def generate_callback_id(self):
randid = shortuuid.uuid()[:8]
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER,
config.MONGO_PASSWORD, config.MONGO_DB)
while mdb.check_callback_id_in_db(randid) is True:
randid = shortuuid.uuid()[:8]
self.callback_id = randid
mdb.register_callback_id(self.callback_id)
def set_error_text(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
if self.error_code:
self.error_text = mdb.get_error_message_from_code(self.error_code)
# We may want a catch if the code is not seen in the database
else:
self.error_text = None
def create_entry_for_study(self):
# Order here matters
data = [self.study_id,
self.callback_id,
self.file_path,
self.md5,
self.assembly,
self.readme,
self.entryUUID,
self.raw_ss
]
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
mdb.insert_new_study(data)
def get_data_for_callback_id(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER,
config.MONGO_PASSWORD, config.MONGO_DB)
data = mdb.get_data_from_callback_id(self.callback_id)
self.get_metadata_errors()
if data is None:
if mdb.check_callback_id_in_db(self.callback_id):
# callback registered but studies not yet added (due to async)
return True
else:
raise RequestedNotFound(
"Couldn't find resource with callback id: {}".format(
self.callback_id))
for study_metadata in data:
study_id = st.set_var_from_dict(study_metadata, 'studyID', None)
callback_id = st.set_var_from_dict(study_metadata, 'callbackID',
None)
file_path = st.set_var_from_dict(study_metadata, 'filePath', None)
md5 = st.set_var_from_dict(study_metadata, 'md5', None)
assembly = st.set_var_from_dict(study_metadata, 'assembly', None)
retrieved = st.set_var_from_dict(study_metadata, 'retrieved', None)
data_valid = st.set_var_from_dict(study_metadata, 'dataValid',
None)
error_code = st.set_var_from_dict(study_metadata, 'errorCode',
None)
readme = st.set_var_from_dict(study_metadata, 'readme', None)
entryUUID = st.set_var_from_dict(study_metadata, 'entryUUID', None)
author_name = st.set_var_from_dict(study_metadata, 'authorName',
None)
pmid = st.set_var_from_dict(study_metadata, 'pmid', None)
gcst = st.set_var_from_dict(study_metadata, 'gcst', None)
raw_ss = st.set_var_from_dict(study_metadata, 'rawSS', None)
study = st.Study(study_id=study_id,
callback_id=callback_id,
file_path=file_path,
md5=md5,
assembly=assembly,
retrieved=retrieved,
data_valid=data_valid,
error_code=error_code,
readme=readme,
entryUUID=entryUUID,
author_name=author_name,
pmid=pmid,
gcst=gcst,
raw_ss=raw_ss)
self.study_obj_list.append(study)
return self.study_obj_list
def get_study_from_db(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
study_metadata = mdb.get_study_metadata(self.study_id)
if study_metadata:
self.study_id = set_var_from_dict(study_metadata, 'studyID', None)
self.callback_id = set_var_from_dict(study_metadata, 'callbackID', None)
self.file_path = set_var_from_dict(study_metadata, 'filePath', None)
self.md5 = set_var_from_dict(study_metadata, 'md5', None)
self.assembly = set_var_from_dict(study_metadata, 'assembly', None)
self.retrieved = set_var_from_dict(study_metadata, 'retrieved', None)
self.data_valid = set_var_from_dict(study_metadata, 'dataValid', None)
self.error_code = set_var_from_dict(study_metadata, 'errorCode', None)
self.readme = set_var_from_dict(study_metadata, 'readme', None)
self.entryUUID = set_var_from_dict(study_metadata, 'entryUUID', None)
self.author_name = set_var_from_dict(study_metadata, 'authorName', None)
self.pmid = set_var_from_dict(study_metadata, 'pmid', None)
self.gcst = set_var_from_dict(study_metadata, 'gcst', None)
self.raw_ss = set_var_from_dict(study_metadata, 'rawSS', None)
self.set_error_text()
return study_metadata
def store_publication_details(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
mdb.update_publication_details(self.study_id, self.author_name, self.pmid, self.gcst)
def store_error_code(self):
# error codes are in the error table (see the DB_SCHEMA)
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
mdb.update_error_code(self.study_id, self.error_code)
def store_data_valid_status(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
mdb.update_data_valid_status(self.study_id, self.data_valid)
def store_retrieved_status(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
mdb.update_retrieved_status(self.study_id, self.retrieved)
def remove(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER, config.MONGO_PASSWORD, config.MONGO_DB)
mdb.delete_study_entry(self.study_id)
def remove_callback_id(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER,
config.MONGO_PASSWORD, config.MONGO_DB)
mdb.remove_callback_id(self.callback_id)
def get_metadata_errors(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER,
config.MONGO_PASSWORD, config.MONGO_DB)
self.metadata_errors = mdb.get_metadata_errors(self.callback_id)
def store_metadata_errors(self):
mdb = mongoClient(config.MONGO_URI, config.MONGO_USER,
config.MONGO_PASSWORD, config.MONGO_DB)
mdb.update_metadata_errors(self.callback_id, self.metadata_errors)
