#@meta {desc: 'linguistic parsing configuration', date: '2024-02-10'}

## Spacy token normalizers

#

# base NLP

[map_filter_token_normalizer]

class_name = zensols.nlp.MapTokenNormalizer

# add the split token mapper to have consistent token symmetry between the

# vanilla langres and mednlp_langres parsers as the MedCAT parser splits

# entities; see section `mednlp_map_filter_token_normalizer`

mapper_class_list = list: filter_token_mapper, split_ent_token_mapper

# medical nlp

[mednlp_map_filter_token_normalizer]

class_name = zensols.nlp.MapTokenNormalizer

mapper_class_list = list: filter_token_mapper

embed_entities = False

## MedCat resources

#

[medcat_resource]

class_name = zensols.mednlp.MedCatResource

installer = instance: medcat_installer

vocab_resource = instance: medcat_vocab_resource

cdb_resource = instance: medcat_cdb_resource

mc_status_resource = instance: medcat_status_resource

umls_tuis = instance: medcat_umls_tuis

umls_groups = instance: medcal_uml_groups

requirements_dir = resource(zensols.mednlp): resources/requirements

cat_config = dict:

  {'general':

    {'spacy_model': '${mednlp_biomed_doc_parser:model_name}'}}

[mednlp_library]

class_name = zensols.mednlp.MedicalLibrary

medcat_resource = instance: medcat_resource

# entity_linker_resource is optionally added in entlink.conf

## Base parser

#

# nlp parser override

[doc_parser]

# midsize model for standard NER

model_name = ${lang}_core_web_md

# install any missing spaCy models at runtime

auto_install_model = True

## Biomedical parsers

#

# ScispaCy parser

[mednlp_biomed_doc_parser]

class_name = zensols.nlp.sparser.SpacyFeatureDocumentParser

lang = ${doc_parser:lang}

# not very useful without using an entity recognizer model

# model_name = en_ner_bionlp13cg_md

# model_name = en_ner_jnlpba_md

model_name = ${lang}_core_sci_md

token_normalizer = instance: map_filter_token_normalizer

token_feature_ids = eval({'import': ['zensols.nlp as n']}):

  n.FeatureToken.FEATURE_IDS

# install any missing spaCy models at runtime

auto_install_model = True

# MedCAT features (CUIs, TUIs etc.)

[mednlp_medcat_doc_parser]

class_name = zensols.mednlp.MedCatFeatureDocumentParser

lang = ${doc_parser:lang}

model_name = ${doc_parser:model_name}

token_normalizer = instance: mednlp_map_filter_token_normalizer

medcat_resource = instance: medcat_resource

# set all features (override in your own configuration if you want them all)

token_feature_ids = eval({'import': ['zensols.nlp as n', 'zensols.mednlp as m']}):

  (n.FeatureToken.FEATURE_IDS | m.MedicalFeatureToken.FEATURE_IDS)

## Combined parsers

#

# adds biomedical ScispaCy features (ent_) to the delegate (doc_parser)

[mednlp_combine_biomed_doc_parser]

class_name = zensols.nlp.combine.MappingCombinerFeatureDocumentParser

delegate = instance: doc_parser

source_parsers = instance: list: mednlp_biomed_doc_parser

# add the FeatureToken attribute regardless

#overwrite_nones = False

# only entities are missing from the medical parser output

yield_features = set: ent_, ent, ent_iob, ent_iob_

# only map token level instead of sentence

merge_sentences = False

token_feature_ids = ${mednlp_biomed_doc_parser:token_feature_ids}

# adds MedCAT features (CUIs, TUIs etc.) to the delegate (doc_parser)

[mednlp_combine_medcat_doc_parser]

class_name = zensols.nlp.combine.MappingCombinerFeatureDocumentParser

delegate = instance: doc_parser

source_parsers = instance: list: mednlp_medcat_doc_parser

# add the FeatureToken attribute regardless

overwrite_nones = True

# only entities are missing from the medical parser output

overwrite_features = eval({'import': ['zensols.mednlp as m']}):

  m.MedicalFeatureToken.FEATURE_IDS

# only map token level instead of sentence

merge_sentences = False

token_feature_ids = ${mednlp_medcat_doc_parser:token_feature_ids}

# adds both biomedical ScispaCy and MedCAT features

[mednlp_combine_biomed_medcat_doc_parser]

class_name = zensols.nlp.combine.MappingCombinerFeatureDocumentParser

delegate = instance: doc_parser

source_parsers = instance: list: mednlp_combine_biomed_doc_parser, mednlp_combine_medcat_doc_parser