def fetch_rois_from_metadata(**kwargs):
'''
DESCRIPTION MISSING
'''
if 'client' not in kwargs.keys():
kwargs['client'] = Client(conf.neuprint_URL, conf.dataset_version,
conf.api_token)
metadata = fetch_meta(client=kwargs['client'])
#print(metadata.keys())
g = fetch_roi_hierarchy(mark_primary=False,
include_subprimary=True,
format='nx',
client=kwargs['client'])
nonhierarchy_rois = metadata['nonHierarchicalROIs']
primary_rois = metadata['primaryRois']
all_rois = list(g.nodes)
toplevel_rois = []
for i, s in enumerate(g.successors('hemibrain')):
toplevel_rois += [s]
return all_rois, primary_rois, nonhierarchy_rois, toplevel_rois
def setup_dataset(dataset, published):
""" Insert or update a data set in Mongo
Keyword arguments:
dataset: data set
published: True=public, False=private
Returns:
last_uid: last UID assigned
action: what to do with bodies in this data set (ignore, insert, or update)
"""
LOGGER.info("Initializing Client for %s %s", ARG.SERVER, dataset)
npc = Client(ARG.SERVER, dataset=dataset)
set_default_client(npc)
result = fetch_meta(client=npc)
if ':' in dataset:
name, version = dataset.split(':')
version = version.replace('v', '')
else:
name = dataset
version = ''
coll = DBM.emDataSet
check = coll.find_one({
"name": name,
"version": version,
"published": published
})
action = 'ignore'
if not check:
if result['dataset'] not in GENDER:
LOGGER.error("%s does not have a gender defined",
result['dataset'])
sys.exit(-1)
payload = {
"class": "org.janelia.model.domain.flyem.EMDataSet",
"ownerKey": "group:flyem",
"readers": ["group:flyem"],
"writers": ["group:flyem"],
"name": result['dataset'],
"version": version,
"gender": GENDER[result['dataset']],
"creationDate": to_datetime(result['lastDatabaseEdit']),
"updatedDate": to_datetime(result['lastDatabaseEdit']),
"active": True,
"published": published
}
if published:
payload['readers'] = ["group:flyem", "group:workstation_users"]
last_uid = generate_uid()
payload['_id'] = last_uid
LOGGER.debug(payload)
if ARG.WRITE:
post_id = coll.insert_one(payload).inserted_id
else:
post_id = last_uid
if post_id != last_uid:
LOGGER.critical("Could not insert to Mongo with requested _id")
sys.exit(-1)
LOGGER.info("Inserted data set %s (UID: %s, datetime: %s)", dataset,
post_id, result['lastDatabaseEdit'])
action = 'insert'
else:
LOGGER.info("%s already exists in Mongo (UID: %s)", dataset,
check['_id'])
last_uid = check['_id']
neuprint_dt = to_datetime(result['lastDatabaseEdit'])
if neuprint_dt > check['updatedDate'] or ARG.FORCE:
LOGGER.warning("Update required for %s (last changed %s)", dataset,
result['lastDatabaseEdit'])
payload = {"updatedDate": datetime.now(), "active": True}
if ARG.WRITE:
coll.update_one({"_id": check['_id']}, {"$set": payload})
action = 'update'
else:
LOGGER.info("No update required for %s (last changed %s)", dataset,
check['updatedDate'])
return last_uid, action
def test_fetch_meta(client):
meta = fetch_meta()
assert isinstance(meta, dict)