#!/usr/bin/env bash ### ------------------------------- ### ### Helper methods for BASH scripts ### ### ------------------------------- ### die() { echo "$@" 1>&2 exit 1 } realpath () { ( TARGET_FILE="$1" CHECK_CYGWIN="$2" cd "$(dirname "$TARGET_FILE")" TARGET_FILE=$(basename "$TARGET_FILE") COUNT=0 while [ -L "$TARGET_FILE" -a $COUNT -lt 100 ] do TARGET_FILE=$(readlink "$TARGET_FILE") cd "$(dirname "$TARGET_FILE")" TARGET_FILE=$(basename "$TARGET_FILE") COUNT=$(($COUNT + 1)) done if [ "$TARGET_FILE" == "." -o "$TARGET_FILE" == ".." ]; then cd "$TARGET_FILE" TARGET_FILEPATH= else TARGET_FILEPATH=/$TARGET_FILE fi # make sure we grab the actual windows path, instead of cygwin's path. if [[ "x$CHECK_CYGWIN" == "x" ]]; then echo "$(pwd -P)/$TARGET_FILE" else echo $(cygwinpath "$(pwd -P)/$TARGET_FILE") fi ) } # TODO - Do we need to detect msys? # Uses uname to detect if we're in the odd cygwin environment. is_cygwin() { local os=$(uname -s) case "$os" in CYGWIN*) return 0 ;; *) return 1 ;; esac } # This can fix cygwin style /cygdrive paths so we get the # windows style paths. cygwinpath() { local file="$1" if is_cygwin; then echo $(cygpath -w $file) else echo $file fi } # Make something URI friendly make_url() { url="$1" local nospaces=${url// /%20} if is_cygwin; then echo "/${nospaces//\\//}" else echo "$nospaces" fi } # This crazy function reads in a vanilla "linux" classpath string (only : are separators, and all /), # and returns a classpath with windows style paths, and ; separators. fixCygwinClasspath() { OLDIFS=$IFS IFS=":" read -a classpath_members <<< "$1" declare -a fixed_members IFS=$OLDIFS for i in "${!classpath_members[@]}" do fixed_members[i]=$(realpath "${classpath_members[i]}" "fix") done IFS=";" echo "${fixed_members[*]}" IFS=$OLDIFS } # Fix the classpath we use for cygwin. fix_classpath() { cp="$1" if is_cygwin; then echo "$(fixCygwinClasspath "$cp")" else echo "$cp" fi } # Detect if we should use JAVA_HOME or just try PATH. get_java_cmd() { # High-priority override for Jlink images if [[ -n "$bundled_jvm" ]]; then echo "$bundled_jvm/bin/java" elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]]; then echo "$JAVA_HOME/bin/java" else echo "java" fi } echoerr () { echo 1>&2 "$@" } vlog () { [[ $verbose || $debug ]] && echoerr "$@" } dlog () { [[ $debug ]] && echoerr "$@" } execRunner () { # print the arguments one to a line, quoting any containing spaces [[ $verbose || $debug ]] && echo "# Executing command line:" && { for arg; do if printf "%s\n" "$arg" | grep -q ' '; then printf "\"%s\"\n" "$arg" else printf "%s\n" "$arg" fi done echo "" } # we use "exec" here for our pids to be accurate. exec "$@" } addJava () { dlog "[addJava] arg = '$1'" java_args+=( "$1" ) } addApp () { dlog "[addApp] arg = '$1'" app_commands+=( "$1" ) } addResidual () { dlog "[residual] arg = '$1'" residual_args+=( "$1" ) } addDebugger () { addJava "-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=$1" } require_arg () { local type="$1" local opt="$2" local arg="$3" if [[ -z "$arg" ]] || [[ "${arg:0:1}" == "-" ]]; then die "$opt requires <$type> argument" fi } is_function_defined() { declare -f "$1" > /dev/null } # Attempt to detect if the script is running via a GUI or not # TODO - Determine where/how we use this generically detect_terminal_for_ui() { [[ ! -t 0 ]] && [[ "${#residual_args}" == "0" ]] && { echo "true" } # SPECIAL TEST FOR MAC [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]] && [[ "${#residual_args}" == "0" ]] && { echo "true" } } # Processes incoming arguments and places them in appropriate global variables. called by the run method. process_args () { local no_more_snp_opts=0 while [[ $# -gt 0 ]]; do case "$1" in --) shift && no_more_snp_opts=1 && break ;; -h|-help) usage; exit 1 ;; -v|-verbose) verbose=1 && shift ;; -d|-debug) debug=1 && shift ;; -no-version-check) no_version_check=1 && shift ;; -mem) echo "!! WARNING !! -mem option is ignored. Please use -J-Xmx and -J-Xms" && shift 2 ;; -jvm-debug) require_arg port "$1" "$2" && addDebugger $2 && shift 2 ;; -main) custom_mainclass="$2" && shift 2 ;; -java-home) require_arg path "$1" "$2" && jre=`eval echo $2` && java_cmd="$jre/bin/java" && shift 2 ;; -D*|-agentlib*|-XX*) addJava "$1" && shift ;; -J*) addJava "${1:2}" && shift ;; *) addResidual "$1" && shift ;; esac done if [[ no_more_snp_opts ]]; then while [[ $# -gt 0 ]]; do addResidual "$1" && shift done fi is_function_defined process_my_args && { myargs=("${residual_args[@]}") residual_args=() process_my_args "${myargs[@]}" } } # Actually runs the script. run() { # TODO - check for sane environment # process the combined args, then reset "$@" to the residuals process_args "$@" set -- "${residual_args[@]}" argumentCount=$# #check for jline terminal fixes on cygwin if is_cygwin; then stty -icanon min 1 -echo > /dev/null 2>&1 addJava "-Djline.terminal=jline.UnixTerminal" addJava "-Dsbt.cygwin=true" fi # check java version if [[ ! $no_version_check ]]; then java_version_check fi if [ -n "$custom_mainclass" ]; then mainclass=("$custom_mainclass") else mainclass=("${app_mainclass[@]}") fi # Now we check to see if there are any java opts on the environment. These get listed first, with the script able to override them. if [[ "$JAVA_OPTS" != "" ]]; then java_opts="${JAVA_OPTS}" fi # run sbt execRunner "$java_cmd" \ ${java_opts[@]} \ "${java_args[@]}" \ -cp "$(fix_classpath "$app_classpath")" \ "${mainclass[@]}" \ "${app_commands[@]}" \ "${residual_args[@]}" local exit_code=$? if is_cygwin; then stty icanon echo > /dev/null 2>&1 fi exit $exit_code } # Loads a configuration file full of default command line options for this script. loadConfigFile() { cat "$1" | sed $'/^\#/d;s/\r$//' } # Now check to see if it's a good enough version # TODO - Check to see if we have a configured default java version, otherwise use 1.6 java_version_check() { readonly java_version=$("$java_cmd" -version 2>&1 | awk -F '"' '/version/ {print $2}') if [[ "$java_version" == "" ]]; then echo echo No java installations was detected. echo Please go to http://www.java.com/getjava/ and download echo exit 1 else local major=$(echo "$java_version" | cut -d'.' -f1) if [[ "$major" -eq "1" ]]; then local major=$(echo "$java_version" | cut -d'.' -f2) fi if [[ "$major" -lt "6" ]]; then echo echo The java installation you have is not up to date echo $app_name requires at least version 1.6+, you have echo version $java_version echo echo Please go to http://www.java.com/getjava/ and download echo a valid Java Runtime and install before running $app_name. echo exit 1 fi fi } ### ------------------------------- ### ### Start of customized settings ### ### ------------------------------- ### usage() { cat < Define a custom main class -jvm-debug Turn on JVM debugging, open at the given port. # java version (default: java from PATH, currently $(java -version 2>&1 | grep version)) -java-home alternate JAVA_HOME # jvm options and output control JAVA_OPTS environment variable, if unset uses "$java_opts" -Dkey=val pass -Dkey=val directly to the java runtime -J-X pass option -X directly to the java runtime (-J is stripped) # special option -- To stop parsing built-in commands from the rest of the command-line. e.g.) enabling debug and sending -d as app argument \$ ./start-script -d -- -d In the case of duplicated or conflicting options, basically the order above shows precedence: JAVA_OPTS lowest, command line options highest except "--". Available main classes: org.geneontology.gaferencer.Main EOM } ### ------------------------------- ### ### Main script ### ### ------------------------------- ### declare -a residual_args declare -a java_args declare -a app_commands declare -r real_script_path="$(realpath "$0")" declare -r app_home="$(realpath "$(dirname "$real_script_path")")" # TODO - Check whether this is ok in cygwin... declare -r lib_dir="$(realpath "${app_home}/../lib")" declare -a app_mainclass=(org.geneontology.gaferencer.Main) declare -r script_conf_file="${app_home}/../conf/application.ini" declare -r app_classpath="$lib_dir/org.geneontology.gaferencer-0.5.jar:$lib_dir/org.scala-lang.scala-library-2.13.3.jar:$lib_dir/net.sourceforge.owlapi.owlapi-distribution-4.5.18.jar:$lib_dir/org.phenoscape.scowl_2.13-1.3.4.jar:$lib_dir/org.semanticweb.elk.elk-owlapi-0.4.3.jar:$lib_dir/org.obolibrary.robot.robot-core-1.7.0.jar:$lib_dir/org.prefixcommons.curie-util-0.0.2.jar:$lib_dir/org.scalaz.scalaz-core_2.13-7.3.2.jar:$lib_dir/io.circe.circe-core_2.13-0.13.0.jar:$lib_dir/io.circe.circe-generic_2.13-0.13.0.jar:$lib_dir/com.outr.scribe-slf4j_2.13-2.8.6.jar:$lib_dir/com.github.alexarchambault.case-app_2.13-2.0.4.jar:$lib_dir/net.sourceforge.owlapi.owlapi-compatibility-4.5.18.jar:$lib_dir/com.fasterxml.jackson.core.jackson-core-2.9.10.jar:$lib_dir/com.fasterxml.jackson.core.jackson-databind-2.9.10.5.jar:$lib_dir/com.fasterxml.jackson.core.jackson-annotations-2.9.10.jar:$lib_dir/org.tukaani.xz-1.6.jar:$lib_dir/org.slf4j.slf4j-api-1.7.30.jar:$lib_dir/org.slf4j.jcl-over-slf4j-1.7.25.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-model-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-api-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-languages-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-datatypes-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-binary-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-n3-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-nquads-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-ntriples-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-rdfjson-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-jsonld-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-rdfxml-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-trix-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-turtle-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-rio-trig-2.4.2.jar:$lib_dir/org.eclipse.rdf4j.rdf4j-util-2.4.2.jar:$lib_dir/com.github.jsonld-java.jsonld-java-0.12.0.jar:$lib_dir/com.github.vsonnier.hppcrt-0.7.5.jar:$lib_dir/com.google.guava.guava-21.0.jar:$lib_dir/com.google.code.findbugs.jsr305-3.0.1.jar:$lib_dir/commons-io.commons-io-2.6.jar:$lib_dir/org.semanticweb.elk.elk-owl-model-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-owl-implementation-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-reasoner-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-util-io-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-util-collections-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-util-logging-0.4.3.jar:$lib_dir/log4j.log4j-1.2.14.jar:$lib_dir/org.apache.jena.jena-arq-3.8.0.jar:$lib_dir/org.apache.jena.jena-tdb-3.8.0.jar:$lib_dir/org.apache.poi.poi-3.15.jar:$lib_dir/org.apache.poi.poi-ooxml-3.15.jar:$lib_dir/org.yaml.snakeyaml-1.18.jar:$lib_dir/com.opencsv.opencsv-4.3.2.jar:$lib_dir/org.geneontology.expression-materializing-reasoner-0.1.3.jar:$lib_dir/org.geneontology.obographs-0.2.1.jar:$lib_dir/com.fasterxml.jackson.dataformat.jackson-dataformat-yaml-2.9.3.jar:$lib_dir/net.sourceforge.owlapi.owlexplanation-2.0.0.jar:$lib_dir/edu.stanford.protege.explanation-workbench-3.0.0.jar:$lib_dir/org.geneontology.owl-diff_2.12-1.1.2.jar:$lib_dir/com.google.code.gson.gson-2.8.0.jar:$lib_dir/junit.junit-4.12.jar:$lib_dir/net.sourceforge.owlapi.org.semanticweb.hermit-1.3.8.413.jar:$lib_dir/net.sourceforge.owlapi.jfact-4.0.4.jar:$lib_dir/net.sf.py4j.py4j-0.10.8.1.jar:$lib_dir/io.circe.circe-numbers_2.13-0.13.0.jar:$lib_dir/org.typelevel.cats-core_2.13-2.1.0.jar:$lib_dir/com.chuusai.shapeless_2.13-2.3.3.jar:$lib_dir/com.outr.scribe_2.13-2.8.6.jar:$lib_dir/com.github.alexarchambault.case-app-annotations_2.13-2.0.4.jar:$lib_dir/com.github.alexarchambault.case-app-util_2.13-2.0.4.jar:$lib_dir/net.sourceforge.owlapi.owlapi-apibinding-4.5.18.jar:$lib_dir/org.apache.httpcomponents.httpclient-4.5.5.jar:$lib_dir/org.apache.httpcomponents.httpclient-cache-4.5.5.jar:$lib_dir/org.apache.httpcomponents.httpclient-osgi-4.5.5.jar:$lib_dir/org.apache.httpcomponents.httpcore-osgi-4.4.9.jar:$lib_dir/org.semanticweb.elk.elk-util-hashing-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-util-concurrent-0.4.3.jar:$lib_dir/org.semanticweb.elk.elk-util-common-0.4.3.jar:$lib_dir/org.apache.jena.jena-core-3.8.0.jar:$lib_dir/org.apache.jena.jena-shaded-guava-3.8.0.jar:$lib_dir/org.apache.thrift.libthrift-0.10.0.jar:$lib_dir/org.apache.commons.commons-lang3-3.8.1.jar:$lib_dir/commons-codec.commons-codec-1.11.jar:$lib_dir/org.apache.commons.commons-collections4-4.2.jar:$lib_dir/org.apache.poi.poi-ooxml-schemas-3.15.jar:$lib_dir/com.github.virtuald.curvesapi-1.04.jar:$lib_dir/org.apache.commons.commons-text-1.3.jar:$lib_dir/commons-beanutils.commons-beanutils-1.9.3.jar:$lib_dir/com.io-informatics.oss.jackson-jsonld-0.0.5.jar:$lib_dir/com.fasterxml.jackson.module.jackson-module-jsonSchema-2.7.2.jar:$lib_dir/com.fasterxml.jackson.dataformat.jackson-dataformat-protobuf-2.7.2.jar:$lib_dir/com.beust.jcommander-1.48.jar:$lib_dir/net.sourceforge.owlapi.telemetry-2.0.0.jar:$lib_dir/org.hamcrest.hamcrest-core-1.3.jar:$lib_dir/commons-logging.commons-logging-1.2.jar:$lib_dir/org.apache.ws.commons.axiom.axiom-api-1.2.14.jar:$lib_dir/org.apache.ws.commons.axiom.a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# java_cmd is overrode in process_args when -java-home is used declare java_cmd=$(get_java_cmd) # if configuration files exist, prepend their contents to $@ so it can be processed by this runner [[ -f "$script_conf_file" ]] && set -- $(loadConfigFile "$script_conf_file") "$@" run "$@"