initial commit

.dockerignore

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+*.zip
+*.tar.gz
+externalData/GNormPlusJava/Dictionary/
+externalData/GNormPlusJava/CRF/
+externalData/tmVarJava/Database/
+externalData/tmVarJava/CRF/
+externalData/data/
+externalData/biobert_ner_models/
+externalData/resources/

.gitignore

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+externalData/**

.gitmodules

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+[submodule "bern"]
+	path = bern
+	url = https://github.com/amalic/bern.git

Dockerfile

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+FROM tensorflow/tensorflow:1.13.1-gpu-py3
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+  apt-get install -y wget default-jre
+
+WORKDIR /app
+COPY externalData/GNormPlusJava/ ./GNormPlusJava/
+COPY externalData/tmVarJava/ ./tmVarJava/
+COPY externalData/CRF++-0.58/ ./GNormPlusJava/CRF/
+COPY externalData/CRF++-0.58/ ./tmVarJava/CRF/
+
+COPY bern/ .
+RUN pip install -r requirements.txt
+
+WORKDIR /app
+RUN cd GNormPlusJava && \
+  cd CRF && \
+  sh ./configure && \
+  make && \
+  make install && \
+  cd .. && \
+  chmod 764 Ab3P && \
+  sed -i 's/= All/= 9606/g' setup.txt; echo "FocusSpecies: from All to 9606 (Human)" && \
+  sh Installation.sh && \
+  wget -O GNormPlusServer.jar --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1g-JlhqeDIlZX5YFk8Y27_M8BXUXcQRSX' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1g-JlhqeDIlZX5YFk8Y27_M8BXUXcQRSX" && \
+  rm -rf /tmp/cookies.txt
+
+WORKDIR /app
+RUN cd tmVarJava && \
+  cd CRF && \
+  sh ./configure && \
+  make && \
+  make install && \
+  cd ..&& \
+  chmod 764 CRF/crf_test && \
+  sh Installation.sh && \
+  wget -O tmVar2Server.jar --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1kQYzLHLFLsU9qKpRRGjXkIYmaYK6bPJm' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1kQYzLHLFLsU9qKpRRGjXkIYmaYK6bPJm"  && \
+  rm -rf /tmp/cookies.txt && \
+  wget https://repo1.maven.org/maven2/org/xerial/sqlite-jdbc/3.20.0/sqlite-jdbc-3.20.0.jar && \
+  wget https://repo1.maven.org/maven2/edu/stanford/nlp/stanford-corenlp/3.5.2/stanford-corenlp-3.5.2.jar
+
+WORKDIR /app
+RUN mkdir logs
+COPY entrypoint.sh .
+
+EXPOSE 8888
+
+ENTRYPOINT ["bash", "-c"]
+CMD ["/app/entrypoint.sh"]

README.md

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+## Prerequisites
+Lot's of disk space
+
+Download following files first:
+- GNormPlus.zip: https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/download/GNormPlus/GNormPlusJava.zip
+- tmVarJava.zip: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/Suppl/tmVar2/tmVarJava.zip
+- CRF++-0.58.tar.gz: https://drive.google.com/uc?id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ
+- biobert_ner_models.zip: https://docs.google.com/uc?export=download&id=1sSVEqvMBVLj1RJmlQDhRKyt_oe-wc5LK
+- data.zip: https://docs.google.com/uc?export=download&id=1NqgG3zJzopG2IqG-0g1o6fH0xVpO4PPN
+- resources.zip: https://docs.google.com/uc?export=download&id=1uU1U6UORqr3l_YYQ5TXeazpLrpeg_OcP
+
+Extract all archives into externalData folder, and delete the archives if not needed any more for other purposes.
+
+## Build
+```
+docker build -t bern-docker
+```
+
+## Run
+```
+docker run -it --gpus all -p 80:8888 \
+  -v $PWD/externalData/GNormPlusJava/Dictionary/:/app/GNormPlusJava/Dictionary/ \
+  -v $PWD/externalData/tmVarJava/Database:/app/tmVarJava/Database \
+  -v $PWD/externalData/biobert_ner_models/:/app/bern/biobert_ner/ \
+  -v $PWD/externalData/data/:/app/normalization/data/ \
+  -v $PWD/externalData/resources/:/app/normalization/resources/ \
+  bern-docker
+```

docker-compose.yaml

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+version: "3"
+
+services:
+
+  bern:
+    build: .
+    ports:
+      - 80:8888
+    volumes:
+      - ./externalData/GNormPlusJava/Dictionary/:/app/GNormPlusJava/Dictionary/
+      - ./externalData/tmVarJava/Database:/app/tmVarJava/Database
+      - ./externalData/biobert_ner_models?:/app/bern/biobert_ner/
+      - ./externalData/data/:/app/normalization/data/
+      - ./externalData/resources/:/app/normalization/resources/
+    networks:
+      - bernnet
+
+networks:
+  bernnet:
+    driver: bridge

entrypoint.sh

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+#!/bin/sh
+
+cd GNormPlusJava/
+nohup java -Xmx16G -Xms16G -jar GNormPlusServer.jar 18895 2>&1 &
+cd ../tmVarJava
+nohup java -Xmx8G -Xms8G -jar tmVar2Server.jar 18896 2>&1 &
+cd ..
+
+sh load_dicts.sh
+
+python3 -u server.py --port 8888 --gnormplus_home /app/GNormPlusJava --gnormplus_port 18895 --tmvar2_home /app/tmVarJava --tmvar2_port 18896