def main(json_path='doid.json', log_dir="./logs", fast_run=True, write=True):
login = wdi_login.WDLogin(user=WDUSER, pwd=WDPASS)
wdi_core.WDItemEngine.setup_logging(log_dir=log_dir, logger_name='WD_logger', log_name=log_name,
header=json.dumps(__metadata__))
with open(json_path) as f:
d = json.load(f)
graphs = {g['id']: g for g in d['graphs']}
graph = graphs['http://purl.obolibrary.org/obo/doid.owl']
# get the has phenotype, has_material_basis_in, and transmitted by edges from another graph
graph['edges'].extend(graphs['http://purl.obolibrary.org/obo/doid/obo/ext.owl']['edges'])
do = DOGraph(graph, login, fast_run)
nodes = sorted(do.nodes.values(), key=lambda x: x.doid)
items = []
for n, node in tqdm(enumerate(nodes), total=len(nodes)):
item = node.create(write=write)
# if n>100:
# sys.exit(0)
if item:
items.append(item)
sleep(10 * 60)
doid_wdid = id_mapper('P699')
frc = items[0].fast_run_container
if not frc:
print("fastrun container not found. not removing deprecated statements")
return None
frc.clear()
for doid in tqdm(doid_wdid.values()):
remove_deprecated_statements(doid, frc, do.release, list(PROPS.values()), login)
print("You have to remove these deprecated diseases manually: ")
print(get_deprecated_nodes(graph))
WDUSER = os.environ['WDUSER']
WDPASS = os.environ['WDPASS']
else:
raise ValueError(
"WDUSER and WDPASS must be specified in local.py or as environment variables"
)
wdi_property_store.wd_properties[PROPS['OMIM ID']]['core_id'] = False
#wdi_property_store.wd_properties[PROPS['MeSH ID']]['core_id'] = False
wdi_property_store.wd_properties[PROPS['Orphanet ID']]['core_id'] = False
wdi_property_store.wd_properties[PROPS['NCI Thesaurus ID']]['core_id'] = False
__metadata__ = {
'name': 'DOIDBot',
'tags': ['disease', 'doid'],
'properties': list(PROPS.values())
}
class DOGraph:
edge_prop = {
# 'http://purl.obolibrary.org/obo/IDO_0000664': 'P828', # has_material_basis_in -> has cause
'http://purl.obolibrary.org/obo/RO_0001025': 'P276', # located in
# 'http://purl.obolibrary.org/obo/RO_0002451': None, # transmitted by. "pathogen transmission process" (P1060)?
'is_a': 'P279'
}
xref_prop = {
'ORDO': 'P1550',
'UMLS_CUI': 'P2892',
'DOID': 'P699',