, response, None)
self.assertTrue(workflow.current_exit_status == 1000)
#response code only
response = 200
workflow.set_exit_code(None, response, None)
self.assertTrue(workflow.current_exit_status ==
workflow.exit_status_by_response[response][1])
#when response code is set to a value other than 200, takes precedent
response = 400
workflow.set_exit_code(None, response, status)
self.assertTrue(workflow.current_exit_status ==
workflow.exit_status_by_response[response][1])
#when response is succesful, exit code is set by workflow_status
response = 200
status = 20000
workflow.set_exit_code(None, response, status)
self.assertTrue(workflow.current_exit_status ==
workflow.exit_status_by_workflow_status[status][1])
def test_transform_workflow_for_None(self):
args = testargs.get_test_args()
workflow_executor = malibuworkflow.WorkflowExecutor(args)
transformed = workflow_executor.transform_workflow_for_output(None)
self.assertIsNotNone(transformed)
self.assertTrue(len(transformed.keys()) == 0)
