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Clinical example fix #632

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Merged
merged 3 commits into from
Feb 9, 2022
Merged

Clinical example fix #632

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dfadb51
debug
hepengfe Feb 4, 2022
7139acc
add elastic search link in the clinical pipeline reademe
hepengfe Feb 9, 2022
6617ccf
Merge branch 'master' into clinical_example_fix
hepengfe Feb 9, 2022
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6 changes: 6 additions & 0 deletions examples/clinical_pipeline/README.md
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Expand Up @@ -24,6 +24,12 @@ python ./download_models.py
**Note**: The above script will save the model in `resources/NCBI-disease`. Use `--path` option to save the
model into a different directory.

## Prepare elastic searcher
You also need to set up elastic searcher by following guide below to run the pipeline.

https://www.elastic.co/guide/en/elasticsearch/reference/current/starting-elasticsearch.html


## Run indexer
First, you should start an Elastic Indexer backend.

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5 changes: 2 additions & 3 deletions examples/clinical_pipeline/clinical_processing_pipeline.py
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Expand Up @@ -10,8 +10,8 @@
from forte.processors.writers import PackIdJsonPackWriter

from fortex.elastic import ElasticSearchPackIndexProcessor
from fortex.hugginface.bio_ner_predictor import BioBERTNERPredictor
from fortex.hugginface.transformers_processor import BERTTokenizer
from fortex.huggingface.bio_ner_predictor import BioBERTNERPredictor
from fortex.huggingface.transformers_processor import BERTTokenizer
from fortex.nltk import NLTKSentenceSegmenter

def main(input_path: str, output_path: str, max_packs: int = -1):
Expand Down Expand Up @@ -40,7 +40,6 @@ def main(input_path: str, output_path: str, max_packs: int = -1):
)

pl.initialize()

for idx, _ in enumerate(pl.process_dataset(input_path)):
if (idx + 1) % 50 == 0:
print(f"{time.strftime('%m-%d %H:%M')}: Processed {idx + 1} packs")
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