def add_study_to_file_mdata(submission_id, file_id, data):
''' Adds a new study to the metadata of this file.
Throws:
InvalidId -- if the submission_id is not corresponding to MongoDB rules (pymongo specific error)
DoesNotExist -- if there is no submission with this id in the DB (Mongoengine specific error)
#### -- NOT ANY MORE! -- ResourceNotFoundException -- my custom exception, thrown if a file
with the file_id does not exist within this submission.
NoEntityCreated - my custom exception, thrown if a request to create an entity was received,
but the entity could not be created because it exists already.
NoEntityIdentifyingFieldsProvided -- my custom exception, thrown if the study
doesn't contain any identifying field (e.g.internal_id, name).
EditConflictException -- my custom exception, thrown when the entity hasn't been inserted, most likely
because of an editing conflict
'''
sender = get_request_source(data)
file_obj = data_access.FileDataAccess.retrieve_submitted_file(file_id)
file_logic = app_logic.FileBusinessLogicBuilder.build_from_type(
file_obj.file_type)
added = file_logic.add_entity_to_filemeta(data, constants.STUDY_TYPE,
sender, file_id, file_obj)
if not added:
raise exceptions.EditConflictException("Study couldn't be added.")
file_logic.status_checker.check_and_update_all_statuses(
file_id, file_obj.reload())
return True
def update_study(submission_id, file_id, study_id, data):
''' Updates the study with the data received from the request.
Throws:
InvalidId -- if the submission_id or file_id is not corresponding to MongoDB rules (pymongo specific error)
DoesNotExist -- if there is no submission nor file_id with this id in the DB (Mongoengine specific error)
## ResourceNotFoundException -- my custom exception, thrown if the study doesn't exist.
NoEntityIdentifyingFieldsProvided -- my custom exception, thrown if the study
doesn't contain any identifying field (e.g.internal_id, name).
DeprecatedDocument -- my custom exception, thrown if the version of the document to be
modified is older than the current document in the DB.
'''
sender = get_request_source(data)
upd = data_access.FileDataAccess.update_study_in_db(data,
sender,
file_id,
study_id=study_id)
logging.info("I AM UPDATING A STUDY - result: %s", upd)
if not upd:
raise exceptions.EditConflictException(
"The study couldn't be updated.")
file_obj = data_access.FileDataAccess.retrieve_submitted_file(file_id)
file_logic = app_logic.FileBusinessLogicBuilder.build_from_type(
file_obj.file_type)
file_logic.status_checker.check_and_update_all_statuses(
file_id, file_obj.reload())
return upd
def delete_study(submission_id, file_id, study_id):
''' Deletes a study specified by study id.
Returns:
True if the study has been successfully deleted. Otherwise it throws exception
Throws:
InvalidId -- if the submission_id is not corresponding to MongoDB rules (pymongo specific error)
DoesNotExist -- if there is no submission with this id in the DB (Mongoengine specific error)
ResourceNotFoundException -- my custom exception, thrown if the study does not exist.
'''
file_obj = data_access.FileDataAccess.retrieve_submitted_file(file_id)
deleted = data_access.FileDataAccess.delete_study(study_id, file_id,
file_obj)
if not deleted:
raise exceptions.EditConflictException(
"The study couldn't be deleted.")
file_logic = app_logic.FileBusinessLogicBuilder.build_from_type(
file_obj.file_type)
file_logic.status_checker.check_and_update_all_statuses(
file_id, file_obj.reload())
return deleted
def add_entity_to_filemeta(cls,
entity_json,
entity_type,
sender,
file_id,
submitted_file=None):
if data_access.FileDataAccess.search_JSON_entity(
entity_json, entity_type, file_id, submitted_file) != None:
raise exceptions.NoEntityCreatedException(
"The entity already exists in the list. For update, please send a PUT request."
)
inserted = data_access.FileDataAccess.insert_JSONentity_in_db(
entity_json, entity_type, sender, file_id, submitted_file)
if inserted == True:
file_obj = data_access.FileDataAccess.retrieve_submitted_file(
file_id)
file_logic = FileBusinessLogicBuilder.build_from_file(
file_id, file_obj)
file_logic.submit_presubmission_tasks(
[constants.UPDATE_MDATA_TASK], file_obj)
return True
else:
raise exceptions.EditConflictException(
"The entity couldn't be inserted.")