def test_get_provenance_history(self):
# in general, the display id (ex: TEST0010-LK-1-1-1) will dictate the corresponding
# number of entity entries returned. Basically, the entity entry count should equal the number of hyphens
# in the display id plus one. For example, TEST0010 will have 1 entity entry. TEST0010-LK will have two: one for the donor TEST0010
# and one for the organ TEST0010-LK.
confdata = Provenance.load_config_file()
conn = Neo4jConnection(confdata['neo4juri'], confdata['neo4jusername'],
confdata['neo4jpassword'])
driver = conn.get_driver()
donor_list = Entity.get_entities_by_type(driver, 'Donor')
prov = Provenance(confdata['appclientid'], confdata['appclientsecret'],
confdata['UUID_WEBSERVICE_URL'])
# walk through the first 5 donors and test them
for x in range(6):
history_data_str = prov.get_provenance_history(
driver, donor_list[x])
history_data = eval(history_data_str)
self.assertEqual(len(history_data['entity']), 1)
sample_list = Entity.get_entities_by_type(driver, 'Sample')
# walk through the first 20 samples and test them
for x in range(20):
sample_item = Entity.get_entity(driver, sample_list[x])
history_data_str = prov.get_provenance_history(
driver, sample_list[x])
history_data = eval(history_data_str)
display_id = sample_item['hubmap_identifier']
hypen_count = str(display_id).count('-')
self.assertEqual(len(history_data['entity']), hypen_count + 1)
def get_provenance_data_object(self, token, groupUUID=None):
provenance_group = None
try:
if groupUUID != None:
provenance_group = self.get_group_by_identifier(groupUUID)
else:
#manually find the group id given the current user:
group_uuid = None
entity = Entity(self.provenance_config['APP_CLIENT_ID'],
self.provenance_config['APP_CLIENT_SECRET'],
self.provenance_config['UUID_WEBSERVICE_URL'])
group_list = entity.get_user_groups(token)
for grp in group_list:
if grp['generateuuid'] == True:
groupUUID = grp['uuid']
# if provenance_group is already set, this means the user belongs to more than one writable group
if provenance_group != None:
ValueError(
'Error: Current user is a member of multiple groups allowed to create new entities. The user must select which one to use'
)
provenance_group = self.get_group_by_identifier(
groupUUID)
#TODO: THIS IS HARDCODED!! WE NEED TO CHANGE THIS TO TRACK TEST GROUPS DIFFERENTLY
# for now if the group is the IEC Testing group, keep looking for a different group
# only use the IEC Testing group if no other writable group is found for the user
# NOTE: this code will simply return the first writable group it encounters
if groupUUID != '5bd084c8-edc2-11e8-802f-0e368f3075e8':
break
if groupUUID == None:
raise ValueError(
'Unauthorized: Current user is not a member of a group allowed to create new entities'
)
except ValueError as ve:
raise ve
ret_provenance_group = {
HubmapConst.PROVENANCE_GROUP_UUID_ATTRIBUTE:
groupUUID,
HubmapConst.PROVENANCE_GROUP_NAME_ATTRIBUTE:
provenance_group['displayname']
}
authcache = None
if AuthHelper.isInitialized() == False:
authcache = AuthHelper.create(
self.provenance_config['appclientid'],
self.provenance_config['appclientsecret'])
else:
authcache = AuthHelper.instance()
userinfo = authcache.getUserInfo(token, True)
ret_provenance_group[
HubmapConst.PROVENANCE_SUB_ATTRIBUTE] = userinfo['sub']
ret_provenance_group[
HubmapConst.PROVENANCE_USER_EMAIL_ATTRIBUTE] = userinfo['email']
ret_provenance_group[
HubmapConst.
PROVENANCE_USER_DISPLAYNAME_ATTRIBUTE] = userinfo['name']
return ret_provenance_group
def write_data_to_neo4j(conf_data, token, data_dict):
conn = Neo4jConnection(conf_data['NEO4J_SERVER'],
conf_data['NEO4J_USERNAME'],
conf_data['NEO4J_PASSWORD'])
driver = conn.get_driver()
with driver.session() as session:
tx = None
try:
tx = session.begin_transaction()
for dict_item in data_dict:
current_uuid = []
try:
current_uuid = Entity.get_uuid_list(
conf_data['UUID_WEBSERVICE_URL'], token, [dict_item])
except ValueError as ve:
print("Unable to resolve UUID for: " + str(dict_item))
continue
# remove single quotes and replace with double quotes
metadata_entry = str(data_dict[dict_item]).replace('\'', '"')
stmt = "MATCH (e)-[:{has_metadata_rel}]-(m) WHERE e.{uuid_attr} = '{uuid}' SET m += {{ {metadata_attr} : '{metadata_entry}' }}".format(
has_metadata_rel=HubmapConst.HAS_METADATA_REL,
uuid_attr=HubmapConst.UUID_ATTRIBUTE,
uuid=current_uuid[0],
metadata_attr=HubmapConst.METADATA_ATTRIBUTE,
metadata_entry=metadata_entry)
print('Executing stmt: ' + stmt)
tx.run(stmt)
except Exception as e:
print("Exception encountered: " + str(e))
tx.rollback()
tx.commit()
def call_index_process(conf_data, token, data_dict):
#reindex this node in elasticsearch
for dict_item in data_dict:
current_uuid = []
try:
try:
current_uuid = Entity.get_uuid_list(
conf_data['UUID_WEBSERVICE_URL'], token, [dict_item])
except ValueError as ve:
print("Unable to resolve UUID for: " + str(dict_item))
continue
rspn = requests.put(
conf_data['SEARCH_WEBSERVICE_URL'] + "/reindex/" +
current_uuid[0],
headers={'Authorization': 'Bearer ' + str(token)})
except:
print("Error happened when calling reindex web service")
def get_collection(self, driver, uuid):
try:
return Entity.get_entity(driver, uuid)
except BaseException as be:
pprint(be)
raise be
def get_metadata_by_source(driver, identifier):
try:
return Entity.get_entities_by_relationship(driver, identifier, HubmapConst.HAS_METADATA_REL)
except BaseException as be:
pprint(be)
raise be
def get_metadata(driver, identifier):
try:
return Entity.get_entity(driver, identifier)
except BaseException as be:
pprint(be)
raise be