def load_cwms(cached=True):
logger.info('Loading CWMS statements')
pkl_name = os.path.join(data_path, 'cwms', 'stmts_regrounded.pkl')
if cached:
if os.path.exists(pkl_name):
with open(pkl_name, 'rb') as fh:
stmts = pickle.load(fh)
logger.info(f'Loaded {len(stmts)} statements')
return stmts
fnames = glob.glob(os.path.join(data_path, 'cwms', 'ekbs', '*.ekb'))
#fnames += glob.glob(os.path.join(data_path, 'cwms', 'j_ekbs', '*.ekb'))
stmts = []
for fname in tqdm.tqdm(fnames):
logger.info(f'Processing {fname}')
try:
cp = cwms.process_ekb_file(fname)
except Exception as e:
continue
stmts += cp.statements
for stmt in stmts:
for ev in stmt.evidence:
ev.annotations['provenance'] = [{
'@type': 'Provenance',
'document': {
'@id': ev.pmid
}
}]
logger.info(f'Loaded {len(stmts)} statements from CWMS')
with open(pkl_name, 'wb') as fh:
pickle.dump(stmts, fh)
return stmts
def process_cwms():
print('Processing CWMS output')
path = 'docs/cwms/20181114/*.ekb'
ekbs = sorted(glob.glob(path))
stmts = []
for ekb in ekbs:
cp = cwms.process_ekb_file(ekb)
stmts += cp.statements
for stmt in stmts:
for ev in stmt.evidence:
prov = [{'document': {'@id': ev.pmid}}]
ev.annotations['provenance'] = prov
return stmts
import glob
from indra.sources import cwms
if __name__ == '__main__':
#fnames = glob.glob('ekbs/*.ekb')
fnames = ['ekbs/t_time-start_20190611T102511_r.ekb']
stmts = []
for fname in fnames:
print('Reading %s' % fname)
cp = cwms.process_ekb_file(fname)
print('Got %d statements' % len(cp.statements))
stmts += cp.statements
do_upload = False
stmts = []
for reader in readers:
version = reader_versions[grounding][reader]
pattern = '*' if reader != 'sofia' \
else ('*_new' if grounding == 'compositional' else '*_old')
fnames = glob.glob('/Users/ben/data/dart/%s/%s/%s' %
(reader, version, pattern))
print('Found %d files for %s' % (len(fnames), reader))
for fname in tqdm.tqdm(fnames):
if reader == 'eidos':
pp = eidos.process_json_file(fname, grounding_mode=grounding)
elif reader == 'hume':
pp = hume.process_jsonld_file(fname, grounding_mode=grounding)
elif reader == 'cwms':
pp = cwms.process_ekb_file(fname, grounding_mode=grounding)
elif reader == 'sofia':
pp = sofia.process_json_file(fname, grounding_mode=grounding)
doc_id = os.path.basename(fname)[:32]
for stmt in pp.statements:
for ev in stmt.evidence:
if 'provenance' not in ev.annotations:
ev.annotations['provenance'] = [{
'document': {
'@id': doc_id
}
}]
else:
prov = ev.annotations['provenance'][0]['document']
prov['@id'] = doc_id
stmts += pp.statements