def add_study(body):
"""Or any study like object. Body should include a title, and primary_investigator_id """
if 'primary_investigator_id' not in body:
raise ApiError(
"missing_pi",
"Can't create a new study without a Primary Investigator.")
if 'title' not in body:
raise ApiError("missing_title",
"Can't create a new study without a title.")
study_model = StudyModel(
user_uid=UserService.current_user().uid,
title=body['title'],
primary_investigator_id=body['primary_investigator_id'],
last_updated=datetime.utcnow(),
status=StudyStatus.in_progress)
session.add(study_model)
StudyService.add_study_update_event(study_model,
status=StudyStatus.in_progress,
event_type=StudyEventType.user,
user_uid=g.user.uid)
errors = StudyService._add_all_workflow_specs_to_study(study_model)
session.commit()
study = StudyService().get_study(study_model.id, do_status=True)
study_data = StudySchema().dump(study)
study_data["errors"] = ApiErrorSchema(many=True).dump(errors)
return study_data
def process_workflow_spec(json_file, directory):
file_path = os.path.join(directory, json_file)
with open(file_path, 'r') as f_open:
data = f_open.read()
data_obj = json.loads(data)
workflow_spec_model = session.query(WorkflowSpecModel).\
filter(WorkflowSpecModel.id == data_obj['id']).\
first()
if not workflow_spec_model:
category_id = None
if data_obj['category'] is not None:
category_id = session.query(
WorkflowSpecCategoryModel.id).filter(
WorkflowSpecCategoryModel.display_name ==
data_obj['category']['display_name']).scalar()
workflow_spec_model = WorkflowSpecModel(
id=data_obj['id'],
display_name=data_obj['display_name'],
description=data_obj['description'],
is_master_spec=data_obj['is_master_spec'],
category_id=category_id,
display_order=data_obj['display_order'],
standalone=data_obj['standalone'],
library=data_obj['library'])
session.add(workflow_spec_model)
session.commit()
return workflow_spec_model
def reset(workflow_model, clear_data=False, delete_files=False):
print('WorkflowProcessor: reset: ')
# Try to execute a cancel notify
try:
wp = WorkflowProcessor(workflow_model)
wp.cancel_notify(
) # The executes a notification to all endpoints that
except Exception as e:
app.logger.error(
f"Unable to send a cancel notify for workflow %s during a reset."
f" Continuing with the reset anyway so we don't get in an unresolvable"
f" state. An %s error occured with the following information: %s"
% (workflow_model.id, e.__class__.__name__, str(e)))
workflow_model.bpmn_workflow_json = None
if clear_data:
# Clear form_data from task_events
task_events = session.query(TaskEventModel). \
filter(TaskEventModel.workflow_id == workflow_model.id).all()
for task_event in task_events:
task_event.form_data = {}
session.add(task_event)
if delete_files:
files = FileModel.query.filter(
FileModel.workflow_id == workflow_model.id).all()
for file in files:
FileService.delete_file(file.id)
session.commit()
return WorkflowProcessor(workflow_model)
def delete_spec_file(file_id):
"""This should remove the record in the file table, and both files on the filesystem."""
sync_file_root = SpecFileService.get_sync_file_root()
file_model = session.query(FileModel).filter(
FileModel.id == file_id).first()
workflow_spec_id = file_model.workflow_spec_id
workflow_spec_model = session.query(WorkflowSpecModel).filter(
WorkflowSpecModel.id == workflow_spec_id).first()
category_name = SpecFileService.get_spec_file_category_name(
workflow_spec_model)
file_model_name = file_model.name
spec_directory_path = os.path.join(sync_file_root, category_name,
workflow_spec_model.display_name)
file_path = os.path.join(spec_directory_path, file_model_name)
json_file_path = os.path.join(spec_directory_path,
f'{file_model_name}.json')
try:
os.remove(file_path)
os.remove(json_file_path)
session.delete(file_model)
session.commit()
except IntegrityError as ie:
session.rollback()
file_model = session.query(FileModel).filter_by(id=file_id).first()
file_model.archived = True
session.commit()
app.logger.info(
"Failed to delete file, so archiving it instead. %i, due to %s"
% (file_id, str(ie)))
def update_workflow_spec_file_model(workflow_spec: WorkflowSpecModel,
file_model: FileModel, binary_data,
content_type):
# Verify the extension
file_extension = FileService.get_extension(file_model.name)
if file_extension not in FileType._member_names_:
raise ApiError(
'unknown_extension',
'The file you provided does not have an accepted extension:' +
file_extension,
status_code=404)
else:
file_model.type = FileType[file_extension]
file_model.content_type = content_type
file_model.archived = False # Unarchive the file if it is archived.
# If this is a BPMN, extract the process id.
if file_model.type == FileType.bpmn:
try:
bpmn: etree.Element = etree.fromstring(binary_data)
file_model.primary_process_id = SpecFileService.get_process_id(
bpmn)
file_model.is_review = FileService.has_swimlane(bpmn)
except etree.XMLSyntaxError as xse:
raise ApiError("invalid_xml",
"Failed to parse xml: " + str(xse),
file_name=file_model.name)
session.add(file_model)
session.commit()
return file_model
def test_update_workflow_specification(self):
self.load_example_data()
category_id = 99
category = WorkflowSpecCategoryModel(id=category_id,
name='trap',
display_name="It's a trap!",
display_order=0)
session.add(category)
session.commit()
db_spec_before: WorkflowSpecModel = session.query(
WorkflowSpecModel).first()
spec_id = db_spec_before.id
self.assertNotEqual(db_spec_before.category_id, category_id)
db_spec_before.category_id = category_id
rv = self.app.put('/v1.0/workflow-specification/%s' % spec_id,
content_type="application/json",
headers=self.logged_in_headers(),
data=json.dumps(
WorkflowSpecModelSchema().dump(db_spec_before)))
self.assert_success(rv)
json_data = json.loads(rv.get_data(as_text=True))
api_spec = WorkflowSpecModelSchema().load(json_data, session=session)
self.assertEqual(db_spec_before, api_spec)
db_spec_after: WorkflowSpecModel = session.query(
WorkflowSpecModel).filter_by(id=spec_id).first()
self.assertIsNotNone(db_spec_after.category_id)
self.assertIsNotNone(db_spec_after.category)
self.assertEqual(db_spec_after.category.display_name,
category.display_name)
self.assertEqual(db_spec_after.category.display_order,
category.display_order)
def delete_workflow_specification(spec_id):
if spec_id is None:
raise ApiError('unknown_spec',
'Please provide a valid Workflow Specification ID.')
spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(
id=spec_id).first()
if spec is None:
raise ApiError(
'unknown_spec',
'The Workflow Specification "' + spec_id + '" is not recognized.')
# Delete all items in the database related to the deleted workflow spec.
files = session.query(FileModel).filter_by(workflow_spec_id=spec_id).all()
for file in files:
FileService.delete_file(file.id)
session.query(TaskEventModel).filter(
TaskEventModel.workflow_spec_id == spec_id).delete()
# Delete all events and workflow models related to this specification
for workflow in session.query(WorkflowModel).filter_by(
workflow_spec_id=spec_id):
StudyService.delete_workflow(workflow)
session.query(WorkflowSpecModel).filter_by(id=spec_id).delete()
session.commit()
def test_delete_study_with_workflow_and_status_etc(self):
self.load_example_data()
workflow = session.query(WorkflowModel).first()
stats1 = StudyEvent(
study_id=workflow.study_id,
status=StudyStatus.in_progress,
comment='Some study status change event',
event_type=StudyEventType.user,
user_uid=self.users[0]['uid'],
)
LdapService.user_info('dhf8r') # Assure that there is a dhf8r in ldap for StudyAssociated.
email = EmailModel(subject="x", study_id=workflow.study_id)
associate = StudyAssociated(study_id=workflow.study_id, uid=self.users[0]['uid'])
event = StudyEvent(study_id=workflow.study_id)
session.add_all([email, associate, event])
stats2 = TaskEventModel(study_id=workflow.study_id, workflow_id=workflow.id, user_uid=self.users[0]['uid'])
session.add_all([stats1, stats2])
session.commit()
rv = self.app.delete('/v1.0/study/%i' % workflow.study_id, headers=self.logged_in_headers())
self.assert_success(rv)
del_study = session.query(StudyModel).filter(StudyModel.id == workflow.study_id).first()
self.assertIsNone(del_study)
def clean_db():
session.flush(
) # Clear out any transactions before deleting it all to avoid spurious errors.
for table in reversed(db.metadata.sorted_tables):
session.execute(table.delete())
session.commit()
session.flush()
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
# Get new status
if 'new_status' in kwargs.keys() or len(args) > 0:
if 'new_status' in kwargs.keys():
new_status = kwargs['new_status']
else:
new_status = args[0]
# Get ProgressStatus object for new_status
try:
progress_status = getattr(ProgressStatus, new_status)
# Invalid argument
except AttributeError as ae:
raise ApiError.from_task(code='invalid_argument',
message=f"We could not find a status matching `{new_status}`. Original message: {ae}.",
task=task)
# Set new status
study_model = session.query(StudyModel).filter(StudyModel.id == study_id).first()
study_model.progress_status = progress_status
session.commit()
return study_model.progress_status.value
# Missing argument
else:
raise ApiError.from_task(code='missing_argument',
message='You must include the new progress status when calling `set_study_progress_status` script. ',
task=task)
def delete_workflow_specification(spec_id):
if spec_id is None:
raise ApiError('unknown_spec',
'Please provide a valid Workflow Specification ID.')
spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(
id=spec_id).first()
category_id = spec.category_id
if spec is None:
raise ApiError(
'unknown_spec',
'The Workflow Specification "' + spec_id + '" is not recognized.')
# Delete all workflow models related to this specification
WorkflowService.delete_workflow_spec_workflow_models(spec_id)
# Delete all files related to this specification
WorkflowService.delete_workflow_spec_files(spec_id)
# Delete all events related to this specification
WorkflowService.delete_workflow_spec_task_events(spec_id)
# .delete() doesn't work when we need a cascade. Must grab the record, and explicitly delete
workflow_spec = session.query(WorkflowSpecModel).filter_by(
id=spec_id).first()
session.delete(workflow_spec)
session.commit()
# Reorder the remaining specs
WorkflowService.cleanup_workflow_spec_display_order(category_id)
def drop_workflow_spec_library(spec_id, library_id):
validate_spec_and_library(spec_id, library_id)
session.query(WorkflowLibraryModel).filter_by(
workflow_spec_id=spec_id, library_spec_id=library_id).delete()
session.commit()
libraries: WorkflowLibraryModel = session.query(
WorkflowLibraryModel).filter_by(workflow_spec_id=spec_id).all()
return WorkflowLibraryModelSchema(many=True).dump(libraries)
def _create_workflow_model(study: StudyModel, spec):
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
study=study,
workflow_spec_id=spec.id,
last_updated=datetime.now())
session.add(workflow_model)
session.commit()
return workflow_model
def add_workflow_spec_category(body):
WorkflowService.cleanup_workflow_spec_category_display_order()
count = session.query(WorkflowSpecCategoryModel).count()
body['display_order'] = count
schema = WorkflowSpecCategoryModelSchema()
new_cat: WorkflowSpecCategoryModel = schema.load(body, session=session)
session.add(new_cat)
session.commit()
return schema.dump(new_cat)
def clean_db():
session.flush() # Clear out any transactions before deleting it all to avoid spurious errors.
engine = session.bind.engine
connection = engine.connect()
for table in reversed(db.metadata.sorted_tables):
if engine.dialect.has_table(connection, table):
session.execute(table.delete())
session.commit()
session.flush()
def update_file(file_model, binary_data, content_type):
session.flush(
) # Assure the database is up-to-date before running this.
latest_data_model = session.query(FileDataModel). \
filter(FileDataModel.file_model_id == file_model.id).\
order_by(desc(FileDataModel.date_created)).first()
md5_checksum = UUID(hashlib.md5(binary_data).hexdigest())
size = len(binary_data)
if (latest_data_model is not None) and (md5_checksum
== latest_data_model.md5_hash):
# This file does not need to be updated, it's the same file. If it is arhived,
# then de-arvhive it.
file_model.archived = False
session.add(file_model)
session.commit()
return file_model
# Verify the extension
file_extension = FileService.get_extension(file_model.name)
if file_extension not in FileType._member_names_:
raise ApiError(
'unknown_extension',
'The file you provided does not have an accepted extension:' +
file_extension,
status_code=404)
else:
file_model.type = FileType[file_extension]
file_model.content_type = content_type
file_model.archived = False # Unarchive the file if it is archived.
if latest_data_model is None:
version = 1
else:
version = latest_data_model.version + 1
try:
user_uid = UserService.current_user().uid
except ApiError as ae:
user_uid = None
new_file_data_model = FileDataModel(data=binary_data,
file_model_id=file_model.id,
file_model=file_model,
version=version,
md5_hash=md5_checksum,
size=size,
user_uid=user_uid)
session.add_all([file_model, new_file_data_model])
session.commit()
session.flush(
) # Assure the id is set on the model before returning it.
return file_model
def test_workflow_spec_reorder_bad_order(self):
self.load_example_data()
self._load_sample_workflow_specs()
ordered = session.query(WorkflowSpecModel).\
filter(WorkflowSpecModel.category_id == 0).\
order_by(WorkflowSpecModel.display_order).\
all()
# Set bad display_orders
spec_model = ordered[0]
spec_model.display_order = 1
session.add(spec_model)
spec_model = ordered[1]
spec_model.display_order = 1
session.add(spec_model)
spec_model = ordered[2]
spec_model.display_order = 1
session.add(spec_model)
session.commit()
bad_orders = session.query(WorkflowSpecModel).\
filter(WorkflowSpecModel.category_id == 0).\
order_by(WorkflowSpecModel.display_order).\
all()
# Not sure how Postgres chooses an order
# when we have multiple specs with display_order == 1
# but it is
# test_spec_1, random_fact, test_spec_2, test_spec_3
self.assertEqual(1, bad_orders[0].display_order)
self.assertEqual('test_spec_1', bad_orders[0].id)
self.assertEqual(1, bad_orders[1].display_order)
self.assertEqual('random_fact', bad_orders[1].id)
self.assertEqual(1, bad_orders[2].display_order)
self.assertEqual('test_spec_2', bad_orders[2].id)
self.assertEqual(3, bad_orders[3].display_order)
self.assertEqual('test_spec_3', bad_orders[3].id)
# Move test_spec_2 up
# This should cause a cleanup of the bad display_order numbers
rv = self.app.put(
f"/v1.0/workflow-specification/test_spec_2/reorder?direction=up",
headers=self.logged_in_headers())
# After moving 2 up, the order should be
# test_spec_1, test_spec_2, random_fact, test_spec_3
# Make sure we have good display_order numbers too
self.assertEqual('test_spec_1', rv.json[0]['id'])
self.assertEqual(0, rv.json[0]['display_order'])
self.assertEqual('test_spec_2', rv.json[1]['id'])
self.assertEqual(1, rv.json[1]['display_order'])
self.assertEqual('random_fact', rv.json[2]['id'])
self.assertEqual(2, rv.json[2]['display_order'])
self.assertEqual('test_spec_3', rv.json[3]['id'])
self.assertEqual(3, rv.json[3]['display_order'])
def create_user(self,
uid="dhf8r",
email="*****@*****.**",
display_name="Hoopy Frood"):
user = session.query(UserModel).filter(UserModel.uid == uid).first()
if user is None:
ldap_user = LdapService.user_info(uid)
user = UserModel(uid=uid, ldap_info=ldap_user)
session.add(user)
session.commit()
return user
def test_waiting_task_error(self):
workflow = self.create_workflow('raise_error')
workflow.status = WorkflowStatus.waiting
session.commit()
status_before = session.query(WorkflowModel.status).filter(WorkflowModel.id == workflow.id).scalar()
WorkflowService.do_waiting()
status_after = session.query(WorkflowModel.status).filter(WorkflowModel.id == workflow.id).scalar()
self.assertEqual('waiting', status_before.value)
self.assertEqual('erroring', status_after.value)
def save(self):
"""Saves the current state of this processor to the database """
self.workflow_model.bpmn_workflow_json = self.serialize()
complete_states = [SpiffTask.CANCELLED, SpiffTask.COMPLETED]
tasks = list(self.get_all_user_tasks())
self.workflow_model.status = self.get_status()
self.workflow_model.total_tasks = len(tasks)
self.workflow_model.completed_tasks = sum(
1 for t in tasks if t.state in complete_states)
self.workflow_model.last_updated = datetime.utcnow()
session.add(self.workflow_model)
session.commit()
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 delete_study(study_id):
session.query(TaskEventModel).filter_by(study_id=study_id).delete()
session.query(TaskLogModel).filter_by(study_id=study_id).delete()
session.query(StudyAssociated).filter_by(study_id=study_id).delete()
session.query(EmailModel).filter_by(study_id=study_id).delete()
session.query(StudyEvent).filter_by(study_id=study_id).delete()
for workflow in session.query(WorkflowModel).filter_by(
study_id=study_id):
StudyService.delete_workflow(workflow.id)
study = session.query(StudyModel).filter_by(id=study_id).first()
session.delete(study)
session.commit()
def stop_impersonating():
if not UserService.has_user():
raise ApiError("logged_out",
"You are no longer logged in.",
status_code=401)
# Clear out the current impersonating user.
if 'impersonate_user' in g:
del g.impersonate_user
admin_session: AdminSessionModel = UserService.get_admin_session()
if admin_session:
session.delete(admin_session)
session.commit()
def add_workflow_specification(body):
category_id = body['category_id']
WorkflowService.cleanup_workflow_spec_display_order(category_id)
count = session.query(WorkflowSpecModel).filter_by(
category_id=category_id).count()
body['display_order'] = count
# Libraries and standalone workflows don't get a category_id
if body['library'] is True or body['standalone'] is True:
body['category_id'] = None
new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(
body, session=session)
session.add(new_spec)
session.commit()
return WorkflowSpecModelSchema().dump(new_spec)
def update_study(study_id, body):
if study_id is None:
raise ApiError('unknown_study', 'Please provide a valid Study ID.')
study_model = session.query(StudyModel).filter_by(id=study_id).first()
if study_model is None:
raise ApiError('unknown_study',
'The study "' + study_id + '" is not recognized.')
study: Study = StudySchema().load(body)
study.update_model(study_model)
session.add(study_model)
session.commit()
return StudySchema().dump(study)
def test_delete_study_with_workflow_and_status(self):
self.load_example_data()
workflow = session.query(WorkflowModel).first()
stats2 = TaskEventModel(study_id=workflow.study_id,
workflow_id=workflow.id,
user_uid=self.users[0]['uid'])
session.add(stats2)
session.commit()
rv = self.app.delete('/v1.0/study/%i' % workflow.study_id,
headers=self.logged_in_headers())
self.assert_success(rv)
del_study = session.query(StudyModel).filter(
StudyModel.id == workflow.study_id).first()
self.assertIsNone(del_study)
def update_irb_code(file_id, irb_doc_code):
"""Create a new file and associate it with the workflow
Please note that the irb_doc_code MUST be a known file in the irb_documents.xslx reference document."""
file_model = session.query(FileModel)\
.filter(FileModel.id == file_id).first()
if file_model is None:
raise ApiError(
"invalid_file_id",
"When updating the irb_doc_code for a file, that file_id must already exist "
"This file_id is not found in the database '%d'" % file_id)
file_model.irb_doc_code = irb_doc_code
session.commit()
return True
def load_example_data(self, use_crc_data=False, use_rrt_data=False):
"""use_crc_data will cause this to load the mammoth collection of documents
we built up developing crc, use_rrt_data will do the same for hte rrt project,
otherwise it depends on a small setup for running tests."""
from example_data import ExampleDataLoader
ExampleDataLoader.clean_db()
# If in production mode, only add the first user.
if app.config['PRODUCTION']:
ldap_info = LdapService.user_info(self.users[0]['uid'])
session.add(
UserModel(uid=self.users[0]['uid'], ldap_info=ldap_info))
else:
for user_json in self.users:
ldap_info = LdapService.user_info(user_json['uid'])
session.add(
UserModel(uid=user_json['uid'], ldap_info=ldap_info))
if use_crc_data:
ExampleDataLoader().load_all()
elif use_rrt_data:
ExampleDataLoader().load_rrt()
else:
ExampleDataLoader().load_test_data()
session.commit()
for study_json in self.studies:
study_model = StudyModel(**study_json)
session.add(study_model)
StudyService._add_all_workflow_specs_to_study(study_model)
session.commit()
update_seq = f"ALTER SEQUENCE %s RESTART WITH %s" % (
StudyModel.__tablename__ + '_id_seq', study_model.id + 1)
print("Update Sequence." + update_seq)
session.execute(update_seq)
session.flush()
specs = session.query(WorkflowSpecModel).all()
self.assertIsNotNone(specs)
for spec in specs:
files = session.query(FileModel).filter_by(
workflow_spec_id=spec.id).all()
self.assertIsNotNone(files)
self.assertGreater(len(files), 0)
for file in files:
# file_data = session.query(FileDataModel).filter_by(file_model_id=file.id).all()
file_data = SpecFileService().get_spec_file_data(file.id).data
self.assertIsNotNone(file_data)
self.assertGreater(len(file_data), 0)
def update_datastore(id, body):
"""allow a modification to a datastore item """
if id is None:
raise ApiError('unknown_id', 'Please provide a valid ID.')
item = session.query(DataStoreModel).filter_by(id=id).first()
if item is None:
raise ApiError('unknown_item',
'The item "' + id + '" is not recognized.')
DataStoreSchema().load(body, instance=item, session=session)
item.last_updated = datetime.utcnow()
session.add(item)
session.commit()
return DataStoreSchema().dump(item)
def update_workflow_specification(spec_id, body):
if spec_id is None:
raise ApiError('unknown_spec',
'Please provide a valid Workflow Spec ID.')
spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
if spec is None:
raise ApiError('unknown_study',
'The spec "' + spec_id + '" is not recognized.')
schema = WorkflowSpecModelSchema()
spec = schema.load(body, session=session, instance=spec, partial=True)
session.add(spec)
session.commit()
return schema.dump(spec)
