docker_run.sh

#!/bin/bash

echo -n "docker: Command recieved::<"
echo -n $@
echo ">"

rawCommand="$(echo -n "$1" | sed -E 's/(^(\s*))|((\s*)$)//g')" # Strip ends of its whitespace
command="biosimulations" # default

echo -n "<"
echo -n $rawCommand
echo ">"

case "$rawCommand" in
  "convert")
    echo 'convert mode requested'
    command="convert"
    shift
    ;;
  "export-omex")
    echo 'export-omex mode requested'
    command="export-omex"
    shift
    ;;
  "export-omex-batch")
    echo 'export-omex-batch mode requested'
    command="export-omex-batch"
    shift
    ;;
  "import-omex")
    echo 'import-omex mode requested'
    command="import-omex"
    shift
    ;;
  "import-omex-batch")
    echo 'import-omex-batch mode requested'
    command="import-omex-batch"
    shift
    ;;
  "model")
    echo 'model mode requested'
    command="model"
    shift
    ;;
  "execute")
    echo 'execute mode requested'
    command="execute"
    shift
    ;;
  "validate")
    echo 'validate mode requested'
    command="validate"
    shift
    ;;
  "version")
  echo 'version mode requested'
    command="version"
    shift
    ;;
  "biosimulations")
  echo 'biosimulations mode requested'
    command="biosimulations"
    shift
    ;;
  "help")
    command="help"
    shift
    ;;
  *)               # Default case: No more options, so break out of the loop.
    echo "Default case selected"
    ;;
esac

# Input validate arugments

arguments="$(echo -n "$@" | sed -E 's/(\s)+/ /g' | sed -E 's/(^(\s*))|((\s*)$)//g')" # convert any whitespace to spaces and strip ends


echo "VCell shall execute <$command" "$arguments>"

java \
  -classpath '/usr/local/app/vcell/lib/*' \
  -XX:MaxRAMPercentage=80 \
  -Dlog4j.configurationFile=/usr/local/app/vcell/installDir/biosimulations_log4j2.xml \
  -Dvcell.softwareVersion=$ENV_SIMULATOR_VERSION \
  -Dvcell.installDir=/usr/local/app/vcell/installDir \
  -Dvcell.server.id="7.3.0.16" \
  -Dvcell.cli="true" \
  -Dvcell.python.executable=/usr/bin/python3 \
  -Dvcell.mongodb.database="localhost" \
  -Dvcell.mongodb.host.internal="localhost" \
  -Dvcell.mongodb.port.internal=27017 \
  -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver \
  -Dvcell.server.dbConnectURL=jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521/ORCLPDB1 \
  -Dcli.workingDir=/usr/local/app/vcell/installDir/python/vcell_cli_utils/ $(if [ $MAX_JAVA_MEM_MB -gt 0 ]; then echo "-Xmx${MAX_JAVA_MEM_MB}m"; fi) \
  org.vcell.cli.CLIStandalone $command $arguments