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_genonce.sh
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_genonce.sh
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#!/bin/bash
publisher_jar=publisher.jar
input_cache_path=./input-cache/
echo Checking internet connection...
curl -sSf tx.fhir.org > /dev/null
if [ $? -eq 0 ]; then
echo "Online"
txoption=""
else
echo "Offline"
txoption="-tx n/a"
fi
#txoption="-tx n/a"
# The NLM server is currently running at R3 and thus not compatible with our current efforts
NLM_TERM="https://cts.nlm.nih.gov/fhir/"
# This is the system we'll likely use in the immediate future
ONTO="https://r4.ontoserver.csiro.au/fhir"
#txoption="-tx $ONTO"
echo "$txoption"
publisher=$input_cache_path/$publisher_jar
if test -f "$publisher"; then
echo java -Djava.awt.headless=true -jar $publisher -ig . $txoption $*
java -Djava.awt.headless=true -jar $publisher -ig . $txoption $*
else
publisher=../$publisher_jar
if test -f "$publisher"; then
java -Djava.awt.headless=true -jar $publisher -ig . $txoption $*
else
echo IG Publisher NOT FOUND in input-cache or parent folder. Please run _updatePublisher. Aborting...
fi
fi