added convenience script for downloading required data

.dockerignore

@@ -1,3 +1,6 @@
+Dockerfile
+docker-compose.yaml
+prerequisites.sh
 *.zip
 *.tar.gz
 externalData/GNormPlusJava/Dictionary/
@@ -6,4 +9,4 @@ externalData/tmVarJava/Database/
 externalData/tmVarJava/CRF/
 externalData/data/
 externalData/biobert_ner_models/
-externalData/resources/
+externalData/resources/

README.md

@@ -21,9 +21,11 @@ work. If not, see <http://creativecommons.org/licenses/by/4.0/>.
 
 Extract all archives into externalData folder within this repository.
 
+or simply run `sh prerequisites.sh`
+
 ## Build
 ```
-docker build -t bern-docker
+docker build -t bern-docker .
 ```
 
 ## Run

prerequisites.sh

@@ -0,0 +1,68 @@
+#!/bin/sh
+set -e
+
+DLDIR="externalData"
+
+if [ ! -d $DLDIR ]; then
+    mkdir $DLDIR
+fi
+
+cd $DLDIR
+
+# GNormPlusJava.zip
+if [ ! -f GNormPlusJava.zip ]; then
+  if [ ! -d GNormPlusJava ]; then
+    wget https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/download/GNormPlus/GNormPlusJava.zip
+    unzip GNormPlusJava.zip
+    rm GNormPlusJava.zip
+  fi
+fi
+
+# tmVarJava.zip
+if [ ! -f tmVarJava.zip ]; then
+  if [ ! -d tmVarJava ]; then
+    wget ftp://ftp.ncbi.nlm.nih.gov/pub/lu/Suppl/tmVar2/tmVarJava.zip 
+    unzip tmVarJava.zip
+    rm tmVarJava.zip
+  fi
+fi
+
+# CRF++-0.58.tar.gz
+if [ ! -f CRF++-0.58.tar.gz ]; then
+  if [ ! -d CRF++-0.58 ]; then
+    wget -O CRF++-0.58.tar.gz  --load-cookies cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies cookies.txt --keep-session-cookies --no-check-certificate 'https://drive.google.com/uc?id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=0B4y35FiV1wh7QVR6VXJ5dWExSTQ"
+    rm -rf cookies.txt
+    tar -xvf CRF++-0.58.tar.gz
+    rm CRF++-0.58.tar.gz
+  fi
+fi
+
+# biobert_ner_models.zip
+if [ ! -f biobert_ner_models.zip ]; then
+  if [ ! -d biobert_ner_models ]; then
+    wget -O biobert_ner_models.zip  --load-cookies cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1sSVEqvMBVLj1RJmlQDhRKyt_oe-wc5LK' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1sSVEqvMBVLj1RJmlQDhRKyt_oe-wc5LK"
+    rm -rf cookies.txt
+    unzip biobert_ner_models.zip
+    rm biobert_ner_models.zip
+  fi
+fi
+
+# data.zip
+if [ ! -f data.zip ]; then
+  if [ ! -d data ]; then
+    wget -O data.zip  --load-cookies cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1NqgG3zJzopG2IqG-0g1o6fH0xVpO4PPN' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1NqgG3zJzopG2IqG-0g1o6fH0xVpO4PPN"
+    rm -rf cookies.txt
+    unzip data.zip
+    rm data.zip
+  fi
+fi
+
+# resources.zip
+if [ ! -f resources.zip ]; then
+  if [ ! -d resources ]; then
+    wget -O resources.zip  --load-cookies cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1uU1U6UORqr3l_YYQ5TXeazpLrpeg_OcP' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1uU1U6UORqr3l_YYQ5TXeazpLrpeg_OcP"
+    rm -rf cookies.txt
+    unzip resources.zip
+    rm resources.zip
+  fi
+fi