def test_get_documents_has_file_details(self, mock_docs):
# mock out the protocol builder
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()
# Add a document to the study with the correct code.
workflow = self.create_workflow('docx')
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)
docs = StudyService().get_documents_status(workflow.study_id)
self.assertIsNotNone(docs)
self.assertEqual("not_started", docs["UVACompl_PRCAppr"]['status'])
self.assertEqual(1, docs["UVACompl_PRCAppr"]['count'])
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0])
self.assertIsNotNone(docs["UVACompl_PRCAppr"]['files'][0]['file_id'])
self.assertEqual(workflow.id,
docs["UVACompl_PRCAppr"]['files'][0]['workflow_id'])
def test_new_approval_requests_after_file_modification_create_new_requests(
self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code="UVACompl_PRCAppr")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
self.assertEqual(2, db.session.query(ApprovalModel).count())
models = db.session.query(ApprovalModel).order_by(
ApprovalModel.version).all()
self.assertEqual(1, models[0].version)
self.assertEqual(2, models[1].version)
def test_delete_irb_document(self):
self.load_example_data()
irb_code = 'Study_Protocol_Document'
workflow = self.create_workflow('add_delete_irb_document')
study_id = workflow.study_id
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
# Should not have any files yet
files = FileService.get_files_for_study(study_id)
self.assertEqual(0, len(files))
self.assertEqual(False, IsFileUploaded.do_task(
IsFileUploaded, first_task, study_id, workflow.id, irb_code))
# Add a file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="filename.txt", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code)
# Assert we have the file
self.assertEqual(True, IsFileUploaded.do_task(
IsFileUploaded, first_task, study_id, workflow.id, irb_code))
# run the workflow, which deletes the file
self.complete_form(workflow, first_task, {'irb_document': irb_code})
workflow_api = self.get_workflow_api(workflow)
second_task = workflow_api.next_task
# make sure it is deleted
self.assertEqual(False, IsFileUploaded.do_task(
IsFileUploaded, second_task, study_id, workflow.id, irb_code))
print('test_delete_irb_document')
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_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_zipped_files(self):
self.load_example_data()
workflow = self.create_workflow('get_zip_file')
study_id = workflow.study_id
workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task
# Add files to use in the test
model_1 = FileService.add_workflow_file(
workflow_id=workflow.id,
name="document_1.png",
content_type="text",
task_spec_name=task.name,
binary_data=b'1234',
irb_doc_code='Study_Protocol_Document')
model_2 = FileService.add_workflow_file(workflow_id=workflow.id,
name="document_2.txt",
content_type="text",
task_spec_name=task.name,
binary_data=b'1234',
irb_doc_code='Study_App_Doc')
model_3 = FileService.add_workflow_file(
workflow_id=workflow.id,
name="document_3.pdf",
content_type="text",
task_spec_name=task.name,
binary_data=b'1234',
irb_doc_code='AD_Consent_Model')
file_ids = [{
'file_id': model_1.id
}, {
'file_id': model_2.id
}, {
'file_id': model_3.id
}]
workflow_api = self.complete_form(workflow, task,
{'file_ids': file_ids})
next_task = workflow_api.next_task
file_model_id = next_task.data['zip_file']['id']
file_data = session.query(FileDataModel).filter(
FileDataModel.file_model_id == file_model_id).first()
# Test what we get back in the zipped file
with zipfile.ZipFile(io.BytesIO(file_data.data), 'r') as zf:
self.assertIsInstance(zf, zipfile.ZipFile)
for name in zf.namelist():
info = zf.getinfo(name)
self.assertIn(os.path.basename(info.filename), [
f'{study_id} Protocol document_1.png',
f'{study_id} Application document_2.txt',
f'{study_id} Model document_3.pdf'
])
file = zf.read(name)
self.assertEqual(b'1234', file)
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
workflow = session.query(WorkflowModel).filter(
WorkflowModel.id == workflow_id).first()
final_document_stream = self.process_template(task, study_id, workflow,
*args, **kwargs)
file_name = args[0]
irb_doc_code = args[1]
FileService.add_workflow_file(workflow_id=workflow_id,
name=file_name,
content_type=CONTENT_TYPES['docx'],
binary_data=final_document_stream.read(),
irb_doc_code=irb_doc_code)
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_workflow_restart_delete_files(self):
self.load_example_data()
irb_code = 'Study_Protocol_Document'
workflow = self.create_workflow('add_delete_irb_document')
study_id = workflow.study_id
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
# Should not have any files yet
files = FileService.get_files_for_study(study_id)
self.assertEqual(0, len(files))
self.assertEqual(
False,
IsFileUploaded.do_task(IsFileUploaded, first_task, study_id,
workflow.id, irb_code))
# Add a file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="filename.txt",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code)
# Assert we have the file
self.assertEqual(
True,
IsFileUploaded.do_task(IsFileUploaded, first_task, study_id,
workflow.id, irb_code))
workflow_api = self.restart_workflow_api(workflow_api,
delete_files=False)
first_task = workflow_api.next_task
# Assert we still have the file
self.assertEqual(
True,
IsFileUploaded.do_task(IsFileUploaded, first_task, study_id,
workflow.id, irb_code))
workflow_api = self.restart_workflow_api(workflow_api,
delete_files=True)
first_task = workflow_api.next_task
# Assert we do not have the file
self.assertEqual(
False,
IsFileUploaded.do_task(IsFileUploaded, first_task, study_id,
workflow.id, irb_code))
def add_file(workflow_id=None, task_spec_name=None, form_field_key=None):
file = connexion.request.files['file']
if workflow_id:
if form_field_key is None:
raise ApiError(
'invalid_workflow_file',
'When adding a workflow related file, you must specify a form_field_key'
)
if task_spec_name is None:
raise ApiError(
'invalid_workflow_file',
'When adding a workflow related file, you must specify a task_spec_name'
)
file_model = FileService.add_workflow_file(
workflow_id=workflow_id,
irb_doc_code=form_field_key,
task_spec_name=task_spec_name,
name=file.filename,
content_type=file.content_type,
binary_data=file.stream.read())
else:
raise ApiError(
"invalid_file",
"You must supply either a workflow spec id or a workflow_id and form_field_key."
)
return FileSchema().dump(to_file_api(file_model))
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_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_get_not_really_csv_content(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('empty_workflow')
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
records = ApprovalService.get_not_really_csv_content()
self.assertEqual(len(records), 2)
def test_create_approval_record(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code="UVACompl_PRCAppr")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
self.assertEqual(1, db.session.query(ApprovalModel).count())
model = db.session.query(ApprovalModel).first()
self.assertEqual(workflow.study_id, model.study_id)
self.assertEqual(workflow.id, model.workflow_id)
self.assertEqual("dhf8r", model.approver_uid)
self.assertEqual(1, model.version)
def test_add_file_from_form_increments_version_and_replaces_on_subsequent_add_with_same_name(
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,
irb_doc_code=irb_code,
name="anything.png",
content_type="text",
binary_data=b'1234')
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="anything.png",
content_type="text",
binary_data=b'5678')
def test_directory_list(self):
self.load_example_data()
irb_code_1 = 'UVACompl_PRCAppr'
irb_code_2 = 'Study_App_Doc'
workflow = self.create_workflow('empty_workflow')
first_task = self.get_workflow_api(workflow).next_task
study_id = workflow.study_id
# Add a file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="something.png",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code_1)
# Add second file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code=irb_code_2)
# Get back the list of documents and their directories.
rv = self.app.get('/v1.0/document_directory/%i' % study_id,
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
print(json_data)
self.assertEqual(2, len(json_data))
self.assertEqual('UVA Compliance', json_data[0]['level'])
self.assertEqual('PRC Approval', json_data[0]['children'][0]['level'])
self.assertEqual(
'something.png',
json_data[0]['children'][0]['children'][0]['file']['name'])
self.assertEqual('Study', json_data[1]['level'])
self.assertEqual('Application', json_data[1]['children'][0]['level'])
self.assertEqual('Document',
json_data[1]['children'][0]['children'][0]['level'])
self.assertEqual(
'anything.png', json_data[1]['children'][0]['children'][0]
['children'][0]['file']['name'])
def test_delete_file_after_approval(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code="UVACompl_PRCAppr")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anotother_anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code="Study_App_Doc")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
file = session.query(FileModel).\
filter(FileModel.workflow_id == workflow.id).\
filter(FileModel.name == "anything.png").first()
self.assertFalse(file.archived)
rv = self.app.get('/v1.0/file/%i' % file.id,
headers=self.logged_in_headers())
self.assert_success(rv)
rv = self.app.delete('/v1.0/file/%i' % file.id,
headers=self.logged_in_headers())
self.assert_success(rv)
session.refresh(file)
self.assertTrue(file.archived)
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
approvals = session.query(ApprovalModel)\
.filter(ApprovalModel.status == ApprovalStatus.PENDING.value)\
.filter(ApprovalModel.study_id == workflow.study_id).all()
self.assertEqual(1, len(approvals))
self.assertEqual(1, len(approvals[0].approval_files))
def test_file_datastore_workflow(self):
self.load_example_data()
# we need to create a file with an IRB code
# for this study
workflow = self.create_workflow('file_data_store')
irb_code = "UVACompl_PRCAppr" # The first file referenced in pb required docs.
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name='task1',
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code)
processor = WorkflowProcessor(workflow)
processor.do_engine_steps()
task_data = processor.bpmn_workflow.last_task.data
self.assertTrue(str(task_data['fileid']) in task_data['fileurl'])
self.assertEqual(task_data['filename'], 'anything.png')
self.assertEqual(task_data['output'], 'me')
self.assertEqual(task_data['output2'], 'nope')
def test_replace_archive_file_unarchives_the_file_and_updates(self):
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.
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')
# Archive the file
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEqual(1, len(file_models))
file_model = file_models[0]
file_model.archived = True
db.session.add(file_model)
# Assure that the file no longer comes back.
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEqual(0, len(file_models))
# Add the file again with different data
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'5678')
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)
self.assertEqual(b'5678', file_data[0].data)
def test_delete_irb_document_list(self):
# try deleting a list of files
self.load_example_data()
irb_code_1 = 'Study_Protocol_Document'
irb_code_2 = 'Study_App_Doc'
irb_codes = [irb_code_1, irb_code_2]
workflow = self.create_workflow('add_delete_irb_document')
study_id = workflow.study_id
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
# Should not have any files yet
files = FileService.get_files_for_study(study_id)
self.assertEqual(0, len(files))
self.assertEqual(False, IsFileUploaded.do_task(IsFileUploaded, first_task, study_id, workflow.id, irb_code_1))
self.assertEqual(False, IsFileUploaded.do_task(IsFileUploaded, first_task, study_id, workflow.id, irb_code_2))
# Add a file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="filename.txt", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code_1)
# Add another file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="filename.txt", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code_2)
self.assertEqual(True, IsFileUploaded.do_task(
IsFileUploaded, first_task, study_id, workflow.id, irb_code_1))
self.assertEqual(True, IsFileUploaded.do_task(
IsFileUploaded, first_task, study_id, workflow.id, irb_code_2))
self.complete_form(workflow, first_task, {'irb_document': irb_codes})
workflow_api = self.get_workflow_api(workflow)
second_task = workflow_api.next_task
self.assertEqual(False, IsFileUploaded.do_task(
IsFileUploaded, second_task, study_id, workflow.id, irb_code_1))
self.assertEqual(False, IsFileUploaded.do_task(
IsFileUploaded, second_task, study_id, workflow.id, irb_code_2))
def test_add_file_from_form_allows_multiple_files_with_different_names(
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,
irb_doc_code=irb_code,
name="anything.png",
content_type="text",
binary_data=b'1234')
# Add the file again with different data
FileService.add_workflow_file(workflow_id=workflow.id,
irb_doc_code=irb_code,
name="a_different_thing.png",
content_type="text",
binary_data=b'5678')
file_models = FileService.get_workflow_files(workflow_id=workflow.id)
self.assertEqual(2, len(file_models))
def test_get_all_studies(self):
user = self.create_user_with_study_and_workflow()
study = db.session.query(StudyModel).filter_by(
user_uid=user.uid).first()
self.assertIsNotNone(study)
# Add a document to the study with the correct code.
workflow1 = self.create_workflow('docx', study=study)
workflow2 = self.create_workflow('empty_workflow', study=study)
# Add files to both workflows.
FileService.add_workflow_file(workflow_id=workflow1.id,
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code="UVACompl_PRCAppr")
FileService.add_workflow_file(workflow_id=workflow1.id,
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code="AD_Consent_Model")
FileService.add_workflow_file(workflow_id=workflow2.id,
name="anything.png",
content_type="text",
binary_data=b'1234',
irb_doc_code="UVACompl_PRCAppr")
studies = StudyService().get_all_studies_with_files()
self.assertEqual(1, len(studies))
self.assertEqual(3, len(studies[0].files))
def test_new_approval_cancels_all_previous_approvals(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code="UVACompl_PRCAppr")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="lb3dp")
current_count = ApprovalModel.query.count()
self.assertTrue(current_count, 2)
FileService.add_workflow_file(workflow_id=workflow.id,
name="borderline.png",
content_type="text",
binary_data=b'906090',
irb_doc_code="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="dhf8r")
current_count = ApprovalModel.query.count()
canceled_count = ApprovalModel.query.filter(
ApprovalModel.status == ApprovalStatus.CANCELED.value)
self.assertTrue(current_count, 2)
self.assertTrue(current_count, 3)
ApprovalService.add_approval(study_id=workflow.study_id,
workflow_id=workflow.id,
approver_uid="lb3dp")
current_count = ApprovalModel.query.count()
self.assertTrue(current_count, 4)
def test_delete_workflow(self):
self.load_example_data()
workflow = session.query(WorkflowModel).first()
FileService.add_workflow_file(workflow_id=workflow.id, task_spec_name='TaskSpec01',
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
workflow_files = session.query(FileModel).filter_by(workflow_id=workflow.id)
self.assertEqual(workflow_files.count(), 1)
workflow_files_ids = [file.id for file in workflow_files]
rv = self.app.delete(f'/v1.0/workflow/{workflow.id}', headers=self.logged_in_headers())
self.assert_success(rv)
# No files should have the deleted workflow id anymore
workflow_files = session.query(FileModel).filter_by(workflow_id=workflow.id)
self.assertEqual(workflow_files.count(), 0)
# Finally, let's confirm the file was archived
workflow_files = session.query(FileModel).filter(FileModel.id.in_(workflow_files_ids))
for file in workflow_files:
self.assertTrue(file.archived)
self.assertIsNone(file.workflow_id)
def test_file_uploaded_pass(self):
self.load_example_data()
irb_code_1 = 'UVACompl_PRCAppr'
irb_code_2 = 'Study_App_Doc'
workflow = self.create_workflow('empty_workflow')
first_task = self.get_workflow_api(workflow).next_task
study_id = workflow.study_id
# We shouldn't have any files yet.
files = FileService.get_files_for_study(study_id)
self.assertEqual(0, len(files))
self.assertEqual(False, IsFileUploaded.do_task(IsFileUploaded, first_task, study_id, workflow.id, irb_code_1))
# Add a file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="something.png", content_type="text",
binary_data=b'1234', irb_doc_code=irb_code_1)
# Make sure we find the file
files = FileService.get_files_for_study(study_id)
self.assertEqual(1, len(files))
self.assertEqual(True, IsFileUploaded.do_task(IsFileUploaded, first_task, study_id, workflow.id, irb_code_1))
# Add second file
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code=irb_code_2)
# Make sure we find both files.
files = FileService.get_files_for_study(study_id)
self.assertEqual(2, len(files))
self.assertEqual(True, IsFileUploaded.do_task(IsFileUploaded, first_task, study_id, workflow.id, irb_code_1))
self.assertEqual(True, IsFileUploaded.do_task(IsFileUploaded, first_task, study_id, workflow.id, irb_code_2))
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)
def test_email_script_attachments(self):
self.load_example_data()
irb_code_1 = 'Study_App_Doc'
irb_code_2 = 'Study_Protocol_Document'
workflow = self.create_workflow('email_script')
workflow_api = self.get_workflow_api(workflow)
first_task = workflow_api.next_task
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="something.png",
content_type="text",
binary_data=b'1234',
irb_doc_code=irb_code_1)
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="another.png",
content_type="text",
binary_data=b'67890',
irb_doc_code=irb_code_1)
FileService.add_workflow_file(workflow_id=workflow.id,
task_spec_name=first_task.name,
name="anything.png",
content_type="text",
binary_data=b'5678',
irb_doc_code=irb_code_2)
with mail.record_messages() as outbox:
self.complete_form(
workflow, first_task, {
'subject':
'My Test Subject',
'recipients':
'*****@*****.**',
'doc_codes': [{
'doc_code': irb_code_1
}, {
'doc_code': irb_code_2
}]
})
self.assertEqual(1, len(outbox))
self.assertEqual(3, len(outbox[0].attachments))
self.assertEqual('image/png',
outbox[0].attachments[0].content_type)
self.assertEqual('something.png',
outbox[0].attachments[0].filename)
self.assertEqual(b'1234', outbox[0].attachments[0].data)
def test_update_from_github(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')
FileService.update_from_github([file_model.id])
file_model_data = FileDataModel.query.filter_by(
file_model_id=file_model.id).order_by(desc(
FileDataModel.version)).first()
self.assertEqual(file_model_data.data, b'Some bytes')