nlpmed_portal.nlp.api.serializers module

class nlpmed_portal.nlp.api.serializers.EscapedNewlineCharField

Bases: CharField

get_initial()

Return a value to use when the field is being returned as a primitive value, without any object instance.

to_internal_value(data)

Transform the incoming primitive data into a native value.

class nlpmed_portal.nlp.api.serializers.EncodingFixerSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of EncodingFixer

fields = ['status']

extra_kwargs = {'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.PatternReplacerSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of PatternReplacer

fields = ['status', 'pattern', 'target']

extra_kwargs = {'pattern': {'initial': '(?:\\s*\\n\\s*){2,}', 'trim_whitespace': False}, 'status': {'initial': 'enabled'}, 'target': {'initial': '\n\n', 'trim_whitespace': False}}

class nlpmed_portal.nlp.api.serializers.WordMaskerSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of WordMasker

fields = ['status', 'words_to_mask', 'mask_char']

extra_kwargs = {'mask_char': {'initial': '*'}, 'status': {'initial': 'enabled'}, 'words_to_mask': {'initial': ['PE CT', 'PE-CT', 'PE/CT', 'CT PE', 'CT/PE', 'CT-PE', 'DVT US', 'DVT U/S', 'DVT ultrasound', 'PE protocol', 'PE study', 'PE technique', 'PE scan', 'DVT protocol', 'DVT study', 'DVT technique', 'DVT scan', 'VTE prophylaxis', 'VTE prophy', 'VTE ppx', 'DVT prophylaxis', 'DVT prophy', 'DVT ppx']}}

class nlpmed_portal.nlp.api.serializers.NoteFilterSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of NoteFilter

fields = ['status', 'words_to_search']

extra_kwargs = {'status': {'initial': 'enabled'}, 'words_to_search': {'initial': ['DVT', 'PE', 'VTE', 'deep vein thrombus', 'deep vein thrombi', 'deep vein thrombosis', 'deep vein thromboses', 'deep vein thromboembolism', 'deep venous thrombus', 'deep venous thrombi', 'deep venous thrombosis', 'deep venous thromboses', 'deep venous thromboembolism', 'pulmonary embolus', 'pulmonary emboli', 'pulmonary embolic', 'pulmonary embolism', 'pulmonary thromboembolism', 'pulmonary artery embolus', 'pulmonary artery emboli', 'pulmonary artery embolic', 'pulmonary artery embolism', 'pulmonary artery thromboembolism', 'pulmonary arterial embolus', 'pulmonary arterial emboli', 'pulmonary arterial embolic', 'pulmonary arterial embolism', 'pulmonary arterial thromboembolism', 'thromboemboli', 'clot', 'embolus', 'emboli', 'embolic', 'embolism', 'embolisms', 'thrombus', 'thrombi', 'thrombotic', 'thrombosis', 'thrombosed', 'phlebitis', 'thrombophlebitis', 'filling defect', 'filling defects']}}

class nlpmed_portal.nlp.api.serializers.SectionSplitterSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of SectionSplitter

fields = ['status', 'delimiter']

extra_kwargs = {'delimiter': {'initial': '\n\n', 'trim_whitespace': False}, 'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.SectionFilterSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of SectionFilter

fields = ['status', 'section_inc_list', 'section_exc_list', 'fallback']

extra_kwargs = {'fallback': {'initial': True}, 'section_exc_list': {'initial': ['review of system', 'system review', 'systems review', 'hematologic history', 'hematological history', 'heme history', 'oncological history', 'oncologic history', 'onc history', 'hematologic hx', 'hematological hx', 'heme hx', 'oncological hx', 'oncologic hx', 'onc hx', 'past h', 'past med', 'past surg', 'medical h', 'social h', 'family h', 'medication', 'allerg', 'physical exam', 'vital', 'ros', 'pmh:', 'pmhx', 'psh:', 'pshx', 'sh:', 'shx', 'fh:', 'fhx', 'med:', 'meds', 'general', 'gen:', 'pe:', 'v/s', 'data', 'lab', 'labs', 'laboratory', 'image', 'imaging', 'radiology', 'pathology', 'path', 'problem', 'problems', 'objective', 'obj', 'o:', 'diagnosis', 'discharge condition', 'disposition', 'discharge medication', 'medication list', 'consults', 'procedures']}, 'section_inc_list': {'initial': ['chief complaint', 'cc:', 'present illness', 'history of present illness', 'hpi', 'clinical presentation', 'clinical history', 'interval history', 'interim history', 'clinical hx', 'interval hx', 'interim hx', 'patient history', 'patient hx', 'subjective', 'subj', 'assessment', 'impression', 'impressions', 'plan', 'suggestion', 'discussion', 'conclusion', 'conclusions', 'recommendation', 'rec', 'recs', 'a&p', 'a &p', 'a& p', 'a/p', 'a /p', 'a/ p', 'ap', 'a p:', 's:', 'a:', 'p:', 'attestation', 'addendum', 'attending note', 'staff note', 'teaching physician note', 'ed course', 'hospital course', 'hospital summary', 'brief summary of hospital course', 'brief hospital course']}, 'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.SentenceSegmenterSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of SentenceSegmenter

fields = ['status', 'model_name', 'batch_size']

extra_kwargs = {'batch_size': {'initial': 10}, 'model_name': {'initial': 'en_core_sci_lg'}, 'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.DuplicateCheckerSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of DuplicateChecker

fields = ['status', 'num_perm', 'sim_threshold', 'length_threshold']

extra_kwargs = {'length_threshold': {'initial': 50}, 'num_perm': {'initial': 256}, 'sim_threshold': {'initial': 0.9}, 'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.SentenceFilterSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of SentenceFilter

fields = ['status', 'words_to_search']

extra_kwargs = {'status': {'initial': 'enabled'}, 'words_to_search': {'initial': ['DVT', 'PE', 'VTE', 'deep vein thrombus', 'deep vein thrombi', 'deep vein thrombosis', 'deep vein thromboses', 'deep vein thromboembolism', 'deep venous thrombus', 'deep venous thrombi', 'deep venous thrombosis', 'deep venous thromboses', 'deep venous thromboembolism', 'pulmonary embolus', 'pulmonary emboli', 'pulmonary embolic', 'pulmonary embolism', 'pulmonary thromboembolism', 'pulmonary artery embolus', 'pulmonary artery emboli', 'pulmonary artery embolic', 'pulmonary artery embolism', 'pulmonary artery thromboembolism', 'pulmonary arterial embolus', 'pulmonary arterial emboli', 'pulmonary arterial embolic', 'pulmonary arterial embolism', 'pulmonary arterial thromboembolism', 'thromboemboli', 'clot', 'embolus', 'emboli', 'embolic', 'embolism', 'embolisms', 'thrombus', 'thrombi', 'thrombotic', 'thrombosis', 'thrombosed', 'phlebitis', 'thrombophlebitis', 'filling defect', 'filling defects']}}

class nlpmed_portal.nlp.api.serializers.SentenceExpanderSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of SentenceExpander

fields = ['status', 'length_threshold']

extra_kwargs = {'length_threshold': {'initial': 50}, 'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.JoinerSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of Joiner

fields = ['status', 'sentence_delimiter', 'section_delimiter']

extra_kwargs = {'section_delimiter': {'initial': '\n\n', 'trim_whitespace': False}, 'sentence_delimiter': {'initial': '\n', 'trim_whitespace': False}, 'status': {'initial': 'enabled'}}

class nlpmed_portal.nlp.api.serializers.MLInferenceSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of MLInference

fields = ['status', 'model_name', 'use_preped_text']

extra_kwargs = {'model_name': {'initial': 'VTE_MULTICLASS'}, 'status': {'initial': 'enabled'}, 'use_preped_text': {'initial': True}}

class nlpmed_portal.nlp.api.serializers.NLPSettingSerializer

Bases: WritableNestedModelSerializer

class Meta

Bases: object

model

alias of NLPSetting

fields = ['debug', 'encoding_fixer', 'pattern_replacer', 'word_masker', 'note_filter', 'section_splitter', 'section_filter', 'sentence_segmenter', 'duplicate_checker', 'sentence_filter', 'sentence_expander', 'joiner', 'ml_inference']

extra_kwargs = {'debug': {'initial': True}}

class nlpmed_portal.nlp.api.serializers.NLPSerializer

Bases: NLPSettingSerializer

class Meta

Bases: Meta

fields = ['input_text', 'debug', 'encoding_fixer', 'pattern_replacer', 'word_masker', 'note_filter', 'section_splitter', 'section_filter', 'sentence_segmenter', 'duplicate_checker', 'sentence_filter', 'sentence_expander', 'joiner', 'ml_inference']

to_internal_value(data)

Dict of native values <- Dict of primitive datatypes.

class nlpmed_portal.nlp.api.serializers.NlpProcessJobSerializer

Bases: ModelSerializer

class Meta

Bases: object

model

alias of NlpProcessJob

fields = '__all__'

read_only_fields = ['job_status', 'error_message', 'created_at', 'updated_at', 'total_count', 'completed_count', 'user']

class nlpmed_portal.nlp.api.serializers.DemoSerializer

Bases: Serializer

to_internal_value(data)

Dict of native values <- Dict of primitive datatypes.