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 index(self):
current_blobs = []
for infile in os.listdir(self.box_path):
if os.path.isdir(infile) or infile == '.meta':
continue
# Get file full path
full_path = os.path.join(self.box_path, infile)
checksum = hash_file(full_path)
timestamp = get_file_timetamp(full_path)
size = get_file_size(full_path)
# Just to ease debugging.
data = '%s:%s:%s:%s\n' % (checksum, infile, timestamp, size)
blobpath = os.path.join(self.registry, checksum)
# Append to current blobs
current_blobs.append({
'checksum': checksum,
'filename': blobpath
})
# Write the blob if we don't already have it.
if not os.path.isfile(blobpath):
try:
# Todo, write much more information to the meta-blob file.
# Last modified, which server modified, ..
print("Writing blob %s (%s)" % (checksum, infile,))
blobfile = open(blobpath, 'w')
blobfile.write(data)
blobfile.close()
except IOError:
raise Exception("Writing a blob failed")
else:
print("Blob %s exists" % checksum)
# Clear orphaned files.
for checksum in os.listdir(self.registry):
blob_path = os.path.join(self.registry, checksum)
content = open(blob_path, 'r').read()
found = False
for current in current_blobs:
if current['checksum'] == checksum:
found = True
break
if not found:
print "Found obsolete %s blob" % checksum
os.unlink(blob_path)
def container_fileinfos(path):
files = odict()
with ZipFile(str(path), 'r') as zf:
l = zf.filelist
for subpath in l:
r = odict()
r['size'] = subpath.file_size
#directories excluded
if subpath.file_size > 0:
with zf.open(subpath.filename, 'r') as f:
hash = hash_file(f);
r[FileInfo.hash_key] = hash
files[subpath.filename] = r
# print(files)
return files
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