Bug for plugging an external recommender for one out of two Features in one Layer

[naudinlo]

Hello, I noticed a bug when I add my external recommender for NER predictions.

My task: I have a Layer Span, with 2 Features:

• Label, for NER annotations, which is of type String
• Assertion for multi-classification annotations, which is of type uima.cas.StringArray [not required]

I have an external recommender which aims to make predictions for Label feature only, based on a NER hugging face model. I have a ValueError when I connect my recommender ValueError: Not a primitive collection type: uima.cas.StringArray.

I noticed I only have the issue when some Spans do not have an annotation for Assertion (even if I did not set it to Required) and everything works perfectly when the only Feature is Label (String) (ie removing Assertion feature).

The issue might come from the fact that:

• when a Span is annotated for Label but not Assertion, its value = fs["Assertion"] is empty and is detected as a string instance, which creates an error when calls _parse_primitive_array
• TYPE_NAME_STRING_ARRAY is not a case in _parse_primitive_array whereas belonging to _PRIMITIVE_COLLECTION_TYPES (not consistant with the error message ValueError: Not a primitive collection type: uima.cas.StringArray)

Issue:

9286-123145460297728 2022-05-16 14:28:50,907 - werkzeug - INFO - 172.16.159.100 - - [16/May/2022 14:28:50] "POST /camembert_ner/predict HTTP/1.1" 500 -
Traceback (most recent call last):
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 2464, in __call__
    return self.wsgi_app(environ, start_response)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 2450, in wsgi_app
    response = self.handle_exception(e)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 1867, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/ariadne/server.py", line 40, in _predict
    req = parse_prediction_request(json_data)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/ariadne/protocol.py", line 75, in parse_prediction_request
    cas = load_cas_from_xmi(document["xmi"], typesystem)
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/cassis/xmi.py", line 95, in load_cas_from_xmi
    return deserializer.deserialize(
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/cassis/xmi.py", line 247, in deserialize
    fs[feature_name] = FSType(elements=self._parse_primitive_array(feature.rangeType, value))
  File "/Users//projects/fhir-lighter/lib/ner_camembert/.venv/lib/python3.9/site-packages/cassis/xmi.py", line 459, in _parse_primitive_array
    raise ValueError(f"Not a primitive collection type: {type_name}")
ValueError: Not a primitive collection type: uima.cas.StringArray

Do you have a way around it? Thanks

[reckart]

Which version of dkpro cassis are you using? If you are not using the latest version, try if upgrading resolves the issue.

[naudinlo]

Thanks, after upgrading all the libs my issue was resolved!