diff --git a/.github/workflows/gradle_test.yml b/.github/workflows/gradle_test.yml index 75e06a740d..faae2a500d 100644 --- a/.github/workflows/gradle_test.yml +++ b/.github/workflows/gradle_test.yml @@ -7,13 +7,14 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - name: Set up JDK 11 - uses: actions/setup-java@v1 + - uses: actions/checkout@v3 + - name: Set up JDK 17 + uses: actions/setup-java@v3 with: - java-version: 11 + java-version: 17 + distribution: temurin - name: Cache Gradle packages - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: | ~/.gradle/caches @@ -30,4 +31,4 @@ jobs: # Restoring these files from a GitHub Actions cache might cause problems for future builds. run: | rm -f ~/.gradle/caches/modules-2/modules-2.lock - rm -f ~/.gradle/caches/modules-2/gc.properties \ No newline at end of file + rm -f ~/.gradle/caches/modules-2/gc.properties diff --git a/build.gradle b/build.gradle index 0f2a391c25..8689038c5f 100644 --- a/build.gradle +++ b/build.gradle @@ -47,6 +47,12 @@ repositories { mavenCentral() } +java { + toolchain { + languageVersion = JavaLanguageVersion.of(17) + } +} + sourceSets { main { resources { @@ -128,10 +134,13 @@ dependencies { ) testImplementation( - [group: 'junit', name: 'junit', version: '4.12'], + [group: 'junit', name: 'junit', version: '4.13'], [group: 'com.sparkjava', name: 'spark-core', version: '2.2'], [group: 'org.glassfish.jersey.core', name: 'jersey-common', version: '2.22.4'] ) + testRuntimeOnly( + [group: 'org.junit.vintage', name:'junit-vintage-engine', version:'5.8.2'] + ) } @@ -179,35 +188,7 @@ tasks.withType(Test) { systemProperties['org.xerial.snappy.tempdir'] = 'build/tmp' maxHeapSize = '2g' maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1 -} - -compileTestJava { - inputs.property("moduleName", moduleName) - doFirst { - options.compilerArgs = [ - '--module-path', classpath.asPath, - '--add-modules', 'junit', - '--patch-module', "$moduleName=" + files(sourceSets.test.java.srcDirs).asPath, - ] - classpath = files() - } -} - -test { - inputs.property("moduleName", moduleName) - - doFirst { - jvmArgs = [ - '-Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize', - '--module-path', classpath.asPath, - '--add-modules', 'junit', - '--add-modules', 'ALL-MODULE-PATH', - '--add-reads', "$moduleName=junit", - '@scripts/test_suite.args', - '--patch-module', "$moduleName=" + files(sourceSets.test.java.outputDir, sourceSets.main.output.resourcesDir).asPath, - ] - classpath = files() - } + useJUnitPlatform() } task createDist(type: Copy, dependsOn: jar) { @@ -244,24 +225,24 @@ tasks.distTar.enabled = false tasks.startScripts.enabled = false task createDistZip(type: Zip, dependsOn: createDist) { - archiveName = "IGV_${version}.zip" + archiveFileName = "IGV_${archiveVersion}.zip" from("${buildDir}/IGV-dist") - into "IGV_${version}" + into "IGV_${archiveVersion}" } task createLinuxDistZip(type: Zip, dependsOn: createDist) { - archiveName = "IGV_Linux_${version}.zip" + archiveFileName = "IGV_Linux_${archiveVersion}.zip" from("${buildDir}/IGV-dist") { exclude "*.bat" exclude "*.command" exclude 'igvtools*' exclude 'lib/genomes' } - into "IGV_Linux_${version}" + into "IGV_Linux_${archiveVersion}" } task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) { - archiveName = "IGV_Linux_${version}_WithJava.zip" + archiveFileName = "IGV_Linux_${archiveVersion}_WithJava.zip" with copySpec { from jdkBundleLinux into "jdk-11" } from("${buildDir}/IGV-dist") { exclude "*.bat" @@ -269,7 +250,7 @@ task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) { exclude 'igvtools*' exclude 'lib/genomes' } - into "IGV_Linux_${version}" + into "IGV_Linux_${archiveVersion}" doLast { if (jdkBundleLinux == "") { throw new GradleException("Required property not set: jdkBundleLinux"); @@ -278,18 +259,19 @@ task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) { } task createMacDistZip(type: Zip, dependsOn: createDist) { - archiveName = "IGV_Mac_${version}.zip" + archiveFileName = "IGV_Mac_${archiveVersion}.zip" from("${buildDir}/IGV-dist") { exclude "*.bat" exclude "*_hidpi*" exclude "igvtools*" exclude 'lib/genomes' } - into "IGV_Mac_${version}" + + into "IGV_Mac_${archiveVersion}" } task createMacWithJavaDistZip(type: Zip, dependsOn: createDist) { - archiveName = "IGV_Mac_${version}_WithJava.zip" + archiveFileName = "IGV_Mac_${archiveVersion}_WithJava.zip" with copySpec { from jdkBundleMac into "jdk-11" } from("${buildDir}/IGV-dist") { exclude "*.bat" @@ -297,7 +279,7 @@ task createMacWithJavaDistZip(type: Zip, dependsOn: createDist) { exclude "igvtools*" exclude 'lib/genomes' } - into "IGV_Mac_${version}" + into "IGV_Mac_${archiveVersion}" doLast { if (jdkBundleMac == "") { throw new GradleException("Required property not set: jdkBundleMac"); @@ -339,7 +321,7 @@ task createMacAppDist(type: Copy, dependsOn: createDist) { } task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) { - archiveName = "IGV_MacApp_${version}.zip" + archiveFileName = "IGV_MacApp_${archiveVersion}.zip" from("${buildDir}/IGV-MacApp-dist") doLast { @@ -348,8 +330,8 @@ task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) { } task createMacAppWithJavaDistZip(type: Zip, dependsOn: createMacAppDist) { - archiveName = "IGV_MacApp_${version}_WithJava.zip" - with copySpec { from jdkBundleMac into "IGV_${version}.app/Contents/jdk-11" } + archiveFileName = "IGV_MacApp_${archiveVersion}_WithJava.zip" + with copySpec { from jdkBundleMac into "IGV_${archiveVersion}.app/Contents/jdk-11" } from("${buildDir}/IGV-MacApp-dist") doLast { @@ -465,7 +447,8 @@ task fullJar(type: Jar, dependsOn: jar) { "Application-Name": "IGV", "Built-By": System.getProperty('user.name'), "Main-Class": mainClassName, - "Class-Path": configurations.default.collect { it.getName() }.join(' ') + + "Class-Path": configurations.runtimeClasspath.collect { it.getName() }.join(' ') ) } } diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index 5c2d1cf016..943f0cbfa7 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index 430dfabc5c..bdc9a83b1e 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,6 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-5.5.1-all.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-8.0.2-bin.zip +networkTimeout=10000 zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index b0d6d0ab5d..65dcd68d65 100755 --- a/gradlew +++ b/gradlew @@ -1,13 +1,13 @@ -#!/usr/bin/env sh +#!/bin/sh # -# Copyright 2015 the original author or authors. +# Copyright © 2015-2021 the original authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # -# http://www.apache.org/licenses/LICENSE-2.0 +# https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, @@ -17,78 +17,113 @@ # ############################################################################## -## -## Gradle start up script for UN*X -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null -APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` +# This is normally unused +# shellcheck disable=SC2034 +APP_BASE_NAME=${0##*/} +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' # Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD="maximum" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + # Determine the Java command to use to start the JVM. if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -97,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" + JAVACMD=java which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the @@ -105,84 +140,105 @@ location of your Java installation." fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC3045 + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC3045 + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) -# For Cygwin, switch paths to Windows format before running java -if $cygwin ; then - APP_HOME=`cygpath --path --mixed "$APP_HOME"` - CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` - JAVACMD=`cygpath --unix "$JAVACMD"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=$((i+1)) + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg done - case $i in - (0) set -- ;; - (1) set -- "$args0" ;; - (2) set -- "$args0" "$args1" ;; - (3) set -- "$args0" "$args1" "$args2" ;; - (4) set -- "$args0" "$args1" "$args2" "$args3" ;; - (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; - (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; - (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; - (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; - (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=$(save "$@") +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Stop when "xargs" is not available. +if ! command -v xargs >/dev/null 2>&1 +then + die "xargs is not available" +fi -# Collect all arguments for the java command, following the shell quoting and substitution rules -eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# -# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong -if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then - cd "$(dirname "$0")" -fi +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat index 15e1ee37a7..6689b85bee 100644 --- a/gradlew.bat +++ b/gradlew.bat @@ -5,7 +5,7 @@ @rem you may not use this file except in compliance with the License. @rem You may obtain a copy of the License at @rem -@rem http://www.apache.org/licenses/LICENSE-2.0 +@rem https://www.apache.org/licenses/LICENSE-2.0 @rem @rem Unless required by applicable law or agreed to in writing, software @rem distributed under the License is distributed on an "AS IS" BASIS, @@ -14,7 +14,7 @@ @rem limitations under the License. @rem -@if "%DEBUG%" == "" @echo off +@if "%DEBUG%"=="" @echo off @rem ########################################################################## @rem @rem Gradle startup script for Windows @@ -25,10 +25,14 @@ if "%OS%"=="Windows_NT" setlocal set DIRNAME=%~dp0 -if "%DIRNAME%" == "" set DIRNAME=. +if "%DIRNAME%"=="" set DIRNAME=. +@rem This is normally unused set APP_BASE_NAME=%~n0 set APP_HOME=%DIRNAME% +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" @@ -37,7 +41,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome set JAVA_EXE=java.exe %JAVA_EXE% -version >NUL 2>&1 -if "%ERRORLEVEL%" == "0" goto init +if %ERRORLEVEL% equ 0 goto execute echo. echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. @@ -51,7 +55,7 @@ goto fail set JAVA_HOME=%JAVA_HOME:"=% set JAVA_EXE=%JAVA_HOME%/bin/java.exe -if exist "%JAVA_EXE%" goto init +if exist "%JAVA_EXE%" goto execute echo. echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% @@ -61,38 +65,26 @@ echo location of your Java installation. goto fail -:init -@rem Get command-line arguments, handling Windows variants - -if not "%OS%" == "Windows_NT" goto win9xME_args - -:win9xME_args -@rem Slurp the command line arguments. -set CMD_LINE_ARGS= -set _SKIP=2 - -:win9xME_args_slurp -if "x%~1" == "x" goto execute - -set CMD_LINE_ARGS=%* - :execute @rem Setup the command line set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + @rem Execute Gradle -"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* :end @rem End local scope for the variables with windows NT shell -if "%ERRORLEVEL%"=="0" goto mainEnd +if %ERRORLEVEL% equ 0 goto mainEnd :fail rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of rem the _cmd.exe /c_ return code! -if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 -exit /b 1 +set EXIT_CODE=%ERRORLEVEL% +if %EXIT_CODE% equ 0 set EXIT_CODE=1 +if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE% +exit /b %EXIT_CODE% :mainEnd if "%OS%"=="Windows_NT" endlocal diff --git a/scripts/test_suite.args b/scripts/test_suite.args deleted file mode 100644 index 6331a3cfcb..0000000000 --- a/scripts/test_suite.args +++ /dev/null @@ -1,75 +0,0 @@ -# Arguments to support running the test suite on Java 9 and 10 -# Need to expose internals to junit for testing. - ---add-exports org.igv/org.broad.igv.annotations=junit ---add-exports org.igv/org.broad.igv.batch=junit ---add-exports org.igv/org.broad.igv.bbfile=junit ---add-exports org.igv/org.broad.igv.bigwig=junit ---add-exports org.igv/org.broad.igv.charts=junit ---add-exports org.igv/org.broad.igv.cli_plugin.ui=junit ---add-exports org.igv/org.broad.igv.data=junit ---add-exports org.igv/org.broad.igv.data.cufflinks=junit ---add-exports org.igv/org.broad.igv.data.expression=junit ---add-exports org.igv/org.broad.igv.data.seg=junit ---add-exports org.igv/org.broad.igv.event=junit ---add-exports org.igv/org.broad.igv.exceptions=junit ---add-exports org.igv/org.broad.igv.feature=junit ---add-exports org.igv/org.broad.igv.feature.aa=junit ---add-exports org.igv/org.broad.igv.feature.basepair=junit ---add-exports org.igv/org.broad.igv.feature.bionano=junit ---add-exports org.igv/org.broad.igv.feature.dranger=junit ---add-exports org.igv/org.broad.igv.feature.dsi=junit ---add-exports org.igv/org.broad.igv.feature.genome=junit ---add-exports org.igv/org.broad.igv.feature.genome.fasta=junit ---add-exports org.igv/org.broad.igv.feature.tribble=junit ---add-exports org.igv/org.broad.igv.feature.tribble.reader=junit ---add-exports org.igv/org.broad.igv.oauth=junit ---add-exports org.igv/org.broad.igv.gwas=junit ---add-exports org.igv/org.broad.igv.lists=junit ---add-exports org.igv/org.broad.igv.maf=junit ---add-exports org.igv/org.broad.igv.methyl=junit ---add-exports org.igv/org.broad.igv.peaks=junit ---add-exports org.igv/org.broad.igv.prefs=junit ---add-exports org.igv/org.broad.igv.repeats=junit ---add-exports org.igv/org.broad.igv.renderer=junit ---add-exports org.igv/org.broad.igv.sam=junit ---add-exports org.igv/org.broad.igv.sam.mods=junit ---add-exports org.igv/org.broad.igv.sam.cram=junit ---add-exports org.igv/org.broad.igv.sam.reader=junit ---add-exports org.igv/org.broad.igv.session=junit ---add-exports org.igv/org.broad.igv.tdf=junit ---add-exports org.igv/org.broad.igv.tools.converters=junit ---add-exports org.igv/org.broad.igv.tools.motiffinder=junit ---add-exports org.igv/org.broad.igv.tools.parsers=junit ---add-exports org.igv/org.broad.igv.tools.sort=junit ---add-exports org.igv/org.broad.igv.tools.ui=junit ---add-exports org.igv/org.broad.igv.track=junit ---add-exports org.igv/org.broad.igv.ui.action=junit ---add-exports org.igv/org.broad.igv.ui.color=junit ---add-exports org.igv/org.broad.igv.ui.commandbar=junit ---add-exports org.igv/org.broad.igv.ui.dnd=junit ---add-exports org.igv/org.broad.igv.ui.filefilters=junit ---add-exports org.igv/org.broad.igv.ui.legend=junit ---add-exports org.igv/org.broad.igv.ui.panel=junit ---add-exports org.igv/org.broad.igv.ui.svg=junit ---add-exports org.igv/org.broad.igv.ui.util=junit ---add-exports org.igv/org.broad.igv.ui.util.download=junit ---add-exports org.igv/org.broad.igv.util=junit ---add-exports org.igv/org.broad.igv.util.blat=junit ---add-exports org.igv/org.broad.igv.util.collections=junit ---add-exports org.igv/org.broad.igv.util.converters=junit ---add-exports org.igv/org.broad.igv.util.extview=junit ---add-exports org.igv/org.broad.igv.util.encode=junit ---add-exports org.igv/org.broad.igv.util.ftp=junit ---add-exports org.igv/org.broad.igv.util.index=junit ---add-exports org.igv/org.broad.igv.util.stream=junit ---add-exports org.igv/org.broad.igv.util.stats=junit ---add-exports org.igv/org.broad.igv.variant=junit ---add-exports org.igv/org.broad.igv.variant.New=junit ---add-exports org.igv/org.broad.igv.variant.util=junit ---add-exports org.igv/org.broad.igv.variant.vcf=junit ---add-exports org.igv/biz.source_code.base64Coder=junit ---add-exports org.igv/org.broad.igv.preprocess=junit ---add-exports org.igv/org.broad.tribble=junit ---add-exports org.igv/util=junit ---add-exports org.igv/org.broad.igv.htsget=junit diff --git a/src/main/java/com/sanityinc/jargs/CmdLineParser.java b/src/main/java/com/sanityinc/jargs/CmdLineParser.java index 970eb00aea..f45c7364c6 100644 --- a/src/main/java/com/sanityinc/jargs/CmdLineParser.java +++ b/src/main/java/com/sanityinc/jargs/CmdLineParser.java @@ -181,7 +181,7 @@ protected Option( String longForm, boolean wantsValue ) { protected Option( char shortForm, String longForm, boolean wantsValue ) { - this(new String(new char[]{shortForm}), longForm, wantsValue); + this(String.valueOf(shortForm), longForm, wantsValue); } private Option( String shortForm, String longForm, boolean wantsValue ) { @@ -281,7 +281,7 @@ public IntegerOption( String longForm ) { protected Integer parseValue( String arg, Locale locale ) throws IllegalOptionValueException { try { - return new Integer(arg); + return Integer.valueOf(arg); } catch (NumberFormatException e) { throw new IllegalOptionValueException(this, arg); } @@ -303,7 +303,7 @@ public LongOption( String longForm ) { protected Long parseValue( String arg, Locale locale ) throws IllegalOptionValueException { try { - return new Long(arg); + return Long.valueOf(arg); } catch (NumberFormatException e) { throw new IllegalOptionValueException(this, arg); } diff --git a/src/main/java/org/broad/igv/feature/genome/Genome.java b/src/main/java/org/broad/igv/feature/genome/Genome.java index 6d96bd4b62..afa928f6b9 100644 --- a/src/main/java/org/broad/igv/feature/genome/Genome.java +++ b/src/main/java/org/broad/igv/feature/genome/Genome.java @@ -334,10 +334,10 @@ public long getCumulativeOffset(String chr) { } offset += getChromosome(c).getLength(); } - cumOffset = new Long(offset); + cumOffset = offset; cumulativeOffsets.put(chr, cumOffset); } - return cumOffset.longValue(); + return cumOffset; } /** diff --git a/src/main/java/org/broad/igv/prefs/IGVPreferences.java b/src/main/java/org/broad/igv/prefs/IGVPreferences.java index 61bf5db497..96d170f034 100644 --- a/src/main/java/org/broad/igv/prefs/IGVPreferences.java +++ b/src/main/java/org/broad/igv/prefs/IGVPreferences.java @@ -1,3 +1,4 @@ + /* * The MIT License (MIT) * @@ -73,9 +74,9 @@ public class IGVPreferences { Set overrideKeys = new HashSet<>(); // Cached non-string preference values - private Map booleanCache = new Hashtable(); - private Map objectCache = new Hashtable(); - private Map colorScaleCache = new Hashtable(); + private Map booleanCache = new Hashtable<>(); + private Map objectCache = new Hashtable<>(); + private Map colorScaleCache = new Hashtable<>(); private PaletteColorTable mutationColorScheme = null; public IGVPreferences() { @@ -141,7 +142,7 @@ public boolean getAsBoolean(String key) { boolValue = Boolean.valueOf(get(key, value)); booleanCache.put(key, boolValue); } - return boolValue.booleanValue(); + return boolValue; } /** @@ -159,7 +160,7 @@ public int getAsInt(String key) { log.warn("No default value for: " + key); return 0; } - value = new Integer(get(key, defValue)); + value = Integer.valueOf(get(key, defValue)); objectCache.put(key, value); } return value.intValue(); @@ -201,7 +202,7 @@ public float getAsFloat(String key) { log.warn("No default value for: " + key); return 0; } - value = new Float(get(key, defValue)); + value = Float.valueOf(get(key, defValue)); objectCache.put(key, value); } return value.floatValue(); @@ -235,7 +236,7 @@ public void addOverrides(Map newPrefs) { public boolean getAntiAliasing() { - if (userPreferences.containsKey(Constants.ENABLE_ANTIALISING) || Globals.IS_LINUX == false) { + if (userPreferences.containsKey(Constants.ENABLE_ANTIALISING) || !Globals.IS_LINUX) { return getAsBoolean(Constants.ENABLE_ANTIALISING); } else { // Linux with no explicit setting @@ -252,9 +253,9 @@ public boolean getAntiAliasing() { private void updateCaches(String key, String value) { key = key.trim(); if (booleanCache.containsKey(key)) { - booleanCache.put(key, new Boolean(value)); + booleanCache.put(key, Boolean.valueOf(value)); } - colorScaleCache.remove(key); + colorScaleCache.remove(key); //TODO color scale cache doesn't use key strings so something here is wrong. objectCache.remove(key); mutationColorScheme = null; } @@ -417,7 +418,7 @@ public void remove(String key) { userPreferences.remove(key); booleanCache.remove(key); objectCache.remove(key); - colorScaleCache.remove(key); + colorScaleCache.remove(key); //TODO same issue of cache not using String keys IGVEventBus.getInstance().post(new PreferencesChangeEvent()); } diff --git a/src/main/java/org/broad/igv/sam/BaseAlignmentCounts.java b/src/main/java/org/broad/igv/sam/BaseAlignmentCounts.java index 936ac7a653..36a82af7f0 100644 --- a/src/main/java/org/broad/igv/sam/BaseAlignmentCounts.java +++ b/src/main/java/org/broad/igv/sam/BaseAlignmentCounts.java @@ -280,27 +280,19 @@ private static void loadKnownSnps(String snpFile) { return; } - knownSnps = new HashMap(); - AsciiLineReader reader = null; - try { - reader = ParsingUtils.openAsciiReader(new ResourceLocator(snpFile)); + knownSnps = new HashMap<>(); + try (AsciiLineReader reader = ParsingUtils.openAsciiReader(new ResourceLocator(snpFile))) { String nextLine = ""; while ((nextLine = reader.readLine()) != null) { String[] tokens = nextLine.split("\t"); String chr = tokens[0]; - Set snps = knownSnps.get(chr); - if (snps == null) { - snps = new HashSet(10000); - knownSnps.put(chr, snps); - } - snps.add(new Integer(tokens[1])); + Set snps = knownSnps.computeIfAbsent(chr, k -> new HashSet<>(10000)); + snps.add(Integer.valueOf(tokens[1])); } } catch (Exception e) { knownSnps = null; log.error("", e); MessageUtils.showMessage("Error loading snps file: " + snpFile + " (" + e.toString() + ")"); - } finally { - reader.close(); } diff --git a/src/main/java/org/broad/igv/sam/SparseAlignmentCounts.java b/src/main/java/org/broad/igv/sam/SparseAlignmentCounts.java index 02de430601..7bfb7f5be6 100644 --- a/src/main/java/org/broad/igv/sam/SparseAlignmentCounts.java +++ b/src/main/java/org/broad/igv/sam/SparseAlignmentCounts.java @@ -439,12 +439,7 @@ protected void incPositionCount(int pos, byte b, byte q, boolean isNegativeStran } private int getIndex(int pos) { - Integer index = indexMap.get(pos); - if (index == null) { - index = new Integer(indexMap.size()); - indexMap.put(pos, index); - } - return index.intValue(); + return indexMap.computeIfAbsent(pos, k -> indexMap.size()); } diff --git a/src/main/java/org/broad/igv/sam/reader/BAMReader.java b/src/main/java/org/broad/igv/sam/reader/BAMReader.java index 1addd6b6a7..9765483e02 100644 --- a/src/main/java/org/broad/igv/sam/reader/BAMReader.java +++ b/src/main/java/org/broad/igv/sam/reader/BAMReader.java @@ -119,7 +119,7 @@ private void loadSequenceDictionary() { if (records.size() > 0) { for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) { String chr = rec.getSequenceName(); - Long size = new Long(rec.getSequenceLength()); + Long size = (long) rec.getSequenceLength(); sequenceNames.add(chr); sequenceDictionary.put(chr, size); diff --git a/src/main/java/org/broad/igv/session/IGVSessionReader.java b/src/main/java/org/broad/igv/session/IGVSessionReader.java index 7a4f750b0a..c4483c780b 100644 --- a/src/main/java/org/broad/igv/session/IGVSessionReader.java +++ b/src/main/java/org/broad/igv/session/IGVSessionReader.java @@ -307,7 +307,7 @@ private void addLeftoverTracks(Collection> tmp) { //For resetting track panels later List> trackPanelAttrs = null; trackPanelAttrs = igv.getTrackPanelAttrs(); - + for (List tracks : tmp) { for (Track track : tracks) { if (track == geneTrack) { @@ -536,10 +536,10 @@ void processResource(Session session, Element element, String sessionPath) { // URL to a database or webservice -- this is not common String serverURL = getAttribute(element, SessionAttribute.SERVER_URL); - + String path = getAttribute(element, SessionAttribute.PATH); - // Older sessions used the "name" attribute for the path. + // Older sessions used the "name" attribute for the path. if (oldSession && name != null) { path = name; int idx = name.lastIndexOf("/"); @@ -630,7 +630,7 @@ private void processRegion(Session session, Element element, String sessionPath) String end = getAttribute(element, SessionAttribute.END_INDEX); String description = getAttribute(element, SessionAttribute.DESCRIPTION); - RegionOfInterest region = new RegionOfInterest(chromosome, new Integer(start), new Integer(end), description); + RegionOfInterest region = new RegionOfInterest(chromosome, Integer.parseInt(start), Integer.parseInt(end), description); igv.addRegionOfInterest(region); NodeList elements = element.getChildNodes(); diff --git a/src/main/java/org/broad/igv/ui/action/MenuAction.java b/src/main/java/org/broad/igv/ui/action/MenuAction.java index 16fd3c51da..dc28269a92 100644 --- a/src/main/java/org/broad/igv/ui/action/MenuAction.java +++ b/src/main/java/org/broad/igv/ui/action/MenuAction.java @@ -50,7 +50,7 @@ public class MenuAction extends AbstractAction { public MenuAction(String name, Icon icon, int mnemonic) { super(name, icon); if(mnemonic >= 0) { - putValue(MNEMONIC_KEY, new Integer(mnemonic)); + putValue(MNEMONIC_KEY, mnemonic); } } diff --git a/src/main/java/org/broad/igv/util/Utilities.java b/src/main/java/org/broad/igv/util/Utilities.java index c5c4a997ad..570900eeaa 100644 --- a/src/main/java/org/broad/igv/util/Utilities.java +++ b/src/main/java/org/broad/igv/util/Utilities.java @@ -164,7 +164,7 @@ public static String getNullSafe(NamedNodeMap attr, String key) { static public Comparator getNumericStringComparator() { - Comparator comparator = new Comparator() { + Comparator comparator = new Comparator() { public int compare(String s1, String s2) { StringTokenizer st1 = new StringTokenizer(s1, " "); @@ -177,10 +177,10 @@ public int compare(String s1, String s2) { int c; try { - Integer i1 = new Integer(t1); - Integer i2 = new Integer(t2); + int i1 = Integer.parseInt(t1); + int i2 = Integer.parseInt(t2); - c = i1.compareTo(i2); + c = Integer.compare(i1, i2); } catch (NumberFormatException e) { c = t1.compareTo(t2); }