def update_task(workflow_id,
task_id,
body,
terminate_loop=None,
update_all=False):
workflow_model = session.query(WorkflowModel).filter_by(
id=workflow_id).first()
if workflow_model is None:
raise ApiError("invalid_workflow_id",
"The given workflow id is not valid.",
status_code=404)
processor = WorkflowProcessor(workflow_model)
task_id = uuid.UUID(task_id)
spiff_task = processor.bpmn_workflow.get_task(task_id)
_verify_user_and_role(processor, spiff_task)
user = UserService.current_user(
allow_admin_impersonate=False) # Always log as the real user.
if not spiff_task:
raise ApiError("empty_task",
"Processor failed to obtain task.",
status_code=404)
if spiff_task.state != spiff_task.READY:
raise ApiError(
"invalid_state",
"You may not update a task unless it is in the READY state. "
"Consider calling a token reset to make this task Ready.")
if terminate_loop and spiff_task.is_looping():
spiff_task.terminate_loop()
# Extract the details specific to the form submitted
form_data = WorkflowService().extract_form_data(body, spiff_task)
# Update the task
__update_task(processor, spiff_task, form_data, user)
# If we need to update all tasks, then get the next ready task and if it a multi-instance with the same
# task spec, complete that form as well.
if update_all:
last_index = spiff_task.task_info()["mi_index"]
next_task = processor.next_task()
while next_task and next_task.task_info()["mi_index"] > last_index:
__update_task(processor, next_task, form_data, user)
last_index = next_task.task_info()["mi_index"]
next_task = processor.next_task()
WorkflowService.update_task_assignments(processor)
workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
return WorkflowApiSchema().dump(workflow_api_model)
def test_do_task(self):
self.load_example_data()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
details = Box({
"title": "My New Title",
"short_title": "My New Short Title",
"pi": "dhf8r",
"short_name": "My Short Name",
"proposal_name": "My Proposal Name"
})
script = UpdateStudy()
# note that we changed where the argument gets evaluated
# previsously, it took the arguments and then evaluated them within the script
# now, it evaluates the arugments in the context of the main script so they get
# evaluated before they are passed to the script -
# this allows us to do a lot more things like strings, functions, etc.
# and it makes the arguments less confusing to use.
script.do_task(task,
workflow.study_id,
workflow.id,
title=details.title,
short_title=details.short_title,
pi=details.pi,
short_name=details.short_name,
proposal_name=details.proposal_name)
self.assertEqual(details.title, workflow.study.title)
self.assertEqual(details.short_title, workflow.study.short_title)
self.assertEqual(details.pi, workflow.study.primary_investigator_id)
self.assertEqual(details.short_name, workflow.study.short_name)
self.assertEqual(details.proposal_name, workflow.study.proposal_name)
def test_file_data_set_changes_irb_code(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
self.load_example_data()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
workflow_model = StudyService._create_workflow_model(
study, workflow_spec_model)
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file = FileService.add_workflow_file(workflow_id=workflow_model.id,
task_spec_name='TaskSpec01',
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
FileDataSet().do_task(task,
study.id,
workflow_model.id,
key="irb_code",
value="Study_App_Doc",
file_id=file.id)
docs = StudyInfo().do_task(task, study.id, workflow_model.id,
"documents")
self.assertTrue(isinstance(docs, Box))
self.assertEqual(1, len(docs.Study_App_Doc.files))
self.assertEqual("Study_App_Doc",
docs.Study_App_Doc.files[0].data_store.irb_code)
def test_add_file_from_task_and_form_errors_on_invalid_form_field_name(
self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
correct_name = task.task_spec.form.fields[0].id
rv = self.app.post(
'/v1.0/file?study_id=%i&workflow_id=%s&task_id=%i&form_field_key=%s'
% (workflow.study_id, workflow.id, task.id, "not_a_known_file"),
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_failure(rv, error_code="invalid_form_field_key")
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
rv = self.app.post(
'/v1.0/file?study_id=%i&workflow_id=%s&task_id=%i&form_field_key=%s'
% (workflow.study_id, workflow.id, task.id, correct_name),
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
def test_get_study_has_details_about_files(self):
# Set up the study and attach a file to it.
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="png",
binary_data=b'1234',
irb_doc_code=irb_code)
api_response = self.app.get('/v1.0/study/%i' % workflow.study_id,
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(api_response)
study = StudySchema().loads(api_response.get_data(as_text=True))
self.assertEqual(1, len(study.files))
self.assertEqual("UVA Compliance/PRC Approval",
study.files[0]["category"])
self.assertEqual("Cancer Center's PRC Approval Form",
study.files[0]["description"])
self.assertEqual("UVA Compliance/PRC Approval.png",
study.files[0]["download_name"])
def test_get_logs_for_study(self):
self.load_example_data()
study = session.query(StudyModel).first()
workflow = self.create_workflow('hello_world', study=study)
processor = WorkflowProcessor(workflow)
task = processor.next_task()
TaskLog().do_task(task, study.id, workflow.id,
level='critical',
code='critical_code',
message='This is my critical message.')
TaskLog().do_task(task, study.id, workflow.id,
level='debug',
code='debug_code',
message='This is my debug message.')
# This workflow adds 3 logs
# some_text = 'variable'
# log('info', 'some_code', 'Some longer message')
# log('info', 'some_other_code', 'Another really long message')
# log('debug', 'debug_code', f'This message has a { some_text }!')
workflow = self.create_workflow('get_logging_for_study', study=study)
workflow_api = self.get_workflow_api(workflow)
task_api = workflow_api.next_task
workflow_api = self.complete_form(workflow, task_api, {})
task_api = workflow_api.next_task
workflow_logs = task_api.data['workflow_logs']
study_logs = task_api.data['study_logs']
self.assertEqual(3, len(workflow_logs))
self.assertEqual(5, len(study_logs))
def test_add_file_from_task_increments_version_and_replaces_on_subsequent_add(
self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code)
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code=irb_code)
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEqual(1, len(file_models))
file_data = FileService.get_workflow_data_files(
workflow_id=workflow.id)
self.assertEqual(1, len(file_data))
self.assertEqual(2, file_data[0].version)
def test_documentation_processing_handles_replacements(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task.task_spec.documentation = "Some simple docs"
docs = WorkflowService._process_documentation(task)
self.assertEqual("Some simple docs", docs)
task.data = {"replace_me": "new_thing"}
task.task_spec.documentation = "{{replace_me}}"
docs = WorkflowService._process_documentation(task)
self.assertEqual("new_thing", docs)
documentation = """
# Bigger Test
* bullet one
* bullet two has {{replace_me}}
# other stuff.
"""
expected = """
# Bigger Test
* bullet one
* bullet two has new_thing
# other stuff.
"""
task.task_spec.documentation = documentation
result = WorkflowService._process_documentation(task)
self.assertEqual(expected, result)
def test_validate_returns_error_if_reference_files_do_not_exist(
self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
self.load_example_data()
self.create_reference_document()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
workflow_model = StudyService._create_workflow_model(
study, workflow_spec_model)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
# Remove the reference file.
file_model = db.session.query(FileModel). \
filter(FileModel.is_reference == True). \
filter(FileModel.name == FileService.DOCUMENT_LIST).first()
if file_model:
db.session.query(FileDataModel).filter(
FileDataModel.file_model_id == file_model.id).delete()
db.session.query(FileModel).filter(
FileModel.id == file_model.id).delete()
db.session.commit()
db.session.flush()
with self.assertRaises(ApiError):
StudyInfo().do_task_validate_only(task, study.id, "documents")
def test_file_data_set_invalid_irb_code_fails(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
self.load_example_data()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
workflow_model = StudyService._create_workflow_model(
study, workflow_spec_model)
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file = FileService.add_workflow_file(workflow_id=workflow_model.id,
task_spec_name='Activity01',
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
with self.assertRaises(ApiError):
FileDataSet().do_task(task,
study.id,
workflow_model.id,
key="irb_code",
value="My_Pretty_Pony",
file_id=file.id)
def test_archive_file_no_longer_shows_up(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
correct_name = task.task_spec.form.fields[0].id
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
rv = self.app.post(
'/v1.0/file?study_id=%i&workflow_id=%s&task_id=%i&form_field_key=%s'
% (workflow.study_id, workflow.id, task.id, correct_name),
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id,
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEqual(1, len(json.loads(rv.get_data(as_text=True))))
file_model = db.session.query(FileModel).filter(
FileModel.workflow_id == workflow.id).all()
self.assertEqual(1, len(file_model))
file_model[0].archived = True
db.session.commit()
rv = self.app.get('/v1.0/file?workflow_id=%s' % workflow.id,
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertEqual(0, len(json.loads(rv.get_data(as_text=True))))
def test_random_data_populate_form_on_auto_complete(self):
self.load_example_data()
workflow = self.create_workflow('enum_options_with_search')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task_api = WorkflowService.spiff_task_to_api_task(task, add_docs_and_forms=True)
WorkflowService.populate_form_with_random_data(task, task_api, required_only=False)
self.assertTrue(isinstance(task.data["sponsor"], dict))
def test_enum_options_from_file(self):
self.load_example_data()
workflow = self.create_workflow('enum_options_from_file')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
WorkflowService.process_options(task, task.task_spec.form.fields[0])
options = task.task_spec.form.fields[0].options
self.assertEqual(28, len(options))
self.assertEqual('1000', options[0]['id'])
self.assertEqual("UVA - INTERNAL - GM USE ONLY", options[0]['name'])
def test_get_current_user_details(self):
self.load_example_data()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
script = Ldap()
g.user = db.session.query(UserModel).filter(
UserModel.uid == 'dhf8r').first()
user_details = script.do_task(task, workflow.study_id, workflow.id)
self.assertEqual(user_details['display_name'], 'Dan Funk')
def test_do_task_with_incorrect_argument(self):
"""This script should raise an error if it can't figure out the approvers."""
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"approvals": {'dhf8r':["invalid"], 'lb3dp':"invalid"}}
script = RequestApproval()
with self.assertRaises(ApiError):
script.do_task(task, workflow.study_id, workflow.id, "approvals")
def test_do_task_validate_only(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"study": {"approval1": "dhf8r", 'approval2':'lb3dp'}}
script = RequestApproval()
script.do_task_validate_only(task, workflow.study_id, workflow.id, "study.approval1")
self.assertEqual(0, db.session.query(ApprovalModel).count())
def test_enum_options_from_file(self):
self.load_example_data()
workflow = self.create_workflow('enum_options_from_file')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
WorkflowService.process_options(task, task.task_spec.form.fields[0])
options = task.task_spec.form.fields[0].options
self.assertEqual(29, len(options))
self.assertEqual('0', options[0].id)
self.assertEqual("Other", options[0].name)
def test_jinja_service_element_documentation(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task.data = {"my_template": "Hi {{name}}, This is a jinja template too!",
"name": "Dan"}
task.task_spec.documentation = """{% include 'my_template' %} Cool Right?"""
docs = WorkflowService._process_documentation(task)
self.assertEqual("Hi Dan, This is a jinja template too! Cool Right?", docs)
def setUp(self):
self.load_example_data()
self.workflow = self.create_workflow('enum_options_all')
self.workflow_api = self.get_workflow_api(self.workflow)
# Assure the form has been loaded at least once.
processor = WorkflowProcessor(self.workflow)
processor.do_engine_steps()
self.task = processor.next_task()
self.assertEqual(self.task.get_name(), 'myFormTask')
self.labelScript = EnumLabel()
def test_get_invalid_user_details(self):
self.load_example_data()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {'PIComputingID': 'rec3z'}
script = Ldap()
user_details = script.do_task(task, workflow.study_id, workflow.id,
"PIComputingID")
self.assertEqual({}, user_details)
def test_do_task(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"details": {"label": "My New Title", "value": "dhf8r"}}
script = UpdateStudy()
script.do_task(task, workflow.study_id, workflow.id,
"title:details.label", "pi:details.value")
self.assertEqual("My New Title", workflow.study.title)
self.assertEqual("dhf8r", workflow.study.primary_investigator_id)
def test_default_values_for_enum_as_checkbox(self):
self.load_test_spec('enum_results')
workflow = self.create_workflow('enum_results')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
service = WorkflowService()
checkbox_enum_field = task.task_spec.form.fields[0]
radio_enum_field = task.task_spec.form.fields[1]
self.assertEqual([],
service.get_default_value(checkbox_enum_field, task))
self.assertEqual(None,
service.get_default_value(radio_enum_field, task))
def test_total_tasks_updated(self, mock_docs):
"""Assure that as a users progress is available when getting a list of studies for that user."""
app.config['PB_ENABLED'] = True
docs_response = self.protocol_builder_response('required_docs.json')
mock_docs.return_value = json.loads(docs_response)
user = self.create_user_with_study_and_workflow()
# The load example data script should set us up a user and at least one study, one category, and one workflow.
studies = StudyService.get_studies_for_user(user)
self.assertTrue(len(studies) == 1)
self.assertTrue(len(studies[0].categories) == 1)
self.assertTrue(len(studies[0].categories[0].workflows) == 1)
workflow = next(iter(
studies[0].categories[0].workflows)) # Workflows is a set.
# workflow should not be started, and it should have 0 completed tasks, and 0 total tasks.
self.assertEqual(WorkflowStatus.not_started, workflow.status)
self.assertEqual(0, workflow.total_tasks)
self.assertEqual(0, workflow.completed_tasks)
# Initialize the Workflow with the workflow processor.
workflow_model = db.session.query(WorkflowModel).filter(
WorkflowModel.id == workflow.id).first()
processor = WorkflowProcessor(workflow_model)
# Assure the workflow is now started, and knows the total and completed tasks.
studies = StudyService.get_studies_for_user(user)
workflow = next(iter(
studies[0].categories[0].workflows)) # Workflows is a set.
# self.assertEqual(WorkflowStatus.user_input_required, workflow.status)
self.assertTrue(workflow.total_tasks > 0)
self.assertEqual(0, workflow.completed_tasks)
self.assertIsNotNone(workflow.spec_version)
# Complete a task
task = processor.next_task()
processor.complete_task(task)
processor.save()
# Assure the workflow has moved on to the next task.
studies = StudyService.get_studies_for_user(user)
workflow = next(iter(
studies[0].categories[0].workflows)) # Workflows is a set.
self.assertEqual(1, workflow.completed_tasks)
# Get approvals
approvals = StudyService.get_approvals(studies[0].id)
self.assertGreater(len(approvals), 0)
self.assertIsNotNone(approvals[0]['display_order'])
def test_hard_reset(self):
self.load_example_data()
# Start the two_forms workflow, and enter some data in the first form.
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
processor = self.get_processor(study, workflow_spec_model)
self.assertEqual(processor.workflow_model.workflow_spec_id,
workflow_spec_model.id)
task = processor.next_task()
task.data = {"color": "blue"}
processor.complete_task(task)
next_task = processor.next_task()
self.assertEqual("Step 2", next_task.task_spec.description)
# Modify the specification, with a major change that alters the flow and can't be serialized effectively.
file_path = os.path.join(app.root_path, '..', 'tests', 'data',
'two_forms', 'mods',
'two_forms_struc_mod.bpmn')
self.replace_file("two_forms.bpmn", file_path)
# Assure that creating a new processor doesn't cause any issues, and maintains the spec version.
processor.workflow_model.bpmn_workflow_json = processor.serialize()
processor2 = WorkflowProcessor(processor.workflow_model)
self.assertFalse(processor2.is_latest_spec) # Still at version 1.
# Do a hard reset, which should bring us back to the beginning, but retain the data.
processor3 = WorkflowProcessor(processor.workflow_model,
hard_reset=True)
self.assertEqual("Step 1",
processor3.next_task().task_spec.description)
self.assertTrue(processor3.is_latest_spec) # Now at version 2.
task = processor3.next_task()
task.data = {"color": "blue"}
processor3.complete_task(task)
self.assertEqual("New Step",
processor3.next_task().task_spec.description)
self.assertEqual("blue", processor3.next_task().data["color"])
def test_do_task_with_blank_second_approver(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
task.data = {"study": {"approval1": "dhf8r", 'approval2':''}}
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code="UVACompl_PRCAppr",
name="anything.png", content_type="text",
binary_data=b'1234')
script = RequestApproval()
script.do_task(task, workflow.study_id, workflow.id, "study.approval1", "study.approval2")
self.assertEqual(1, db.session.query(ApprovalModel).count())
def test_no_validation_error_when_correct_file_exists(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
self.load_example_data()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
workflow_model = StudyService._create_workflow_model(
study, workflow_spec_model)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
StudyInfo().do_task_validate_only(task, study.id, workflow_model.id,
"documents")
def test_documentation_processing_handles_conditionals(self):
self.load_example_data()
workflow = self.create_workflow('random_fact')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
task.task_spec.documentation = "This test {% if works == 'yes' %}works{% endif %}"
docs = WorkflowService._process_documentation(task)
self.assertEqual("This test ", docs)
task.data = {"works": 'yes'}
docs = WorkflowService._process_documentation(task)
self.assertEqual("This test works", docs)
def test_timer_event(self):
workflow = self.create_workflow('timer_event')
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task = processor.next_task()
processor.complete_task(task)
tasks = processor.get_ready_user_tasks()
self.assertEqual(tasks, [])
processor.save()
time.sleep(.3) # our timer is at .25 sec so we have to wait for it
# get done waiting
WorkflowService.do_waiting()
wf = db.session.query(WorkflowModel).filter(
WorkflowModel.id == workflow.id).first()
self.assertTrue(wf.status != WorkflowStatus.waiting)
def test_study_info_returns_a_box_object(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
self.load_example_data()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
workflow_model = StudyService._create_workflow_model(
study, workflow_spec_model)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
docs = StudyInfo().do_task(task, study.id, workflow_model.id,
"documents")
self.assertTrue(isinstance(docs, Box))
docs = StudyInfo().do_task_validate_only(task, study.id,
workflow_model.id,
"documents")
self.assertTrue(isinstance(docs, Box))
def test_publish_to_github_updates(self, mock_github):
mock_github.return_value = FakeGithub()
self.load_example_data()
workflow = self.create_workflow('file_upload_form')
processor = WorkflowProcessor(workflow)
task = processor.next_task()
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
file_model = FileService.add_workflow_file(
workflow_id=workflow.id,
irb_doc_code=irb_code,
task_spec_name=task.get_name(),
name="anything.png",
content_type="text",
binary_data=b'1234')
result = FileService.publish_to_github([file_model.id])
self.assertEqual(result['updated'], True)