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fixed minor file path typos #6

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fixed minor file path typos #6

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6 changes: 3 additions & 3 deletions bin/process_CDR/process_CDR.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env bash

word_piece_vocab=data/cdr/word_piece_vocabs/just_train_2500/word_pieces.txt
word_piece_vocab=${CDR_IE_ROOT}/data/cdr/word_piece_vocabs/just_train_2500/word_pieces.txt
input_dir=${CDR_IE_ROOT}/data/cdr
processed_dir=${input_dir}/processed/just_train_2500
proto_dir=${processed_dir}/protos
Expand All @@ -21,7 +21,7 @@ echo "Processing Test data"
python ${CDR_IE_ROOT}/src/processing/utils/process_CDR_data.py --input_file ${input_dir}/CDR_TestSet.PubTator.txt.gz --output_dir ${processed_dir} --output_file_suffix CDR_test.txt --max_seq ${max_len} --full_abstract True --word_piece_codes ${word_piece_vocab}

for f in CDR_dev CDR_train CDR_test; do
python ${CDR_IE_ROOT}/src/processing/utils/filter_hypernyms.py -p ${processed_dir}/positive_0_${f}.txt -n ${processed_dir}/negative_0_${f}.txt -m data/2017MeshTree.txt -o ${processed_dir}/negative_0_${f}_filtered.txt
python ${CDR_IE_ROOT}/src/processing/utils/filter_hypernyms.py -p ${processed_dir}/positive_0_${f}.txt -n ${processed_dir}/negative_0_${f}.txt -m ${CDR_IE_ROOT}/data/2017MeshTree.txt -o ${processed_dir}/negative_0_${f}_filtered.txt
done


Expand All @@ -33,4 +33,4 @@ mv ${proto_dir}/negative_0_CDR_dev_filtered.txt.proto ${proto_dir}/negative_0_CD
mv ${proto_dir}/positive_0_CDR_dev.txt.proto ${proto_dir}/positive_0_CDR_train_dev.txt.proto

# convert ner data to tf protos
python ${CDR_IE_ROOT}/src/processing/ner_to_tfrecords.py --in_files ${processed_dir}/ner_\* --out_dir ${proto_dir} --load_vocab ${proto_dir} --num_threads 5
python ${CDR_IE_ROOT}/src/processing/ner_to_tfrecords.py --in_files ${processed_dir}/ner_\* --out_dir ${proto_dir} --load_vocab ${proto_dir} --num_threads 5