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))
maker = EntityMaker(mediawiki_api_url, sparql_endpoint_url, username,
password)
item_engine = wdi_core.WDItemEngine.wikibase_item_engine_factory(
mediawiki_api_url, sparql_endpoint_url)
login = wdi_login.WDLogin("testbot",
"password",
mediawiki_api_url=mediawiki_api_url)
else:
sparql_endpoint_url = 'https://query.wikidata.org/sparql'
item_engine = wdi_core.WDItemEngine
login = wd_login
cu = wikicurie.CurieUtil()
h = wdi_helpers.WikibaseHelper(sparql_endpoint_url=sparql_endpoint_url)
for k, v in PROPS.items():
try:
PROPS[k] = h.get_pid(v)
except Exception:
PROPS[k] = None
OMIM_QID = h.get_qid("Q241953")
EXT_ID_MAP = dict()
def retrieve_qid_from_curie(curie):
pid, ext_id_value = cu.parse_curie(curie)
pid = h.get_pid(pid)
if pid not in EXT_ID_MAP:
EXT_ID_MAP[pid] = wdi_helpers.id_mapper(pid,
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',