def test_change_primary_bpmn(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()
data = {}
data['file'] = io.BytesIO(
self.minimal_bpmn("abcdef")), 'my_new_file.bpmn'
# Add a new BPMN file to the specification
rv = self.app.post('/v1.0/file?workflow_spec_id=%s' % spec.id,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
# Delete the primary BPMN file for the workflow.
orig_model = session.query(FileModel).\
filter(FileModel.primary == True).\
filter(FileModel.workflow_spec_id == spec.id).first()
rv = self.app.delete('/v1.0/file?file_id=%s' % orig_model.id,
headers=self.logged_in_headers())
# Set that new file to be the primary BPMN, assure it has a primary_process_id
file.primary = True
rv = self.app.put('/v1.0/file/%i' % file.id,
content_type="application/json",
data=json.dumps(FileModelSchema().dump(file)),
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertTrue(json_data['primary'])
self.assertIsNotNone(json_data['primary_process_id'])
def test_create_file(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()
data = {'file': (io.BytesIO(b"abcdef"), 'random_fact.svg')}
rv = self.app.post('/v1.0/file?workflow_spec_id=%s' % spec.id,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(FileType.svg, file.type)
self.assertFalse(file.primary)
self.assertEqual("image/svg+xml", file.content_type)
self.assertEqual(spec.id, file.workflow_spec_id)
rv = self.app.get('/v1.0/file/%i' % file.id,
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
file2 = FileModelSchema().load(json_data, session=session)
self.assertEqual(file, file2)
def test_list_reference_files(self):
ExampleDataLoader.clean_db()
file_name = DocumentService.DOCUMENT_LIST
filepath = os.path.join(app.root_path, 'static', 'reference',
'irb_documents.xlsx')
with open(filepath, 'rb') as myfile:
file_data = myfile.read()
data = {'file': (io.BytesIO(file_data), file_name)}
rv = self.app.post('/v1.0/reference_file',
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/reference_file',
follow_redirects=True,
content_type="application/json",
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(1, len(json_data))
file = FileModelSchema(many=True).load(json_data, session=session)
self.assertEqual(file_name, file[0].name)
self.assertTrue(file[0].is_reference)
def write_file_info_to_system(file_path, file_model):
json_file_path = f'{file_path}.json'
latest_file_model = session.query(FileModel).filter(
FileModel.id == file_model.id).first()
file_schema = FileModelSchema().dumps(latest_file_model)
with open(json_file_path, 'w') as j_handle:
j_handle.write(file_schema)
def test_document_added_to_workflow_shows_up_in_file_list(self):
self.load_example_data()
self.create_reference_document()
workflow = self.create_workflow('docx')
# get the first form in the two form workflow.
task = self.get_workflow_api(workflow).next_task
data = {
"full_name": "Buck of the Wild",
"date": "5/1/2020",
"title": "Leader of the Pack",
"company": "In the company of wolves",
"last_name": "Mr. Wolf"
}
workflow_api = self.complete_form(workflow, task, data)
self.assertIsNotNone(workflow_api.next_task)
self.assertEqual("EndEvent_0evb22x", workflow_api.next_task.name)
self.assertTrue(workflow_api.status == WorkflowStatus.complete)
rv = self.app.get('/v1.0/file?workflow_id=%i' % workflow.id,
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
files = FileModelSchema(many=True).load(json_data, session=session)
self.assertTrue(len(files) == 1)
# Assure we can still delete the study even when there is a file attached to a workflow.
rv = self.app.delete('/v1.0/study/%i' % workflow.study_id,
headers=self.logged_in_headers())
self.assert_success(rv)
def get_protocol(study_id):
"""Returns the study protocol, if it has been uploaded."""
file = db.session.query(FileModel)\
.filter_by(study_id=study_id)\
.filter_by(form_field_key='Study_Protocol_Document')\
.first()
return FileModelSchema().dump(file)
def update_reference_file_info(self, old_file_model, body):
file_data = self.get_reference_file_data(old_file_model.name)
old_file_path = self.get_reference_file_path(old_file_model.name)
self.delete_reference_file_data(old_file_path)
self.delete_reference_file_info(old_file_path)
new_file_model = FileModelSchema().load(body, session=session)
new_file_path = self.get_reference_file_path(new_file_model.name)
self.write_reference_file_data_to_system(new_file_path, file_data.data)
self.write_reference_file_info_to_system(new_file_path, new_file_model)
return new_file_model
def test_update_file_info(self):
self.load_example_data()
file: FileModel = session.query(FileModel).first()
file.name = "silly_new_name.bpmn"
rv = self.app.put('/v1.0/file/%i' % file.id,
content_type="application/json",
data=json.dumps(FileModelSchema().dump(file)),
headers=self.logged_in_headers())
self.assert_success(rv)
db_file = session.query(FileModel).filter_by(id=file.id).first()
self.assertIsNotNone(db_file)
self.assertEqual(file.name, db_file.name)
def update_file_info(file_id, body):
if file_id is None:
raise ApiError('no_such_file', 'Please provide a valid File ID.')
file_model = session.query(FileModel).filter_by(id=file_id).first()
if file_model is None:
raise ApiError('unknown_file_model', 'The file_model "' + file_id + '" is not recognized.')
file_model = FileModelSchema().load(body, session=session)
session.add(file_model)
session.commit()
return FileSchema().dump(to_file_api(file_model))
def test_list_files_for_workflow_spec(self):
self.load_example_data(use_crc_data=True)
spec_id = 'core_info'
spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
rv = self.app.get('/v1.0/file?workflow_spec_id=%s' % spec_id,
follow_redirects=True,
content_type="application/json",
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(5, len(json_data))
files = FileModelSchema(many=True).load(json_data, session=session)
file_names = [f.name for f in files]
self.assertTrue("%s.bpmn" % spec.name in file_names)
def update_spec_file_info(self, old_file_model, body):
file_data = self.get_spec_file_data(old_file_model.id)
old_file_path = self.get_path_from_spec_file_model(old_file_model)
self.delete_spec_file_data(old_file_path)
self.delete_spec_file_info(old_file_path)
new_file_model = FileModelSchema().load(body, session=session)
new_file_path = self.get_path_from_spec_file_model(new_file_model)
self.write_file_data_to_system(new_file_path, file_data.data)
self.write_file_info_to_system(new_file_path, new_file_model)
print('update_spec_file_info')
return new_file_model
def test_set_reference_file(self):
file_name = "irb_document_types.xls"
data = {'file': (io.BytesIO(b"abcdef"), "does_not_matter.xls")}
rv = self.app.put('/v1.0/reference_file/%s' % file_name,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(FileType.xls, file.type)
self.assertTrue(file.is_reference)
self.assertEqual("application/vnd.ms-excel", file.content_type)
def test_add_reference_file(self):
ExampleDataLoader().load_reference_documents()
file_name = 'new.xlsx'
data = {'file': (io.BytesIO(b"abcdef"), file_name)}
rv = self.app.post('/v1.0/reference_file',
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(FileType.xlsx, file.type)
self.assertFalse(file.primary)
self.assertEqual(True, file.is_reference)
def process_workflow_spec_file(session, workflow_spec_file,
workflow_spec_file_path):
# workflow_spec_file_path = os.path.join
os.makedirs(os.path.dirname(workflow_spec_file_path), exist_ok=True)
file_data_model = session.query(FileDataModel). \
filter(FileDataModel.file_model_id == workflow_spec_file.id). \
order_by(sa.desc(FileDataModel.version)). \
first()
with open(workflow_spec_file_path, 'wb') as f_handle:
f_handle.write(file_data_model.data)
json_file_path = f'{workflow_spec_file_path}.json'
workflow_spec_file_model = session.query(FileModel).filter(
FileModel.id == file_data_model.file_model_id).first()
workflow_spec_file_schema = FileModelSchema().dumps(
workflow_spec_file_model)
with open(json_file_path, 'w') as j_handle:
j_handle.write(workflow_spec_file_schema)
def test_update_file_data(self):
self.load_example_data()
spec = session.query(WorkflowSpecModel).first()
data = {}
data['file'] = io.BytesIO(
self.minimal_bpmn("abcdef")), 'my_new_file.bpmn'
rv = self.app.post('/v1.0/file?workflow_spec_id=%s' % spec.id,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
data['file'] = io.BytesIO(
self.minimal_bpmn("efghijk")), 'my_new_file.bpmn'
rv = self.app.put('/v1.0/file/%i/data' % file.id,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
file_json = json.loads(rv.get_data(as_text=True))
self.assertEqual(2, file_json['latest_version'])
self.assertEqual(FileType.bpmn.value, file_json['type'])
self.assertEqual("application/octet-stream", file_json['content_type'])
self.assertEqual(spec.id, file.workflow_spec_id)
# Assure it is updated in the database and properly persisted.
file_model = session.query(FileModel).filter(
FileModel.id == file.id).first()
file_data = FileService.get_file_data(file_model.id)
self.assertEqual(2, file_data.version)
rv = self.app.get('/v1.0/file/%i/data' % file.id,
headers=self.logged_in_headers())
self.assert_success(rv)
data = rv.get_data()
self.assertIsNotNone(data)
self.assertEqual(self.minimal_bpmn("efghijk"), data)
def test_list_reference_files(self):
ExampleDataLoader.clean_db()
file_name = FileService.DOCUMENT_LIST
data = {'file': (io.BytesIO(b"abcdef"), file_name)}
rv = self.app.put('/v1.0/reference_file/%s' % file_name,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
rv = self.app.get('/v1.0/reference_file',
follow_redirects=True,
content_type="application/json",
headers=self.logged_in_headers())
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
self.assertEqual(1, len(json_data))
file = FileModelSchema(many=True).load(json_data, session=session)
self.assertEqual(file_name, file[0].name)
self.assertTrue(file[0].is_reference)
def test_update_reference_file_data(self):
self.load_example_data()
file_name = "documents.xlsx"
filepath = os.path.join(app.root_path, 'static', 'reference',
'irb_documents.xlsx')
with open(filepath, 'rb') as myfile:
file_data = myfile.read()
data = {'file': (io.BytesIO(file_data), file_name)}
rv = self.app.put('/v1.0/reference_file/%s/data' % file_name,
data=data,
follow_redirects=True,
content_type='multipart/form-data',
headers=self.logged_in_headers())
self.assert_success(rv)
self.assertIsNotNone(rv.get_data())
json_data = json.loads(rv.get_data(as_text=True))
file = FileModelSchema().load(json_data, session=session)
self.assertEqual(FileType.xlsx, file.type)
self.assertTrue(file.is_reference)
self.assertEqual(
"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
file.content_type)
def test_update_file_info(self):
self.load_example_data()
file: FileModel = session.query(FileModel).filter(
column('workflow_spec_id').isnot(None)).first()
file_model = FileModel(id=file.id,
name="silly_new_name.bpmn",
type=file.type,
content_type=file.content_type,
is_reference=file.is_reference,
primary=file.primary,
primary_process_id=file.primary_process_id,
workflow_id=file.workflow_id,
workflow_spec_id=file.workflow_spec_id,
archived=file.archived)
# file.name = "silly_new_name.bpmn"
rv = self.app.put('/v1.0/spec_file/%i' % file.id,
content_type="application/json",
data=json.dumps(FileModelSchema().dump(file_model)),
headers=self.logged_in_headers())
self.assert_success(rv)
db_file = session.query(FileModel).filter_by(id=file.id).first()
self.assertIsNotNone(db_file)
self.assertEqual("silly_new_name.bpmn", db_file.name)