def download_all(self):
path_fn = 'tmp/'
t1 = time()
if not self.fake:
download_file(self.url_all_tpl, path_fn)
session = ctx.Session()
# save parsed entries into database
print("Parsing HMDB finished! Took {} seconds".format(round(time() - t1, 2)))
session.commit()
session.close()
if refs_multiple:
meta.ref_etc = refs_multiple.copy()
if 'hmdb_id' in refs_multiple:
for hmdb_id in refs_multiple['hmdb_id']:
if len(hmdb_id) == 9 and 'HMDB00'+hmdb_id[4:] in meta.ref_etc['hmdb_id']:
# redundant secondary HMDB id
meta.ref_etc['hmdb_id'].remove(hmdb_id)
return meta
path_fn = '../../tmp/ChEBI_complete.sdf'
i = 0
session = ctx.Session()
print("Starting ChEBI bulk import prototype")
t1 = time()
# migrate DB
if not ctx.table_exists('chebi_data'):
ctx.create_database()
else:
print("Truncated data")
ctx.truncate('chebi_data')
for me in parse_iter_sdf(path_fn):
meta: CHEBIData = sdfdict_to_entity(me)