def _qrun(queries, mmjar):
out = {}
# run one query at a time for more efficient caching
for k, v in queries.iteritems():
q = {k: v}
tmp = tempfile.NamedTemporaryFile()
qfn = tmp.name
f = codecs.open(qfn, "w", encoding="utf-8")
for qid, qtxt in q.iteritems():
print >> f, "%s:%s" % (qid, qtxt)
f.close()
d = _run(qfn, mmjar, cache_file=cache_file(CACHEDIR,
[hash_file(qfn),
hash_file(mmjar)],
"metamap"))
d = longest_concepts(d)
for kk, vv in d.iteritems():
if kk in out:
print >> sys.stderr, "error: duplicate key:", kk
print >> sys.stderr, out
sys.exit(1)
else:
out[kk] = vv
tmp.close()
return out
def _qrun(queries, mmjar):
out = {}
# run one query at a time for more efficient caching
for k, v in queries.iteritems():
q = {k: v}
tmp = tempfile.NamedTemporaryFile()
qfn = tmp.name
f = codecs.open(qfn, "w", encoding="utf-8")
for qid, qtxt in q.iteritems():
print >> f, "%s:%s" % (qid, qtxt)
f.close()
d = _run(qfn,
mmjar,
cache_file=cache_file(
CACHEDIR,
[hash_file(qfn), hash_file(mmjar)], "metamap"))
d = longest_concepts(d)
for kk, vv in d.iteritems():
if kk in out:
print >> sys.stderr, "error: duplicate key:", kk
print >> sys.stderr, out
sys.exit(1)
else:
out[kk] = vv
tmp.close()
return out
def _txtrun(text, mmjar, no_cache, long_concepts):
if not text:
print '[metamap info] empty query'
return {'txt': {'concepts': []}}
# tmp = tempfile.NamedTemporaryFile()
# tfn = tmp.name
#
# with codecs.open(tfn, 'wb', encoding='utf-8') as f:
# print >> f, u"txt:{0}".format(text)
cf = cache_file(CACHEDIR, [hash_obj(text), hash_file(mmjar)], "metamap")
# for some inesplicable reason, the Java MetaMap API client
# throws a java.lang.StringIndexOutOfBoundsException exception
# instead of gracefully returning nothing when a text has no concepts.
try:
d = _run(text, mmjar, no_cache=no_cache, cache_file=cf)
except ValueError:
print '[metamap info] no concepts found'
d = {'txt': {'concepts': []}}
return d
def _txtrun(text, mmjar, no_cache, long_concepts):
if not text:
print '[metamap info] empty query'
return {'txt': {'concepts': []}}
# tmp = tempfile.NamedTemporaryFile()
# tfn = tmp.name
#
# with codecs.open(tfn, 'wb', encoding='utf-8') as f:
# print >> f, u"txt:{0}".format(text)
cf = cache_file(CACHEDIR, [hash_obj(text), hash_file(mmjar)], "metamap")
# for some inesplicable reason, the Java MetaMap API client
# throws a java.lang.StringIndexOutOfBoundsException exception
# instead of gracefully returning nothing when a text has no concepts.
try:
d = _run(text, mmjar, no_cache=no_cache, cache_file=cf)
except ValueError:
print '[metamap info] no concepts found'
d = {'txt': {'concepts': []}}
return d
