def test_info_script_documents(self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
response = ProtocolBuilderService.get_required_docs(self.test_study_id)
study_info, second_task = self.do_work(info_type='documents')
self.assertEqual(study_info, second_task.data['info'])
self.assertEqual(0, len(study_info['Grant_App']['files']),
"Grant_App has not files yet.")
# Add a grant app file
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
rv = self.app.post(
'/v1.0/file?study_id=%i&workflow_id=%s&task_spec_name=%s&form_field_key=%s'
% (self.workflow.study_id, self.workflow.id, second_task.name,
'Grant_App'),
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
file_data = json.loads(rv.get_data(as_text=True))
# Now get the study info again.
study_info = StudyInfo().do_task(self.workflow_api.study_id,
self.workflow.study.id,
self.workflow.id, 'documents')
# The data should contain a file.
self.assertEqual(1, len(study_info['Grant_App']['files']),
"Grant_App has exactly one file.")
# This file data returned should be the same as what we get back about the file when we uploaded it,
# but the details on the document should be removed, because that would be recursive.
del file_data['document']
self.assertEqual(file_data, study_info['Grant_App']['files'][0])
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_study_roles_returns_box(self, mock_investigators):
investigators_response = self.protocol_builder_response(
'investigators.json')
mock_investigators.return_value = json.loads(investigators_response)
docs = StudyInfo().do_task(self.task, self.study.id,
self.workflow_model.id, "roles")
self.assertTrue(isinstance(docs, Box))
def test_study_info_returns_a_box_object_for_all_validations(
self, mock_get):
app.config['PB_ENABLED'] = True
mock_get.return_value.ok = True
for option in StudyInfo.type_options:
if option == 'info':
mock_get.return_value.text = self.protocol_builder_response(
'irb_info.json')
elif option == 'investigators':
mock_get.return_value.text = self.protocol_builder_response(
'investigators.json')
elif option == 'roles':
mock_get.return_value.text = self.protocol_builder_response(
'investigators.json')
elif option == 'details':
mock_get.return_value.text = self.protocol_builder_response(
'study_details.json')
elif option == 'documents':
mock_get.return_value.text = self.protocol_builder_response(
'required_docs.json')
elif option == 'sponsors':
mock_get.return_value.text = self.protocol_builder_response(
'sponsors.json')
data = StudyInfo().do_task_validate_only(self.task, self.study.id,
self.workflow_model.id,
option)
if isinstance(data, list):
for x in data:
self.assertIsInstance(
x, Box, "this is not a list of boxes:" + option)
else:
self.assertIsInstance(data, Box, "this is not a box:" + option)
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_study_sponsors_returns_box(self, mock):
response = self.protocol_builder_response('sponsors.json')
mock.return_value = json.loads(response)
data = StudyInfo().do_task(self.task, self.study.id,
self.workflow_model.id, "sponsors")
self.assertTrue(isinstance(data, list))
for x in data:
self.assertIsInstance(x, Box)
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_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 do_work(self, info_type):
app.config['PB_ENABLED'] = True
self.load_example_data()
self.workflow = self.create_workflow('study_info_script')
self.workflow_api = self.get_workflow_api(self.workflow)
# grab study_info directly from script
study_info = StudyInfo().do_task(self.workflow_api.study_id,
self.workflow.study.id,
self.workflow.id, info_type)
# grab study info through a workflow
first_task = self.workflow_api.next_task
self.complete_form(self.workflow, first_task, {'which': info_type})
workflow_api = self.get_workflow_api(self.workflow)
second_task = workflow_api.next_task
return study_info, second_task
def test_study_details_returns_box(self, mock_details):
details_response = self.protocol_builder_response('study_details.json')
mock_details.return_value = json.loads(details_response)
data = StudyInfo().do_task(self.task, self.study.id,
self.workflow_model.id, "details")
self.assertTrue(isinstance(data, Box))
def test_study_info_returns_a_box_object(self):
docs = StudyInfo().do_task(self.task, self.study.id,
self.workflow_model.id, "info")
self.assertTrue(isinstance(docs, Box))