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prepare_env.sh
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# ---------------------------------------------------------------------------
# Install utilities
# ---------------------------------------------------------------------------
#apt install wget
#apt install git
#apt install rar
#pip install git+https://github.com/OntoGene/PyBioC.git
# ---------------------------------------------------------------------------
# Get and install JAVA
# ---------------------------------------------------------------------------
#apt-get update
#apt-get install -y default-jdk
#apt-get autoclean -y
#apt-get update && apt-get install -y default-jdk && apt-get autoclean -y
# ---------------------------------------------------------------------------
# Install requirements
# ---------------------------------------------------------------------------
#pip install -r requirements.txt
# ---------------------------------------------------------------------------
# Eliminate annoying messages during Tensorflow execution
# ---------------------------------------------------------------------------
#export TF_CPP_MIN_LOG_LEVEL=3
#export AUTOGRAPH_VERBOSITY=0
# ---------------------------------------------------------------------------
# Download and prepare abbreviation detector AB3P
# ---------------------------------------------------------------------------
cd src/abbreviation_detector/
#git clone https://github.com/ncbi-nlp/NCBITextLib.git
#wget https://github.com/ncbi-nlp/NCBITextLib/archive/refs/heads/master.zip
#unzip master.zip
#mv NCBITextLib-master NCBITextLib
## 1. Install NCBITextLib
#cd NCBITextLib/lib/
#make
#cd ../../
## 2. Install Ab3P
#git clone https://github.com/ncbi-nlp/Ab3P.git
wget https://github.com/ncbi-nlp/Ab3P/archive/refs/heads/master.zip
unzip master.zip
mv Ab3P-master Ab3P
cd Ab3P
sed -i 's/** location of NCBITextLib **/../NCBITextLib/' Makefile
make
cd ../../
#------------------------------------------------------------------------------
# GENERATE ANNOTATION DATASETS DICTIONARIES
#------------------------------------------------------------------------------
#python src/setup/annotations_dicts/dataset_entities