def _dep(xml, source_element='basic-dependencies'):
soup = _soup(xml)
token_by_ids = _token_by_ids(soup)
ann_by_ids = defaultdict(dict)
for s_id, t_id, ann in _pos(xml):
ann_by_ids[s_id][t_id] = ann
yield ann
curr_rel_id = 1
for sent_e in _find_sentences_element(soup).iter('sentence'):
sent_id = int(sent_e.get('id'))
deps_e = sent_e.findall(source_element)
assert len(deps_e) == 1
deps_e = deps_e[0]
for dep_e in deps_e:
if dep_e.tag != 'dep':
# To be on the safe side
continue
dep_type = dep_e.get('type')
assert dep_type is not None
gov_tok_id = int(dep_e.find('governor').get('idx'))
dep_tok_id = int(dep_e.find('dependent').get('idx'))
yield BinaryRelationAnnotation('R%s' % curr_rel_id, dep_type,
'Governor',
ann_by_ids[sent_id][gov_tok_id].id,
'Dependent',
ann_by_ids[sent_id][dep_tok_id].id,
'')
curr_rel_id += 1
def _create_relation(ann_obj, projectconf, mods, origin, target, type,
attributes, old_type, old_target, undo_resp={}):
attributes = _parse_attributes(attributes)
if old_type is not None or old_target is not None:
assert type in projectconf.get_relation_types(), (
('attempting to convert relation to non-relation "%s" ' % (target.type, )) +
('(legit types: %s)' % (unicode(projectconf.get_relation_types()), )))
sought_target = (old_target
if old_target is not None else target.id)
sought_type = (old_type
if old_type is not None else type)
# We are to change the type, target, and/or attributes
found = None
for ann in ann_obj.get_relations():
if ann.arg2 == sought_target and ann.type == sought_type:
found = ann
break
if found is None:
# TODO: better response
Messager.error('_create_relation: failed to identify target relation (type %s, target %s) (deleted?)' % (str(old_type), str(old_target)))
elif found.arg2 == target.id and found.type != type:
# no changes to type or target
pass
else:
# type and/or target changed, mark.
before = unicode(found)
found.arg2 = target.id
found.type = type
mods.change(before, found)
target_ann = found
else:
# Create a new annotation
new_id = ann_obj.get_new_id('R')
rel = projectconf.get_relation_by_type(type)
assert rel is not None and len(rel.arg_list) == 2
a1l, a2l = rel.arg_list
ann = BinaryRelationAnnotation(new_id, type, a1l, origin.id, a2l, target.id, '\t')
mods.addition(ann)
ann_obj.add_annotation(ann)
target_ann = ann
# process attributes
if target_ann is not None:
_set_attributes(ann_obj, ann, attributes, mods, undo_resp)
elif attributes != None:
Messager.error('_create_relation: cannot set arguments: failed to identify target relation (type %s, target %s) (deleted?)' % (str(old_type), str(old_target)))
return target_ann
def _dep(xml, source_element='basic-dependencies'):
soup = _soup(xml)
token_by_ids = _token_by_ids(soup)
ann_by_ids = defaultdict(dict)
for s_id, t_id, ann in _pos(xml):
ann_by_ids[s_id][t_id] = ann
yield ann
curr_rel_id = 1
for sent_e in _find_sentences_element(soup).getiterator('sentence'):
sent_id = int(sent_e.get('id'))
# Attempt to find dependencies as distinctly named elements as they
# were stored in the Stanford XML format prior to 2013.
deps_e = sent_e.findall(source_element)
if len(deps_e) == 0:
# Perhaps we are processing output following the newer standard,
# check for the same identifier but as a type attribute for
# general "dependencies" elements.
deps_e = list(e for e in sent_e.getiterator('dependencies')
if e.attrib['type'] == source_element)
assert len(deps_e) == 1
deps_e = deps_e[0]
for dep_e in deps_e:
if dep_e.tag != 'dep':
# To be on the safe side
continue
dep_type = dep_e.get('type')
assert dep_type is not None
if dep_type == 'root':
# Skip dependencies to the root node, this behaviour conforms
# with how we treated the pre-2013 format.
continue
gov_tok_id = int(dep_e.find('governor').get('idx'))
dep_tok_id = int(dep_e.find('dependent').get('idx'))
yield BinaryRelationAnnotation(
'R%s' % curr_rel_id, dep_type,
'Governor', ann_by_ids[sent_id][gov_tok_id].id,
'Dependent', ann_by_ids[sent_id][dep_tok_id].id,
''
)
curr_rel_id += 1
mods = ModificationTracker()
cidmap = {}
for cid, ann in ((i, a) for i, a in json_resp.iteritems()
if _is_relation(a)):
assert 'rel_type' in ann, 'Tagger response lacks rel_type'
rel_type = ann['rel_type']
assert 'arg1' in ann, 'Tagger response lacks arg1'
arg1 = ann['arg1']
assert 'arg2' in ann, 'Tagger response lacks arg2'
arg2 = ann['arg2']
_id = ann_obj.get_new_id('R')
cidmap[cid] = _id
tb = BinaryRelationAnnotation(_id, rel_type, 'Arg1', arg1, 'Arg2',
arg2, "")
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')