Merge remote-tracking branch 'origin/main' into main
diff --git a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/ctakes_cnlpt_py/src/ctakes_cnlpt/ae/negation_delegator.py b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/ctakes_cnlpt_py/src/ctakes_cnlpt/ae/negation_delegator.py
index 262cde6..53129c0 100644
--- a/ctakes-examples/src/user/resources/org/apache/ctakes/examples/ctakes_cnlpt_py/src/ctakes_cnlpt/ae/negation_delegator.py
+++ b/ctakes-examples/src/user/resources/org/apache/ctakes/examples/ctakes_cnlpt_py/src/ctakes_cnlpt/ae/negation_delegator.py
@@ -9,12 +9,31 @@
sem = asyncio.Semaphore(1)
+async def init_caller():
+ await negation_rest.startup_event()
+
+
+async def negation_caller(cas, text, event_mentions, offsets):
+ e_doc = EntityDocument(doc_text=text, entities=offsets)
+ # async with sem:
+ negation_output = await negation_rest.process(e_doc)
+ i = 0
+ for e in event_mentions:
+ # -1 represents that it had happened, 1 represents that it is negated
+ e.polarity = negation_output.statuses[i] * -1
+ i += 1
+
+
+def a_sort_by(a):
+ return a.begin
+
+
class NegationDelegator(cas_annotator.CasAnnotator):
# Initializes the cNLPT, which loads its Negation model.
def initialize(self):
print(time.ctime((time.time())), "Initializing cnlp-transformers negation ...")
- asyncio.run(self.init_caller())
+ asyncio.run(init_caller())
print(time.ctime((time.time())), "Done.")
# Processes the document to get Negation on Events from cNLPT.
@@ -23,6 +42,7 @@
# print(time.ctime((time.time())), "Processing cnlp-transformers negation on", get_document_id(cas), "...")
sentences = cas.select(ctakes_types.Sentence)
event_mentions = cas.select(ctakes_types.EventMention)
+ event_mentions.sort(key=a_sort_by)
sentence_events = get_covered_list(sentences, event_mentions)
i = 0
@@ -31,19 +51,6 @@
print(time.ctime((time.time())), "Processing cnlp-transformers negation on sentence",
str(i), "of", str(len(sentences)), "...")
offsets = get_windowed_offsets(sentence_events[i], sentences[i].begin)
- asyncio.run(self.negation_caller(cas, sentences[i].get_covered_text(), sentence_events[i], offsets))
+ asyncio.run(negation_caller(cas, sentences[i].get_covered_text(), sentence_events[i], offsets))
i += 1
print(time.ctime((time.time())), "cnlp-transformers negation Done.")
-
- async def init_caller(self):
- await negation_rest.startup_event()
-
- async def negation_caller(self, cas, text, event_mentions, offsets):
- e_doc = EntityDocument(doc_text=text, entities=offsets)
- # async with sem:
- negation_output = await negation_rest.process(e_doc)
- i = 0
- for e in event_mentions:
- # -1 represents that it had happened, 1 represents that it is negated
- e.polarity = negation_output.statuses[i] * -1
- i += 1
diff --git a/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/event_creator.py b/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/event_creator.py
index 71ebaed..ebb6088 100644
--- a/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/event_creator.py
+++ b/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/event_creator.py
@@ -4,7 +4,7 @@
class EventCreator:
def __init__(self, cas):
- self.event_mention_type = cas.typesystem.get_type
+ self.event_mention_type = cas.typesystem.get_type(ctakes_types.EventMention)
self.event_type = cas.typesystem.get_type(ctakes_types.Event)
self.event_properties_type = cas.typesystem.get_type(ctakes_types.EventProperties)
diff --git a/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/helper_functions.py b/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/helper_functions.py
index 96987bd..2c8f1ef 100644
--- a/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/helper_functions.py
+++ b/ctakes-pbj/src/user/resources/org/apache/ctakes/pbj/ctakes_pbj_py/src/ctakes_pbj/pbj_tools/helper_functions.py
@@ -24,8 +24,7 @@
if b == begin:
return e_mentions[i]
i += 1
- i = 0
- event_men_type = cas.typesystem.get_type(ctakes_types.Procedure)
+ event_men_type = cas.typesystem.get_type(ctakes_types.EventMention)
return create_type.add_type(cas, event_men_type, begin, end)
