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seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new 8062b41 event_creator.py Replaced missing type EventMention
helper_functions.py Fixed Procedure != EventMention, removed unnecessary i=0
reset negation_delegator.py Made callers static functions, sort the
EventMentions before calling get_covered_list
new cd926ab Merge remote-tracking branch 'origin/main' into main
8062b41 is described below
commit 8062b410cd422748b8a247810852ece419f6bd75
Author: Sean Finan <[email protected]>
AuthorDate: Mon Feb 20 17:26:18 2023 -0500
event_creator.py Replaced missing type EventMention
helper_functions.py Fixed Procedure != EventMention, removed unnecessary
i=0 reset
negation_delegator.py Made callers static functions, sort the EventMentions
before calling get_covered_list
---
.../src/ctakes_cnlpt/ae/negation_delegator.py | 37 +++++++++++++---------
.../src/ctakes_pbj/pbj_tools/event_creator.py | 2 +-
.../src/ctakes_pbj/pbj_tools/helper_functions.py | 3 +-
3 files changed, 24 insertions(+), 18 deletions(-)
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 @@ from ctakes_pbj.pbj_tools.helper_functions import *
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 @@ class NegationDelegator(cas_annotator.CasAnnotator):
# 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 @@ class NegationDelegator(cas_annotator.CasAnnotator):
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 @@ from ctakes_pbj.type_system import ctakes_types
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 @@ def get_event_mention(cas, e_mentions, e_m_begins, begin,
end):
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)
