def tag(collection, document, tagger):
pconf = ProjectConfiguration(real_directory(collection))
for tagger_token, _, _, tagger_service_url in pconf.get_annotator_config():
if tagger == tagger_token:
break
else:
raise UnknownTaggerError(tagger)
doc_path = path_join(real_directory(collection), document)
with TextAnnotations(path_join(real_directory(collection),
document)) as ann_obj:
try:
# Note: Can we actually fit a whole document in here?
quoted_doc_text = quote_plus(ann_obj.get_document_text())
resp = urlopen(tagger_service_url % quoted_doc_text, None,
QUERY_TIMEOUT)
except URLError:
raise TaggerConnectionError(tagger_token)
# TODO: Check for errors
json_resp = loads(resp.read())
mods = ModificationTracker()
for ann_data in json_resp.itervalues():
offsets = ann_data['offsets']
# Note: We do not support discontinuous spans at this point
assert len(offsets) == 1, 'discontinuous/null spans'
start, end = offsets[0]
_id = ann_obj.get_new_id('T')
tb = TextBoundAnnotationWithText(
start, end,
_id,
ann_data['type'],
ann_data['text']
)
mods.addition(tb)
ann_obj.add_annotation(tb)
mod_resp = mods.json_response()
mod_resp['annotations'] = _json_from_ann(ann_obj)
return mod_resp
assert 'offsets' in ann_data, 'Tagger response lacks offsets'
offsets = ann_data['offsets']
assert 'type' in ann_data, 'Tagger response lacks type'
_type = ann_data['type']
assert 'texts' in ann_data, 'Tagger response lacks texts'
texts = ann_data['texts']
# sanity
assert len(offsets) != 0, 'Tagger response has empty offsets'
assert len(texts) == len(offsets), 'Tagger response has different numbers of offsets and texts'
# Note: We do not support discontinuous spans at this point
assert len(offsets) < 2, 'Tagger response has multiple offsets (discontinuous spans not supported)'
start, end = offsets[0]
text = texts[0]
_id = ann_obj.get_new_id('T')
tb = TextBoundAnnotationWithText(((start, end),), _id, _type, text)
mods.addition(tb)
ann_obj.add_annotation(tb)
mod_resp = mods.json_response()
mod_resp['annotations'] = _json_from_ann(ann_obj)
return mod_resp
if __name__ == '__main__':
# Silly test, but helps
tag('/BioNLP-ST_2011_ID_devel', 'PMC1874608-01-INTRODUCTION', 'random')
texts = ann_data['texts']
# sanity
assert len(offsets) != 0, 'Tagger response has empty offsets'
assert len(texts) == len(
offsets
), 'Tagger response has different numbers of offsets and texts'
# Note: We do not support discontinuous spans at this point
assert len(
offsets
) < 2, 'Tagger response has multiple offsets (discontinuous spans not supported)'
start, end = offsets[0]
text = texts[0]
_id = ann_obj.get_new_id('T')
tb = TextBoundAnnotationWithText(start, end, _id, _type, text)
mods.addition(tb)
ann_obj.add_annotation(tb)
mod_resp = mods.json_response()
mod_resp['annotations'] = _json_from_ann(ann_obj)
return mod_resp
if __name__ == '__main__':
# Silly test, but helps
tag('/BioNLP-ST_2011_ID_devel', 'PMC1874608-01-INTRODUCTION', 'random')
def tag(collection, document, tagger):
pconf = ProjectConfiguration(real_directory(collection))
print("tagger", tagger, file=sys.stderr)
for tagger_token, _, _, tagger_service_url in pconf.get_annotator_config():
if tagger == tagger_token:
break
else:
raise UnknownTaggerError(tagger)
path_join(real_directory(collection), document)
# print("path_join(real_directory(collection), document)", path_join(real_directory(collection), document), file=sys.stderr)
# print("tagger_token", tagger_token, file=sys.stderr)
with TextAnnotations(path_join(real_directory(collection),
document)) as ann_obj:
# print("ann_obj", document, file=sys.stderr)
url_soup = urlparse(tagger_service_url)
if url_soup.scheme == 'http':
Connection = HTTPConnection
# print("HTTPConnection", HTTPConnection, file=sys.stderr)
elif url_soup.scheme == 'https':
# Delayed HTTPS import since it relies on SSL which is commonly
# missing if you roll your own Python, for once we should not
# fail early since tagging is currently an edge case and we
# can't allow it to bring down the whole server.
from http.client import HTTPSConnection
Connection = HTTPSConnection
else:
raise InvalidConnectionSchemeError(tagger_token, url_soup.scheme)
conn = None
try:
conn = Connection(url_soup.netloc)
req_headers = {
'Content-type': 'text/plain; charset=utf-8',
'Accept': 'application/json',
}
# Build a new service URL since the request method doesn't accept
# a parameters argument
service_url = url_soup.path + ('?' + url_soup.query
if url_soup.query else '')
try:
# Note: Trout slapping for anyone sending Unicode objects here
data = str(path_join(
real_directory(collection),
document)) + "#*^$#" + ann_obj.get_document_text()
data = data.encode('utf-8')
# print("data", type(data),data, file=sys.stderr)
# print("data", ann_obj, file=sys.stderr)
req_headers['Content-length'] = len(data)
# Note: Trout slapping for anyone sending Unicode objects here
conn.request(
'POST',
# As per: http://bugs.python.org/issue11898
# Force the url to be an ascii string
str(service_url),
data,
headers=req_headers)
# httpConnection = http.client.HTTPConnection(url_soup.netloc)
# httpConnection.request('GET', str(service_url), headers=req_headers)
# response = httpConnection.getresponse()
except SocketError as e:
raise TaggerConnectionError(tagger_token, e)
resp = conn.getresponse()
# print("resp-------------", resp.read(), file=sys.stderr)
# Did the request succeed?
if resp.status != 200:
raise TaggerConnectionError(
tagger_token, '%s %s' % (resp.status, resp.reason))
# Finally, we can read the response data
resp_data = resp.read()
finally:
if conn is not None:
conn.close()
try:
json_resp = loads(resp_data)
# print("json_resp", json_resp, file=sys.stderr)
except ValueError:
raise InvalidTaggerResponseError(tagger_token, resp_data)
mods = ModificationTracker()
cidmap = {}
# print("json_resp.items:::::::::::::", json_resp.items(), file=sys.stderr)
for cid, ann in ((i, a) for i, a in json_resp.items()
if _is_textbound(a)):
assert 'offsets' in ann, 'Tagger response lacks offsets'
offsets = ann['offsets']
# print("json_resp.items:::::::::::::", offsets, file=sys.stderr)
assert 'type' in ann, 'Tagger response lacks type'
_type = ann['type']
assert 'texts' in ann, 'Tagger response lacks texts'
texts = ann['texts']
# sanity
assert len(offsets) != 0, 'Tagger response has empty offsets'
assert len(texts) == len(
offsets
), 'Tagger response has different numbers of offsets and texts'
start, end = offsets[0]
text = texts[0]
# print("offsets, _type, texts, text:", offsets, _type, texts, text, file=sys.stderr)
_id = ann_obj.get_new_id('T')
print("_id", _id, file=sys.stderr)
cidmap[cid] = _id
tb = TextBoundAnnotationWithText(offsets, _id, _type, text,
" " + ' '.join(texts[1:]))
mods.addition(tb)
ann_obj.add_annotation(tb)
for norm in (a for a in json_resp.values() if _is_normalization(a)):
try:
_type = norm['type']
target = norm['target']
refdb = norm['refdb']
refid = norm['refid']
except KeyError as e:
raise # TODO
_id = ann_obj.get_new_id('N')
target = cidmap[target]
na = NormalizationAnnotation(_id, _type, target, refdb, refid, '')
mods.addition(na)
ann_obj.add_annotation(na)
mod_resp = mods.json_response()
mod_resp['annotations'] = _json_from_ann(ann_obj)
return mod_resp
def tag(collection, document, tagger):
pconf = ProjectConfiguration(real_directory(collection))
for tagger_token, _, _, tagger_service_url in pconf.get_annotator_config():
if tagger == tagger_token:
break
else:
raise UnknownTaggerError(tagger)
path_join(real_directory(collection), document)
with TextAnnotations(path_join(real_directory(collection),
document)) as ann_obj:
url_soup = urlparse(tagger_service_url)
if url_soup.scheme == 'http':
Connection = HTTPConnection
elif url_soup.scheme == 'https':
# Delayed HTTPS import since it relies on SSL which is commonly
# missing if you roll your own Python, for once we should not
# fail early since tagging is currently an edge case and we
# can't allow it to bring down the whole server.
from http.client import HTTPSConnection
Connection = HTTPSConnection
else:
raise InvalidConnectionSchemeError(tagger_token, url_soup.scheme)
conn = None
try:
conn = Connection(url_soup.netloc)
req_headers = {
'Content-type': 'text/plain; charset=utf-8',
'Accept': 'application/json',
}
# Build a new service URL since the request method doesn't accept
# a parameters argument
service_url = url_soup.path + (
'?' + url_soup.query if url_soup.query else '')
try:
data = ann_obj.get_document_text().encode('utf-8')
req_headers['Content-length'] = len(data)
# Note: Trout slapping for anyone sending Unicode objects here
conn.request('POST',
# As per: http://bugs.python.org/issue11898
# Force the url to be an ascii string
str(service_url),
data,
headers=req_headers)
except SocketError as e:
raise TaggerConnectionError(tagger_token, e)
resp = conn.getresponse()
# Did the request succeed?
if resp.status != 200:
raise TaggerConnectionError(
tagger_token, '%s %s' %
(resp.status, resp.reason))
# Finally, we can read the response data
resp_data = resp.read()
finally:
if conn is not None:
conn.close()
try:
json_resp = loads(resp_data)
except ValueError:
raise InvalidTaggerResponseError(tagger_token, resp_data)
mods = ModificationTracker()
cidmap = {}
for cid, ann in ((i, a) for i, a in json_resp.items()
if _is_textbound(a)):
assert 'offsets' in ann, 'Tagger response lacks offsets'
offsets = ann['offsets']
assert 'type' in ann, 'Tagger response lacks type'
_type = ann['type']
assert 'texts' in ann, 'Tagger response lacks texts'
texts = ann['texts']
# sanity
assert len(offsets) != 0, 'Tagger response has empty offsets'
assert len(texts) == len(
offsets), 'Tagger response has different numbers of offsets and texts'
start, end = offsets[0]
text = texts[0]
_id = ann_obj.get_new_id('T')
cidmap[cid] = _id
tb = TextBoundAnnotationWithText(
offsets, _id, _type, text, " " + ' '.join(texts[1:]))
mods.addition(tb)
ann_obj.add_annotation(tb)
for norm in (a for a in json_resp.values()
if _is_normalization(a)):
try:
_type = norm['type']
target = norm['target']
refdb = norm['refdb']
refid = norm['refid']
except KeyError as e:
raise # TODO
_id = ann_obj.get_new_id('N')
target = cidmap[target]
na = NormalizationAnnotation(_id, _type, target, refdb, refid, '')
mods.addition(na)
ann_obj.add_annotation(na)
mod_resp = mods.json_response()
mod_resp['annotations'] = _json_from_ann(ann_obj)
return mod_resp