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fix(medcat): Relcat addon fix deserialise_from to match metacat behavior#542

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fix/medcat/relcat-deserialize-error
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fix(medcat): Relcat addon fix deserialise_from to match metacat behavior#542
alhendrickson wants to merge 6 commits into
mainfrom
fix/medcat/relcat-deserialize-error

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@alhendrickson alhendrickson commented Jun 15, 2026 •
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Error

When I save a model pack in medcat trainer, that has a relcat addon, then it errors the page and returns 500

The error looks like the RelCAT addon isn't as safe as the Metacat addon.

This change updates the relcat deserialise_from method to match the metacat one, by adding defaults and some safety into it. It should look like MetaCATAddon

Trainer



2026-06-15 16:01:27.406 | [medcattrainer] INFO 2026-06-15 15:01:27,406 cat.py l:784:Unziping the model pack and loading models.
2026-06-15 16:01:31.444 | [medcattrainer] [15/Jun/2026 15:01:31] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:01:39.503 | [medcattrainer] [15/Jun/2026 15:01:39] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:01:45.148 | [medcattrainer] INFO 2026-06-15 15:01:45,147 serialisers.py l:314:Determined serialised of type dill off disk
2026-06-15 16:01:47.901 | [medcattrainer] [15/Jun/2026 15:01:47] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:01:55.852 | [medcattrainer] [15/Jun/2026 15:01:55] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:03.842 | [medcattrainer] [15/Jun/2026 15:02:03] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:11.930 | [medcattrainer] [15/Jun/2026 15:02:11] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:24.381 | [medcattrainer] [15/Jun/2026 15:02:24] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:28.315 | [medcattrainer] [15/Jun/2026 15:02:28] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:36.492 | [medcattrainer] [15/Jun/2026 15:02:36] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:51.299 | [medcattrainer] [15/Jun/2026 15:02:51] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:02:52.463 | [medcattrainer] [15/Jun/2026 15:02:52] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:03:01.825 | [medcattrainer] INFO 2026-06-15 15:03:01,825 serialisers.py l:314:Determined serialised of type dill off disk
2026-06-15 16:03:01.836 | [medcattrainer] [15/Jun/2026 15:03:01] "GET /api/prep-docs-bg-tasks/ HTTP/1.1" 200 36
2026-06-15 16:03:03.869 | [medcattrainer] INFO 2026-06-15 15:03:03,869 serialisers.py l:149:Deserialising manually based on medcat.components.addons.relation_extraction.rel_cat.RelCATAddon
2026-06-15 16:03:04.951 | [medcattrainer] Internal Server Error: /api/modelpacks/
2026-06-15 16:03:04.951 | [medcattrainer] Traceback (most recent call last):
2026-06-15 16:03:04.951 | [medcattrainer]   File "/home/api/api/models.py", line 119, in save
2026-06-15 16:03:04.951 | [medcattrainer]     addons = CAT.load_addons(unpacked_model_pack_path)
2026-06-15 16:03:04.951 | [medcattrainer]              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.951 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/cat.py", line 937, in load_addons
2026-06-15 16:03:04.951 | [medcattrainer]     deserialise(addon_path)
2026-06-15 16:03:04.951 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/storage/serialisers.py", line 366, in deserialise
2026-06-15 16:03:04.951 | [medcattrainer]     return Serialiser.deserialise_manually(folder_path, man_cls_path,
2026-06-15 16:03:04.951 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.951 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/storage/serialisers.py", line 159, in deserialise_manually
2026-06-15 16:03:04.952 | [medcattrainer]     return man_cls.deserialise_from(folder_path, **init_kwargs)
2026-06-15 16:03:04.952 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/components/addons/relation_extraction/rel_cat.py", line 100, in deserialise_from
2026-06-15 16:03:04.953 | [medcattrainer]     base_tokenizer=init_kwargs['tokenizer'],
2026-06-15 16:03:04.953 | [medcattrainer]                    ~~~~~~~~~~~^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer] KeyError: 'tokenizer'
2026-06-15 16:03:04.953 | [medcattrainer] 
2026-06-15 16:03:04.953 | [medcattrainer] The above exception was the direct cause of the following exception:
2026-06-15 16:03:04.953 | [medcattrainer] 
2026-06-15 16:03:04.953 | [medcattrainer] Traceback (most recent call last):
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/core/handlers/exception.py", line 55, in inner
2026-06-15 16:03:04.953 | [medcattrainer]     response = get_response(request)
2026-06-15 16:03:04.953 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/core/handlers/base.py", line 197, in _get_response
2026-06-15 16:03:04.953 | [medcattrainer]     response = wrapped_callback(request, *callback_args, **callback_kwargs)
2026-06-15 16:03:04.953 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/views/decorators/csrf.py", line 65, in _view_wrapper
2026-06-15 16:03:04.953 | [medcattrainer]     return view_func(request, *args, **kwargs)
2026-06-15 16:03:04.953 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/viewsets.py", line 125, in view
2026-06-15 16:03:04.953 | [medcattrainer]     return self.dispatch(request, *args, **kwargs)
2026-06-15 16:03:04.953 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 515, in dispatch
2026-06-15 16:03:04.953 | [medcattrainer]     response = self.handle_exception(exc)
2026-06-15 16:03:04.953 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 475, in handle_exception
2026-06-15 16:03:04.953 | [medcattrainer]     self.raise_uncaught_exception(exc)
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 486, in raise_uncaught_exception
2026-06-15 16:03:04.953 | [medcattrainer]     raise exc
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 512, in dispatch
2026-06-15 16:03:04.953 | [medcattrainer]     response = handler(request, *args, **kwargs)
2026-06-15 16:03:04.953 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/mixins.py", line 19, in create
2026-06-15 16:03:04.953 | [medcattrainer]     self.perform_create(serializer)
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/mixins.py", line 24, in perform_create
2026-06-15 16:03:04.953 | [medcattrainer]     serializer.save()
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/serializers.py", line 210, in save
2026-06-15 16:03:04.953 | [medcattrainer]     self.instance = self.create(validated_data)
2026-06-15 16:03:04.953 | [medcattrainer]                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.953 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/serializers.py", line 991, in create
2026-06-15 16:03:04.954 | [medcattrainer]     instance = ModelClass._default_manager.create(**validated_data)
2026-06-15 16:03:04.954 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/db/models/manager.py", line 87, in manager_method
2026-06-15 16:03:04.954 | [medcattrainer]     return getattr(self.get_queryset(), name)(*args, **kwargs)
2026-06-15 16:03:04.954 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/db/models/query.py", line 665, in create
2026-06-15 16:03:04.954 | [medcattrainer]     obj.save(force_insert=True, using=self.db)
2026-06-15 16:03:04.954 | [medcattrainer]   File "/usr/local/lib/python3.12/contextlib.py", line 81, in inner
2026-06-15 16:03:04.954 | [medcattrainer]     return func(*args, **kwds)
2026-06-15 16:03:04.954 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/api/api/models.py", line 133, in save
2026-06-15 16:03:04.954 | [medcattrainer]     raise MedCATLoadException(f'Failure loading MetaCAT models - {unpacked_model_pack_path}') from exc
2026-06-15 16:03:04.954 | [medcattrainer] api.models.MedCATLoadException: Failure loading MetaCAT models - /home/api/media/MedCAT_Snomed2025_w_RelCAT_FULL_v1
2026-06-15 16:03:04.954 | [medcattrainer] ERROR 2026-06-15 15:03:04,940 log.py l:253:Internal Server Error: /api/modelpacks/
2026-06-15 16:03:04.954 | [medcattrainer] Traceback (most recent call last):
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/api/api/models.py", line 119, in save
2026-06-15 16:03:04.954 | [medcattrainer]     addons = CAT.load_addons(unpacked_model_pack_path)
2026-06-15 16:03:04.954 | [medcattrainer]              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/cat.py", line 937, in load_addons
2026-06-15 16:03:04.954 | [medcattrainer]     deserialise(addon_path)
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/storage/serialisers.py", line 366, in deserialise
2026-06-15 16:03:04.954 | [medcattrainer]     return Serialiser.deserialise_manually(folder_path, man_cls_path,
2026-06-15 16:03:04.954 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.954 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/storage/serialisers.py", line 159, in deserialise_manually
2026-06-15 16:03:04.959 | [medcattrainer]     return man_cls.deserialise_from(folder_path, **init_kwargs)
2026-06-15 16:03:04.959 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/medcat/components/addons/relation_extraction/rel_cat.py", line 100, in deserialise_from
2026-06-15 16:03:04.959 | [medcattrainer]     base_tokenizer=init_kwargs['tokenizer'],
2026-06-15 16:03:04.959 | [medcattrainer]                    ~~~~~~~~~~~^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer] KeyError: 'tokenizer'
2026-06-15 16:03:04.959 | [medcattrainer] 
2026-06-15 16:03:04.959 | [medcattrainer] The above exception was the direct cause of the following exception:
2026-06-15 16:03:04.959 | [medcattrainer] 
2026-06-15 16:03:04.959 | [medcattrainer] Traceback (most recent call last):
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/core/handlers/exception.py", line 55, in inner
2026-06-15 16:03:04.959 | [medcattrainer]     response = get_response(request)
2026-06-15 16:03:04.959 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/core/handlers/base.py", line 197, in _get_response
2026-06-15 16:03:04.959 | [medcattrainer]     response = wrapped_callback(request, *callback_args, **callback_kwargs)
2026-06-15 16:03:04.959 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/views/decorators/csrf.py", line 65, in _view_wrapper
2026-06-15 16:03:04.959 | [medcattrainer]     return view_func(request, *args, **kwargs)
2026-06-15 16:03:04.959 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/viewsets.py", line 125, in view
2026-06-15 16:03:04.959 | [medcattrainer]     return self.dispatch(request, *args, **kwargs)
2026-06-15 16:03:04.959 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 515, in dispatch
2026-06-15 16:03:04.959 | [medcattrainer]     response = self.handle_exception(exc)
2026-06-15 16:03:04.959 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 475, in handle_exception
2026-06-15 16:03:04.959 | [medcattrainer]     self.raise_uncaught_exception(exc)
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 486, in raise_uncaught_exception
2026-06-15 16:03:04.959 | [medcattrainer]     raise exc
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/views.py", line 512, in dispatch
2026-06-15 16:03:04.959 | [medcattrainer]     response = handler(request, *args, **kwargs)
2026-06-15 16:03:04.959 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/mixins.py", line 19, in create
2026-06-15 16:03:04.959 | [medcattrainer]     self.perform_create(serializer)
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/mixins.py", line 24, in perform_create
2026-06-15 16:03:04.959 | [medcattrainer]     serializer.save()
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/serializers.py", line 210, in save
2026-06-15 16:03:04.959 | [medcattrainer]     self.instance = self.create(validated_data)
2026-06-15 16:03:04.959 | [medcattrainer]                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/rest_framework/serializers.py", line 991, in create
2026-06-15 16:03:04.959 | [medcattrainer]     instance = ModelClass._default_manager.create(**validated_data)
2026-06-15 16:03:04.959 | [medcattrainer]                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/db/models/manager.py", line 87, in manager_method
2026-06-15 16:03:04.959 | [medcattrainer]     return getattr(self.get_queryset(), name)(*args, **kwargs)
2026-06-15 16:03:04.959 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/.venv/lib/python3.12/site-packages/django/db/models/query.py", line 665, in create
2026-06-15 16:03:04.959 | [medcattrainer]     obj.save(force_insert=True, using=self.db)
2026-06-15 16:03:04.959 | [medcattrainer]   File "/usr/local/lib/python3.12/contextlib.py", line 81, in inner
2026-06-15 16:03:04.959 | [medcattrainer]     return func(*args, **kwds)
2026-06-15 16:03:04.959 | [medcattrainer]            ^^^^^^^^^^^^^^^^^^^
2026-06-15 16:03:04.959 | [medcattrainer]   File "/home/api/api/models.py", line 133, in save
2026-06-15 16:03:04.959 | [medcattrainer]     raise MedCATLoadException(f'Failure loading MetaCAT models - {unpacked_model_pack_path}') from exc
2026-06-15 16:03:04.959 | [medcattrainer] api.models.MedCATLoadException: Failure loading MetaCAT models - /home/api/media/MedCAT_Snomed2025_w_RelCAT_FULL_v1
2026-06-15 16:03:04.959 | [medcattrainer] [15/Jun/2026 15:03:04] "POST /api/modelpacks/ HTTP/1.1" 500 167524

Medcat

This is the error in medcat, after making a unit test to check this load_addons function.

ERROR: test_can_load_rel_cat_via_load_addons (tests.components.addons.relation_extraction.test_rel_cat_in_model_pack.LoadedRelCATTests.test_can_load_rel_cat_via_load_addons)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/ali/workspace/CogStack/cogstack-nlp/medcat-v2/tests/components/addons/relation_extraction/test_rel_cat_in_model_pack.py", line 89, in test_can_load_rel_cat_via_load_addons
    addons = CAT.load_addons(self.model_pack_path)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ali/workspace/CogStack/cogstack-nlp/medcat-v2/medcat/cat.py", line 939, in load_addons
    deserialise(addon_path)
  File "/home/ali/workspace/CogStack/cogstack-nlp/medcat-v2/medcat/storage/serialisers.py", line 366, in deserialise
    return Serialiser.deserialise_manually(folder_path, man_cls_path,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ali/workspace/CogStack/cogstack-nlp/medcat-v2/medcat/storage/serialisers.py", line 159, in deserialise_manually
    return man_cls.deserialise_from(folder_path, **init_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ali/workspace/CogStack/cogstack-nlp/medcat-v2/medcat/components/addons/relation_extraction/rel_cat.py", line 100, in deserialise_from
    base_tokenizer=init_kwargs['tokenizer'],
                   ~~~~~~~~~~~^^^^^^^^^^^^^
KeyError: 'tokenizer'

----------------------------------------------------------------------
Ran 1 test in 142.944s

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@alhendrickson