rerun = False
# Download the papers if they are not available yet
for pmcid in pmc_ids:
prefix = folder + "/" + pmcid
if not have_file(prefix + ".nxml") and not have_file(prefix + ".txt"):
txt, txt_format = get_full_text(pmcid)
if txt_format == "nxml":
fname = prefix + ".nxml"
else:
fname = prefix + ".txt"
with open(fname, "wt") as fh:
fh.write(txt.encode("utf-8"))
# Read each paper if it hasn't been read yet.
# Otherwise use the existing json extractions.
for pmcid, pmid in zip(pmc_ids, pmids):
prefix = folder + "/" + pmcid
print "Processing %s..." % pmcid
# If REACH already processed it then don't run it again
if rerun or not have_file(prefix + ".json"):
if have_file(prefix + ".txt"):
txt = open(prefix + ".txt").read().decode("utf-8")
rp = reach.process_text(txt, citation=pmid, offline=True)
elif have_file(prefix + ".nxml"):
rp = reach.process_nxml_file(prefix + ".nxml", citation=pmid, offline=True)
shutil.move("reach_output.json", prefix + ".json")
else:
rp = reach.process_json_file(prefix + ".json", citation=pmid)
run_assembly(rp.statements, folder, pmcid)
for pmcid in pmc_ids:
prefix = folder + '/' + pmcid
if not have_file(prefix + '.nxml') and\
not have_file(prefix + '.txt'):
txt, txt_format = get_full_text(pmcid)
if txt_format == 'nxml':
fname = prefix + '.nxml'
else:
fname = prefix + '.txt'
with open(fname, 'wt') as fh:
fh.write(txt.encode('utf-8'))
pmids.append(id_lookup(pmcid)['pmid'])
# Read each paper if it hasn't been read yet.
# Otherwise use the existing json extractions.
for pmcid, pmid in zip(pmc_ids, pmids):
prefix = folder + '/' + pmcid
print 'Processing %s...' % pmcid
# If REACH already processed it then don't run it again
if rerun or not have_file(prefix + '.json'):
if have_file(prefix + '.txt'):
txt = open(prefix + '.txt').read().decode('utf-8')
rp = reach.process_text(txt, citation=pmid)
elif have_file(prefix + '.nxml'):
rp = reach.process_nxml_file(prefix + '.nxml', citation=pmid)
shutil.move('reach_output.json', prefix + '.json')
else:
rp = reach.process_json_file(prefix + '.json', citation=pmid)
run_assembly(rp.statements, folder, pmcid)