def _text_for_offsets(text, offsets):
"""
Given a text and a list of (start, end) integer offsets, returns
the (catenated) text corresponding to those offsets, joined
appropriately for use in a TextBoundAnnotation(WithText).
"""
try:
return DISCONT_SEP.join(text[s:e] for s,e in offsets)
except Exception:
Messager.error('_text_for_offsets: failed to get text for given offsets (%s)' % str(offsets))
raise ProtocolArgumentError
def _text_for_offsets(text, offsets):
"""Given a text and a list of (start, end) integer offsets, returns the
(catenated) text corresponding to those offsets, joined appropriately for
use in a TextBoundAnnotation(WithText)."""
try:
return DISCONT_SEP.join(text[s:e] for s, e in offsets)
except Exception:
Messager.error(
'_text_for_offsets: failed to get text for given offsets (%s)' %
str(offsets))
raise ProtocolArgumentError
def __create_span(ann_obj, mods, type, offsets, txt_file_path,
projectconf, attributes):
# For event types, reuse trigger if a matching one exists.
found = None
if projectconf.is_event_type(type):
for tb_ann in ann_obj.get_textbounds():
try:
if (_offsets_equal(tb_ann.spans, offsets)
and tb_ann.type == type):
found = tb_ann
break
except AttributeError:
# Not a trigger then
pass
if found is None:
# Get a new ID
new_id = ann_obj.get_new_id('T') # XXX: Cons
# Get the text span
with open_textfile(txt_file_path, 'r') as txt_file:
text = txt_file.read()
text_span = _text_for_offsets(text, offsets)
# The below code resolves cases where there are newlines in the
# offsets by creating discontinuous annotations for each span
# separated by newlines. For most cases it preserves the offsets.
seg_offsets = []
for o_start, o_end in offsets:
pos = o_start
for text_seg in text_span.split('\n'):
if not text_seg and o_start != o_end:
# Double new-line, skip ahead
pos += 1
continue
start = pos
end = start + len(text_seg)
# For the next iteration the position is after the newline.
pos = end + 1
# Adjust the offsets to compensate for any potential leading
# and trailing whitespace.
start += len(text_seg) - len(text_seg.lstrip())
end -= len(text_seg) - len(text_seg.rstrip())
# If there is any segment left, add it to the offsets.
if start != end:
seg_offsets.append((start, end, ))
# if we're dealing with a null-span
if not seg_offsets:
seg_offsets = offsets
ann_text = DISCONT_SEP.join((text[start:end]
for start, end in seg_offsets))
ann = TextBoundAnnotationWithText(seg_offsets, new_id, type, ann_text)
ann_obj.add_annotation(ann)
mods.addition(ann)
else:
ann = found
if ann is not None:
if projectconf.is_physical_entity_type(type):
# TODO: alert that negation / speculation are ignored if set
event = None
else:
# Create the event also
new_event_id = ann_obj.get_new_id('E') # XXX: Cons
event = EventAnnotation(
ann.id, [], str(new_event_id), type, '')
ann_obj.add_annotation(event)
mods.addition(event)
else:
# We got a newline in the span, don't take any action
event = None
return ann, event
