CU-8695ucw9b deid transformers fix (#490)

* CU-8695ucw9b: Fix older DeID models due to changes in transformers.

Since transformers 4.42.0, the tokenizer is expected to have the 'split_special_tokens' attribute. But the version we've saved does not. So when it's loaded, this causes an exception to be raised (which is currently caught and logged by medcat).

* CU-8695ucw9b: Add functionality for transformers NER to spectacularly fail upon consistent consecutive exceptions.

The idea is that this way, if something in the underlying models is consistently failing, the exception is raised rather than simply logged

* CU-8695ucw9b: Add tests for exception raising after a pre-defined number of failed document processes

* CU-8695ucw9b: Change conditions for raising exception on consecutive failure.

Now only raise the exception if the consecutive failure is identical (or similar). We determine that from the type and string-representation of the exception being raised.

* CU-8695ucw9b: Small additional cleanup on successful TNER processing

* CU-8695ucw9b: Use custom exception when failing due to consecutive exceptions

* CU-8695ucw9b: Remove try-except when processing transformers NER to force immediate raising of exception

Author: mart-r

medcat/ner/transformers_ner.py

@@ -4,7 +4,7 @@
 import datasets
 from spacy.tokens import Doc
 from datetime import datetime
-from typing import Iterable, Iterator, Optional, Dict, List, cast, Union, Tuple, Callable
+from typing import Iterable, Iterator, Optional, Dict, List, cast, Union, Tuple, Callable, Type
 from spacy.tokens import Span
 import inspect
 from functools import partial
@@ -87,7 +87,13 @@ def create_eval_pipeline(self):
             # NOTE: this will fix the DeID model(s) created before medcat 1.9.3
             #       though this fix may very well be unstable
             self.ner_pipe.tokenizer._in_target_context_manager = False
+        # if not hasattr(self.ner_pipe.tokenizer, 'split_special_tokens'):
+        #     # NOTE: this will fix the DeID model(s) created with transformers before 4.42
+        #     #       and allow them to run with later transforemrs
+        #     self.ner_pipe.tokenizer.split_special_tokens = False
         self.ner_pipe.device = self.model.device
+        self._consecutive_identical_failures = 0
+        self._last_exception: Optional[Tuple[str, Type[Exception]]] = None
 
     def get_hash(self) -> str:
         """A partial hash trying to catch differences between models.
@@ -390,34 +396,33 @@ def _process(self,
             #all_text_processed = self.tokenizer.encode_eval(all_text)
             # For now we will process the documents one by one, should be improved in the future to use batching
             for doc in docs:
-                try:
-                    res = self.ner_pipe(doc.text, aggregation_strategy=self.config.general['ner_aggregation_strategy'])
-                    doc.ents = []  # type: ignore
-                    for r in res:
-                        inds = []
-                        for ind, word in enumerate(doc):
-                            end_char = word.idx + len(word.text)
-                            if end_char <= r['end'] and end_char > r['start']:
-                                inds.append(ind)
-                            # To not loop through everything
-                            if end_char > r['end']:
-                                break
-                        if inds:
-                            entity = Span(doc, min(inds), max(inds) + 1, label=r['entity_group'])
-                            entity._.cui = r['entity_group']
-                            entity._.context_similarity = r['score']
-                            entity._.detected_name = r['word']
-                            entity._.id = len(doc._.ents)
-                            entity._.confidence = r['score']
-
-                            doc._.ents.append(entity)
-                    create_main_ann(self.cdb, doc)
-                    if self.cdb.config.general['make_pretty_labels'] is not None:
-                        make_pretty_labels(self.cdb, doc, LabelStyle[self.cdb.config.general['make_pretty_labels']])
-                    if self.cdb.config.general['map_cui_to_group'] is not None and self.cdb.addl_info.get('cui2group', {}):
-                        map_ents_to_groups(self.cdb, doc)
-                except Exception as e:
-                    logger.warning(e, exc_info=True)
+                res = self.ner_pipe(doc.text, aggregation_strategy=self.config.general['ner_aggregation_strategy'])
+                doc.ents = []  # type: ignore
+                for r in res:
+                    inds = []
+                    for ind, word in enumerate(doc):
+                        end_char = word.idx + len(word.text)
+                        if end_char <= r['end'] and end_char > r['start']:
+                            inds.append(ind)
+                        # To not loop through everything
+                        if end_char > r['end']:
+                            break
+                    if inds:
+                        entity = Span(doc, min(inds), max(inds) + 1, label=r['entity_group'])
+                        entity._.cui = r['entity_group']
+                        entity._.context_similarity = r['score']
+                        entity._.detected_name = r['word']
+                        entity._.id = len(doc._.ents)
+                        entity._.confidence = r['score']
+
+                        doc._.ents.append(entity)
+                create_main_ann(self.cdb, doc)
+                if self.cdb.config.general['make_pretty_labels'] is not None:
+                    make_pretty_labels(self.cdb, doc, LabelStyle[self.cdb.config.general['make_pretty_labels']])
+                if self.cdb.config.general['map_cui_to_group'] is not None and self.cdb.addl_info.get('cui2group', {}):
+                    map_ents_to_groups(self.cdb, doc)
+                self._consecutive_identical_failures = 0  # success
+                self._last_exception = None
             yield from docs
 
     # Override