diff --git a/services/nlp-services/applications/medcat/config/env_app b/services/nlp-services/applications/medcat/config/env_app index f65a11e8..4024cbc9 100644 --- a/services/nlp-services/applications/medcat/config/env_app +++ b/services/nlp-services/applications/medcat/config/env_app @@ -2,7 +2,7 @@ # IMPORTANT : log level set # CRITICAL - 50, ERROR - 40, WARNING - 30, INFO - 20, DEBUG - 10, NOTSET - 0 -APP_LOG_LEVEL=ERROR +APP_LOG_LEVEL=INFO # can include only one model for NER APP_NAME=MedCAT @@ -23,7 +23,7 @@ APP_MEDCAT_MODEL_PACK= # APP_MODEL_CUI_FILTER_PATH=/cat/models/cui_filter.txt # NLP processing -APP_BULK_NPROC=16 +APP_BULK_NPROC=8 APP_TRAINING_MODE=False # Flask server config @@ -31,8 +31,8 @@ SERVER_HOST=0.0.0.0 SERVER_PORT=5000 SERVER_WORKERS=1 SERVER_WORKER_TIMEOUT=300 -SERVER_THREADS=16 +SERVER_THREADS=1 # GPU SETTING # CAUTION, use only if you are using the GPU docker image. -APP_TORCH_THREADS=0 \ No newline at end of file +APP_TORCH_THREADS=-1 \ No newline at end of file diff --git a/services/nlp-services/applications/medcat/config/env_medcat b/services/nlp-services/applications/medcat/config/env_medcat index c9b95a9b..b1f5ff0f 100644 --- a/services/nlp-services/applications/medcat/config/env_medcat +++ b/services/nlp-services/applications/medcat/config/env_medcat @@ -2,7 +2,7 @@ TYPE=NOT_UMLS # IMPORTANT : log level set # CRITICAL - 50, ERROR - 40, WARNING - 30, INFO - 20, DEBUG - 10, NOTSET - 0 -LOG_LEVEL=20 +LOG_LEVEL=40 NESTED_ENTITIES=False @@ -31,3 +31,9 @@ SPACY_MODEL= # (the NiFi groovy scripts and annotation ingester are two such services that process the output, and so they might require further customisation) # POSSIBLE VALUES: [list, dict], if left empty then "dict" is the default. ANNOTATIONS_ENTITY_OUTPUT_MODE=dict + +# you will need a De-ID model for this, otherwise there might be unexpected behaviour +DEID_MODE=False + +# replaces the type of the de-id entity e.g patient name: [Name] with patient name: [****] +DEID_REDACT=True \ No newline at end of file