From 3f8dcb45270ca39e8fcb29db9a42c1a82a7ca8cf Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 24 Oct 2019 19:41:27 +0100 Subject: [PATCH] JAL-3120 consistent paths/property interpolation in build.gradle. Test classes. Clean task corrections. --- .gitignore | 2 + build.gradle | 401 +++++++++++---------- gradle.properties | 14 +- utils/jalviewjs/test/src/jalview/bin/Jalview.java | 11 + utils/jalviewjs/test/test/jalview/bin/Test.java | 11 + 5 files changed, 240 insertions(+), 199 deletions(-) create mode 100644 utils/jalviewjs/test/src/jalview/bin/Jalview.java create mode 100644 utils/jalviewjs/test/test/jalview/bin/Test.java diff --git a/.gitignore b/.gitignore index 9c0d393..c30231b 100644 --- a/.gitignore +++ b/.gitignore @@ -33,3 +33,5 @@ TESTNG /.j2s /template.html /jalviewjsTest.html +/site1 +/site2 diff --git a/build.gradle b/build.gradle index 63665a9..48033f1 100644 --- a/build.gradle +++ b/build.gradle @@ -53,97 +53,97 @@ def compile_source_compatibility def compile_target_compatibility ext { - getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}" getdownDir = "" reportRsyncCmd = false buildDist = true buildProperties = buildPropertiesFile - getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher + getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}" switch (CHANNEL) { case "BUILD": // TODO: get bamboo build artifact URL for getdown artifacts getdown_channel_base = bamboo_channelbase - getdown_channel_name = bamboo_planKey + '/'+JAVA_VERSION - getdown_app_base = bamboo_channelbase + '/'+ bamboo_planKey + bamboo_getdown_channel_suffix + '/'+JAVA_VERSION + getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}" + getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}" getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" break case "RELEASE": getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" getdown_app_dir = getdown_app_dir_release - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" reportRsyncCommand = true break case "ARCHIVE": - getdown_channel_name = CHANNEL.toLowerCase()+"/"+JALVIEW_VERSION - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir + getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}" + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" getdown_app_dir = getdown_app_dir_alt - if (!file(ARCHIVEDIR+"/"+packageDir).exists()) { + if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { print "Must provide an ARCHIVEDIR value to produce an archive distribution" exit } else { - packageDir = ARCHIVEDIR + "/" + packageDir - buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile + packageDir = "${ARCHIVEDIR}/${packageDir}" + buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}" buildDist = false } reportRsyncCommand = true break case "ARCHIVELOCAL": - getdown_channel_name = "archive" + "/" + JALVIEW_VERSION - getdownDir = getdown_channel_name + "/" + JAVA_VERSION + getdown_channel_name = "archive/${JALVIEW_VERSION}" + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" getdown_app_base = file(getdownWebsiteDir).toURI().toString() getdown_app_dir = getdown_app_dir_alt - if (!file(ARCHIVEDIR+"/"+packageDir).exists()) { + if (!file("${ARCHIVEDIR}/${packageDir}").exists()) { print "Must provide an ARCHIVEDIR value to produce an archive distribution" exit } else { - packageDir = ARCHIVEDIR + "/" + packageDir - buildProperties = ARCHIVEDIR +"/" + classesDir + "/" + buildPropertiesFile + packageDir = "${ARCHIVEDIR}/${packageDir}" + buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}" buildDist = false } reportRsyncCommand = true - getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local + getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}" break case "DEVELOP": getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" reportRsyncCommand = true break case "TEST-RELEASE": getdown_channel_name = CHANNEL.toLowerCase() - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" reportRsyncCommand = true break case ~/^SCRATCH(|-[-\w]*)$/: getdown_channel_name = CHANNEL - getdownDir = getdown_channel_name + "/" + JAVA_VERSION - getdown_app_base = getdown_channel_base + "/" + getdownDir + getdownDir = "${getdown_channel_name}/${JAVA_VERSION}" + getdown_app_base = "${getdown_channel_base}/${getdownDir}" getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile + buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" reportRsyncCommand = true break case "LOCAL": getdown_app_base = file(getdownWebsiteDir).toURI().toString() getdown_app_dir = getdown_app_dir_alt - buildProperties = jalviewDir + "/" + classesDir +"/" + buildPropertiesFile - getdownLauncher = jalviewDir + '/' + getdown_lib_dir + '/' + getdown_launcher_local + buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}" + getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}" break default: // something wrong specified @@ -153,15 +153,15 @@ ext { } - println("Using a "+CHANNEL+" profile. appbase="+getdown_app_base) - getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir - //getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir - getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir - getdownInstallDir = getdownWebsiteDir + '/' + getdown_install_dir - getdownFilesDir = jalviewDir + '/' + getdown_files_dir + '/' + JAVA_VERSION + '/' - getdownFilesInstallDir = getdownFilesDir+"/"+getdown_install_dir + println("Using a ${CHANNEL} profile. appbase=${getdown_app_base}") + getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}" + //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}" + getdownResourceDir = "${getdownWebsiteDir}/${getdown_resource_dir}" + getdownInstallDir = "${getdownWebsiteDir}/${getdown_install_dir}" + getdownFilesDir = "${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/" + getdownFilesInstallDir = "${getdownFilesDir}/${getdown_install_dir}" /* compile without modules -- using classpath libraries - modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"]) + modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"]) modules_runtimeClasspath = modules_compileClasspath */ gitHash = "" @@ -222,25 +222,25 @@ if (JAVA_VERSION.equals("1.8")) { ] */ } else { - throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview") + throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview") } sourceSets { main { java { - srcDirs "$jalviewDir/$sourceDir" - outputDir = file("$classes") + srcDirs "${jalviewDir}/${sourceDir}" + outputDir = file("${classes}") } resources { - srcDirs "$jalviewDir/$resourceDir" + srcDirs "${jalviewDir}/${resourceDir}" } - jar.destinationDir = file("$jalviewDir/$packageDir") + jar.destinationDir = file("${jalviewDir}/${packageDir}") compileClasspath = files(sourceSets.main.java.outputDir) - compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath } @@ -257,16 +257,16 @@ sourceSets { compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir ) compileClasspath += files(sourceSets.main.java.outputDir) compileClasspath += sourceSets.main.compileClasspath - compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"]) - compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) runtimeClasspath = compileClasspath } test { java { - srcDirs "$jalviewDir/$testSourceDir" - outputDir = file("$jalviewDir/$testOutputDir") + srcDirs "${jalviewDir}/${testSourceDir}" + outputDir = file("${jalviewDir}/${testOutputDir}") } resources { @@ -281,9 +281,9 @@ sourceSets { compileClasspath += files(sourceSets.main.java.outputDir) } - compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"]) - compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testnglibs", include: ["**/*.jar"]) - compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir/testlibs", include: ["**/*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"]) + compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"]) runtimeClasspath = compileClasspath } @@ -332,7 +332,7 @@ eclipse { HashMap alreadyAddedSrcPath = new HashMap<>(); cp.entries.each { entry -> if (entry.kind == 'src') { - if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test")) { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) { removeTheseToo += entry } else { alreadyAddedSrcPath.putAt(entry.path, true) @@ -341,8 +341,8 @@ eclipse { } cp.entries.removeAll(removeTheseToo) - if (file(eclipse_bin_dir+"/main").isDirectory()) { - cp.entries += new Output(eclipse_bin_dir+"/main") + if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) { + cp.entries += new Output("${eclipse_bin_dir}/main") } if (file(helpParentDir).isDirectory()) { cp.entries += new Library(fileReference(helpParentDir)) @@ -360,7 +360,7 @@ eclipse { return } def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { // make relative path itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) } @@ -381,7 +381,7 @@ eclipse { return false // groovy "break" in .each closure } def itPath = it.toString() - if (itPath.startsWith(jalviewDirAbsolutePath+"/")) { + if (itPath.startsWith("${jalviewDirAbsolutePath}/")) { itPath = itPath.substring(jalviewDirAbsolutePath.length()+1) } if (alreadyAddedLibPath.get(itPath)) { @@ -412,7 +412,7 @@ eclipse { file { withProperties { props -> def jalview_prefs = new Properties() - def ins = new FileInputStream(jalviewDirAbsolutePath+"/"+eclipse_extra_jdt_prefs_file) + def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}") jalview_prefs.load(ins) ins.close() jalview_prefs.forEach { t, v -> @@ -550,9 +550,9 @@ task setGitVals { task createBuildProperties(type: WriteProperties) { dependsOn setGitVals - inputs.dir("$jalviewDir/$sourceDir") - inputs.dir("$classes") - inputs.dir("$jalviewDir/$resourceDir") + inputs.dir("${jalviewDir}/${sourceDir}") + inputs.dir("${classes}") + inputs.dir("${jalviewDir}/${resourceDir}") outputFile (buildProperties) // taking time specific comment out to allow better incremental builds comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss") @@ -563,7 +563,7 @@ task createBuildProperties(type: WriteProperties) { outputs.file(outputFile) } -def buildingHTML = "$jalviewDir/$docDir/building.html" +def buildingHTML = "${jalviewDir}/${docDir}/building.html" task cleanBuildingHTML(type: Delete) { doFirst { delete buildingHTML @@ -572,8 +572,8 @@ task cleanBuildingHTML(type: Delete) { task convertBuildingMD(type: Exec) { dependsOn cleanBuildingHTML - def buildingMD = "$jalviewDir/$docDir/building.md" - def css = "$jalviewDir/$docDir/github.css" + def buildingMD = "${jalviewDir}/${docDir}/building.md" + def css = "${jalviewDir}/${docDir}/github.css" def pandoc = null pandoc_exec.split(",").each { @@ -612,17 +612,17 @@ clean { task syncDocs(type: Sync) { dependsOn convertBuildingMD - def syncDir = "$classes/$docDir" - from fileTree("$jalviewDir/$docDir") + def syncDir = "${classes}/${docDir}" + from fileTree("${jalviewDir}/${docDir}") into syncDir } -def helpFile = "$classes/$helpDir/help.jhm" +def helpFile = "${classes}/${helpDir}/help.jhm" task copyHelp(type: Copy) { - def inputDir = "$jalviewDir/$helpParentDir/$helpDir" - def outputDir = "$classes/$helpDir" + def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" + def outputDir = "${classes}/${helpDir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' @@ -642,16 +642,16 @@ task copyHelp(type: Copy) { } task syncLib(type: Sync) { - def syncDir = "$classes/$libDistDir" - from fileTree("$jalviewDir/$libDistDir") + def syncDir = "${classes}/${libDistDir}" + from fileTree("${jalviewDir}/${libDistDir}") into syncDir } task syncResources(type: Sync) { - from "$jalviewDir/$resourceDir" + from "${jalviewDir}/${resourceDir}" include "**/*.*" exclude "install4j" - into "$classes" + into "${classes}" preserve { include "**" } @@ -694,59 +694,59 @@ task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" - workingDir = "$classes/$helpDir" + workingDir = "${classes}/${helpDir}" def argDir = "html" args = [ argDir ] - inputs.dir("$workingDir/$argDir") + inputs.dir("${workingDir}/${argDir}") - outputs.dir("$classes/doc") - outputs.dir("$classes/help") - outputs.file("$workingDir/JavaHelpSearch/DOCS") - outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB") - outputs.file("$workingDir/JavaHelpSearch/OFFSETS") - outputs.file("$workingDir/JavaHelpSearch/POSITIONS") - outputs.file("$workingDir/JavaHelpSearch/SCHEMA") - outputs.file("$workingDir/JavaHelpSearch/TMAP") + outputs.dir("${classes}/doc") + outputs.dir("${classes}/help") + outputs.file("${workingDir}/JavaHelpSearch/DOCS") + outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") + outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") + outputs.file("${workingDir}/JavaHelpSearch/POSITIONS") + outputs.file("${workingDir}/JavaHelpSearch/SCHEMA") + outputs.file("${workingDir}/JavaHelpSearch/TMAP") } task compileLinkCheck(type: JavaCompile) { options.fork = true - classpath = files("$jalviewDir/$utilsDir") - destinationDir = file("$jalviewDir/$utilsDir") - source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) + classpath = files("${jalviewDir}/${utilsDir}") + destinationDir = file("${jalviewDir}/${utilsDir}") + source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"]) - inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java") - inputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.java") - outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class") - outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class") + inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java") + inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java") + outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class") + outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class") } -def helplinkscheckertouchfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.touch") +def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch") task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck - classpath = files("$jalviewDir/$utilsDir") + classpath = files("${jalviewDir}/${utilsDir}") main = "HelpLinksChecker" workingDir = jalviewDir - def help = "$classes/$helpDir" - args = [ "$classes/$helpDir", "-nointernet" ] + def help = "${classes}/${helpDir}" + args = [ "${classes}/${helpDir}", "-nointernet" ] doLast { helplinkscheckertouchfile.createNewFile() } - inputs.dir("$classes/$helpDir") + inputs.dir("${classes}/${helpDir}") outputs.file(helplinkscheckertouchfile) } // import the pubhtmlhelp target -ant.properties.basedir = "$jalviewDir" -ant.properties.helpBuildDir = jalviewDirAbsolutePath+"/$classes/$helpDir" -ant.importBuild "$utilsDir/publishHelp.xml" +ant.properties.basedir = "${jalviewDir}" +ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}" +ant.importBuild "${utilsDir}/publishHelp.xml" task cleanPackageDir(type: Delete) { doFirst { - delete fileTree("$jalviewDir/$packageDir").include("*.jar") + delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar") } } @@ -762,7 +762,7 @@ jar { "Codebase": application_codebase } - destinationDir = file("$jalviewDir/$packageDir") + destinationDir = file("${jalviewDir}/${packageDir}") archiveName = rootProject.name+".jar" exclude "cache*/**" @@ -771,19 +771,19 @@ jar { exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir("$classes") - outputs.file("$jalviewDir/$packageDir/$archiveName") + inputs.dir("${classes}") + outputs.file("${jalviewDir}/${packageDir}/${archiveName}") } task copyJars(type: Copy) { - from fileTree("$classes").include("**/*.jar").include("*.jar").files - into "$jalviewDir/$packageDir" + from fileTree(dir: "${classes}", include: "**/*.jar").files + into "${jalviewDir}/${packageDir}" } // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well task syncJars(type: Sync) { - from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files - into "$jalviewDir/$packageDir" + from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files + into "${jalviewDir}/${packageDir}" preserve { include jar.archiveName } @@ -798,7 +798,7 @@ task makeDist { dependsOn cleanPackageDir dependsOn syncJars dependsOn jar - outputs.dir("$jalviewDir/$packageDir") + outputs.dir("${jalviewDir}/${packageDir}") } task cleanDist { @@ -812,7 +812,7 @@ shadowJar { if (buildDist) { dependsOn makeDist } - from ("$jalviewDir/$libDistDir") { + from ("${jalviewDir}/${libDistDir}") { include("*.jar") } manifest { @@ -847,7 +847,7 @@ task getdownWebsite() { rename(buildPropertiesFile, getdown_build_properties) into project.ext.getdownAppDir } - getdownWebsiteResourceFilenames += getdown_app_dir+"/"+getdown_build_properties + getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}" // go through properties looking for getdown_txt_... def props = project.properties.sort { it.key } @@ -865,7 +865,7 @@ task getdownWebsite() { if (prop.startsWith("getdown_txt_multi_")) { def key = prop.substring(18) val.split(",").each{ v -> - def line = key + " = " + v + "\n" + def line = "${key} = ${v}\n" getdownTextString += line } } else { @@ -877,16 +877,16 @@ task getdownWebsite() { r = file(val) } else if (val.indexOf('/') > 0) { // relative path (relative to jalviewDir) - r = file( jalviewDir + '/' + val ) + r = file( "${jalviewDir}/${val}" ) } if (r.exists()) { - val = getdown_resource_dir + '/' + r.getName() + val = "${getdown_resource_dir}/" + r.getName() getdownWebsiteResourceFilenames += val getdownResourceFilenames += r.getPath() } } if (! prop.startsWith("getdown_txt_resource")) { - def line = prop.substring(12) + " = " + val + "\n" + def line = prop.substring(12) + " = ${val}\n" getdownTextString += line } } @@ -894,7 +894,7 @@ task getdownWebsite() { } getdownWebsiteResourceFilenames.each{ filename -> - getdownTextString += "resource = "+filename+"\n" + getdownTextString += "resource = ${filename}\n" } getdownResourceFilenames.each{ filename -> copy { @@ -913,7 +913,8 @@ task getdownWebsite() { } } codeFiles.sort().each{f -> - def line = "code = " + getdown_app_dir + '/' + f.getName() + "\n" + def name = f.getName() + def line = "code = ${getdown_app_dir}/${name}\n" getdownTextString += line copy { from f.getPath() @@ -924,9 +925,10 @@ task getdownWebsite() { // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist /* if (JAVA_VERSION.equals("11")) { - def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles() + def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles() j11libFiles.sort().each{f -> - def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n" + def name = f.getName() + def line = "code = ${getdown_j11lib_dir}/${name}\n" getdownTextString += line copy { from f.getPath() @@ -938,13 +940,13 @@ task getdownWebsite() { // getdown-launcher.jar should not be in main application class path so the main application can move it when updated. Listed as a resource so it gets updated. //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n" - getdownTextString += "resource = " + getdown_launcher_new + "\n" - getdownTextString += "class = " + mainClass + "\n" + getdownTextString += "resource = ${getdown_launcher_new}\n" + getdownTextString += "class = ${mainClass}\n" - def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt") + def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt") getdown_txt.write(getdownTextString) - def launch_jvl = file(project.ext.getdownWebsiteDir + "/" + getdown_launch_jvl) + def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}") launch_jvl.write("appbase="+props.get("getdown_txt_appbase")) copy { @@ -965,7 +967,7 @@ task getdownWebsite() { copy { from getdown_txt from getdownLauncher - from getdownWebsiteDir+"/"+getdown_build_properties + from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } @@ -982,7 +984,7 @@ task getdownWebsite() { from getdown_txt from launch_jvl from getdownLauncher - from getdownWebsiteDir+"/"+getdown_build_properties + from "${getdownWebsiteDir}/${getdown_build_properties}" if (file(getdownLauncher).getName() != getdown_launcher) { rename(file(getdownLauncher).getName(), getdown_launcher) } @@ -991,12 +993,12 @@ task getdownWebsite() { copy { from getdownResourceDir - into project.ext.getdownFilesDir + '/' + getdown_resource_dir + into "${project.ext.getdownFilesDir}/${getdown_resource_dir}" } } if (buildDist) { - inputs.dir(jalviewDir + '/' + packageDir) + inputs.dir("${jalviewDir}/${packageDir}") } outputs.dir(project.ext.getdownWebsiteDir) outputs.dir(project.ext.getdownFilesDir) @@ -1007,12 +1009,12 @@ task getdownDigest(type: JavaExec) { description = "Digest the getdown website folder" dependsOn getdownWebsite doFirst { - classpath = files(getdownWebsiteDir + '/' + getdown_launcher) + classpath = files("${getdownWebsiteDir}/${getdown_launcher}") } main = "com.threerings.getdown.tools.Digester" args project.ext.getdownWebsiteDir inputs.dir(project.ext.getdownWebsiteDir) - outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt") + outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt") } task getdown() { @@ -1021,8 +1023,8 @@ task getdown() { dependsOn getdownDigest doLast { if (reportRsyncCommand) { - def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith("/")?"":"/") - def toDir = getdown_rsync_dest + "/" + getdownDir + (getdownDir.endsWith("/")?"":"/") + def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/') + def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/') println "LIKELY RSYNC COMMAND:" println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'" if (RUNRSYNC == "true") { @@ -1069,15 +1071,15 @@ def macosJavaVMDir def macosJavaVMTgz def windowsJavaVMDir def windowsJavaVMTgz -def install4jDir = "$jalviewDir/$install4jResourceDir" -def install4jConfFile = "jalview-installers-java"+JAVA_VERSION+".install4j" -install4jConf = "$install4jDir/$install4jConfFile" +def install4jDir = "${jalviewDir}/${install4jResourceDir}" +def install4jConfFile = "jalview-installers-java${JAVA_VERSION}.install4j" +install4jConf = "${install4jDir}/${install4jConfFile}" task copyInstall4jTemplate(type: Copy) { - macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre" - macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz" - windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre" - windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz" + macosJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre" + macosJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz" + windowsJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre" + windowsJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz" from (install4jDir) { include install4jTemplate rename (install4jTemplate, install4jConfFile) @@ -1110,7 +1112,7 @@ task copyInstall4jTemplate(type: Copy) { doLast { // include file associations in installer - def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text + def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text ant.replaceregexp( byline: false, flags: "s", @@ -1140,7 +1142,7 @@ task installers(type: com.install4j.gradle.Install4jTask) { projectFile = file(install4jConf) println("Using projectFile "+projectFile) variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH] - destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION" + destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}" buildSelected = true if (OSX_KEYPASS) { @@ -1152,7 +1154,7 @@ task installers(type: com.install4j.gradle.Install4jTask) { inputs.file(install4jConf) inputs.dir(macosJavaVMDir) inputs.dir(windowsJavaVMDir) - outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION") + outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}") } @@ -1165,7 +1167,7 @@ clean { task sourceDist (type: Tar) { def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_") - def outputFileName = project.name + "_" + VERSION_UNDERSCORES + ".tar.gz" + def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz" // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09] try { archiveFileName = outputFileName @@ -1182,7 +1184,7 @@ task sourceDist (type: Tar) { ,"benchmarking/*" ,"**/.*" ,"*.class" - ,"**/*.class","$j11modDir/**/*.jar","appletlib","**/*locales" + ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales" ,"*locales/**", ,"utils/InstallAnywhere"] def PROCESS_FILES=[ "AUTHORS", @@ -1222,7 +1224,7 @@ task sourceDist (type: Tar) { exclude (getdown_website_dir) // exluding these as not using jars as modules yet - exclude ("$j11modDir/**/*.jar") + exclude ("${j11modDir}/**/*.jar") } // from (jalviewDir) { // // explicit includes for stuff that seemed to not get included @@ -1236,8 +1238,8 @@ task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("$classes/$helpDir") - outputs.dir("$helpOutputDir") + inputs.dir("${classes}/${helpDir}") + outputs.dir("${helpOutputDir}") } def jalviewjsBuildDir @@ -1246,12 +1248,12 @@ def jalviewjsTransferSiteDir task jalviewjsSitePath { def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs" - if (jalviewjs_site_dir.startsWith("/")) { + if (jalviewjs_site_dir.startsWith('/')) { jalviewjsSiteDir = jalviewjs_site_dir } else { - jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir + jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" } - jalviewjsTransferSiteDir = jalviewjsBuildDir + "/tmp/site" + jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site" } def eclipseWorkspace @@ -1298,8 +1300,8 @@ task jalviewjsSetEclipseWorkspace { task jalviewjsUnzipFiles { dependsOn jalviewjsSitePath - def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip") - zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip + def zipFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_libjs_dir}", include: "*.zip") + zipFiles += "${jalviewjs_utils_dir}/${jalviewjs_swingjs_zip}" doLast { zipFiles.each { file_zip -> @@ -1327,31 +1329,34 @@ task jalviewjsEclipsePaths { } if (OperatingSystem.current().isMacOsX()) { eclipseRoot += "/Eclipse.app" - eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins" - eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse" - eclipseProduct = eclipseRoot+"/Contents/Eclipse/.eclipseproduct" + eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins" + eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" + eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" } else if (OperatingSystem.current().isWindows()) { // check these paths!! - if (file(eclipseRoot+"/eclipse").isDirectory() && file(eclipseRoot+"/eclipse/.eclipseproduct").exists()) { + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" } - eclipseDropinsDir = eclipseRoot+"/dropins" - eclipseBinary = eclipseRoot+"/eclipse" - eclipseProduct = eclipseRoot+"/.eclipseproduct" + eclipseDropinsDir = "${eclipseRoot}/dropins" + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" } else { // linux or unix - if (file(eclipseRoot+"/eclipse").isDirectory() && file(eclipseRoot+"/eclipse/.eclipseproduct").exists()) { + if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" } - eclipseDropinsDir = eclipseRoot+"/dropins" - eclipseBinary = eclipseRoot+"/eclipse" - eclipseProduct = eclipseRoot+"/.eclipseproduct" + eclipseDropinsDir = "${eclipseRoot}/dropins" + eclipseBinary = "${eclipseRoot}/eclipse" + eclipseProduct = "${eclipseRoot}/.eclipseproduct" } - def fis = new FileInputStream(eclipseProduct) - def props = new Properties() - props.load(fis) - eclipseVersion = props.getProperty("version") - fis.close() - println("ECLIPSE_VERSION=${eclipseVersion}") + eclipseVersion = "4.12" // default + if (file(eclipseProduct).exists()) { + def fis = new FileInputStream(eclipseProduct) + def props = new Properties() + props.load(fis) + eclipseVersion = props.getProperty("version") + fis.close() + println("ECLIPSE_VERSION=${eclipseVersion}") + } String[] v = eclipseVersion.split("\\.") def v0 = Integer.valueOf(v[0]) def v1 = Integer.valueOf(v[1]) @@ -1362,18 +1367,17 @@ task jalviewjsEclipsePaths { } } -task OLDjalviewjsEclipseCopyDropins { +task jalviewjsEclipseCopyDropins { dependsOn jalviewjsEclipsePaths - def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+fromDropinsDir, include: "*.jar") + def inputFiles = fileTree(dir: "${jalviewjs_utils_dir}/${fromDropinsDir}", include: "*.jar") def outputDir = eclipseDropinsDir inputs.files inputFiles inputFiles.each { file -> - outputs.file(outputDir+"/"+file.name) + outputs.file("${outputDir}/${file.name}") } doLast { - def outputFiles = [] inputFiles.each { file -> copy { from file @@ -1384,22 +1388,23 @@ task OLDjalviewjsEclipseCopyDropins { } // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir -task jalviewjsEclipseCopyDropins(type: Copy) { +task NEWjalviewjsEclipseCopyDropins(type: Copy) { + dependsOn jalviewjsEclipsePaths from fromDropinsDir into eclipseDropinsDir } task jalviewjsCreateJ2sSettings(type: WriteProperties) { dependsOn jalviewjsSitePath - outputFile (jalviewDir+"/"+jalviewjs_j2s_settings) + outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}") def props = project.properties.sort { it.key } def siteDirProperty = "j2s.site.directory" def setSiteDir = false props.each { prop, val -> if (prop.startsWith("j2s.") && val != null) { if (prop == siteDirProperty) { - if (!(val.startsWith("/") || val.startsWith("file://") )) { - val = jalviewjsTransferSiteDir+"/"+val + if (!(val.startsWith('/') || val.startsWith("file://") )) { + val = "${jalviewjsTransferSiteDir}/${val}" } setSiteDir = true } @@ -1422,13 +1427,13 @@ task jalviewjsEclipseSetup { task jalviewjsCopyResources (type: Copy) { dependsOn jalviewjsSitePath def inputFiles = fileTree(dir: jalviewjs_resource_dir) - def outputDir = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir + def outputDir = "${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles into outputDir def outputFiles = [] rename { filename -> - outputFiles += outputDir+"/"+filename + outputFiles += "${outputDir}/${filename}" null } outputs.files outputFiles @@ -1437,33 +1442,20 @@ task jalviewjsCopyResources (type: Copy) { task jalviewjsCopySiteResources (type: Copy) { dependsOn jalviewjsSitePath - def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir) + def inputFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_site_resource_dir}") def outputDir = jalviewjsSiteDir from inputFiles into outputDir def outputFiles = [] rename { filename -> - outputFiles += outputDir+"/"+filename + outputFiles += "${outputDir}/${filename}" null } outputs.files outputFiles inputs.files inputFiles } -task cleanJalviewjsAll { - group "JalviewJS" - description "Delete all configuration and build artifacts to do with JalviewJS build" - dependsOn cleanJalviewjsSite - - doFirst { - delete jalviewjsBuildDir - delete jalviewDir+"/"+eclipse_bin_dir - delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") - delete jalviewDir+"/"+jalviewjs_j2s_settings - } -} - task jalviewjsProjectImport(type: Exec) { // work out how to do this! dependsOn eclipseProject @@ -1473,9 +1465,12 @@ task jalviewjsProjectImport(type: Exec) { dependsOn jalviewjsEclipseSetup executable(eclipseBinary) args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath]) + if (eclipse_debug == "true") { + args += "-debug" + } def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core" - inputs.file(jalviewDir+"/.project") + inputs.file("${jalviewDir}/.project") outputs.dir(projdir) outputs.upToDateWhen { file(projdir).exists() } } @@ -1485,7 +1480,10 @@ task jalviewjsTranspile(type: Exec) { dependsOn jalviewjsProjectImport dependsOn jalviewjsEclipsePaths executable(eclipseBinary) - args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ]) + args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipseBuildArg}", eclipse_project_name ]) + if (eclipse_debug == "true") { + args += "-debug" + } def stdout def stderr @@ -1531,7 +1529,7 @@ task jalviewjsTranspile(type: Exec) { } inputs.dir(sourceDir) - outputs.dir(eclipse_bin_dir+"/main") + outputs.dir("${eclipse_bin_dir}/main") outputs.dir(jalviewjsTransferSiteDir) outputs.upToDateWhen { file("${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } @@ -1603,7 +1601,7 @@ task jalviewjsServer { def url while(port < start+1000 && !running) { try { - def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir) + def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}") def jalviewjsServer = factory.start(doc_root, port) running = true url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource) @@ -1626,6 +1624,19 @@ task jalviewjsServer { outputs.file(htmlFile) } +task cleanJalviewjsAll { + group "JalviewJS" + description "Delete all configuration and build artifacts to do with JalviewJS build" + dependsOn cleanJalviewjsSite + + doFirst { + delete jalviewjsBuildDir + delete "${jalviewDir}/${eclipse_bin_dir}" + delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") + delete "${jalviewDir}/${jalviewjs_j2s_settings}" + } +} + task jalviewjs { group "JalviewJS" description "Build the site" diff --git a/gradle.properties b/gradle.properties index c035a59..f2834c7 100644 --- a/gradle.properties +++ b/gradle.properties @@ -2,6 +2,13 @@ jalviewDir = . #JAVA_VERSION = 1.8 JAVA_VERSION = 11 + +sourceDir = src +#sourceDir = utils/jalviewjs/test/src + +testSourceDir = test +#testSourceDir = utils/jalviewjs/test/test + JALVIEW_VERSION = DEVELOPMENT INSTALLATION = Source jalview_keystore = keys/.keystore @@ -23,7 +30,6 @@ helpParentDir = help helpDir = help helpOutputDir = build/distributions/help docDir = doc -sourceDir = src schemaDir = schemas classesDir = classes examplesDir = examples @@ -35,7 +41,6 @@ packageDir = dist ARCHIVEDIR = outputJar = jalview.jar -testSourceDir = test testOutputDir = tests utilsDir = utils @@ -141,8 +146,9 @@ bamboo_getdown_channel_suffix = /latest/artifact/shared/getdown-channel eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs eclipse_project_name = jalview eclipse_bin_dir = bin +eclipse_debug = false -jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-09 +jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-06 jalviewjs_utils_dir = utils/jalviewjs jalviewjs_eclipse_dropins_dir = eclipse/dropins @@ -167,7 +173,7 @@ j2s.compiler.status = enable #j2s.log.methods.declared = j2s_methods_declared.log #j2s.log.methods.called = j2s_methods_called.log #a semicolon-separated list of package-level file paths to be excluded -#j2s.excluded.paths = test;testng;util +j2s.excluded.paths = test;testng;util #j2s.include.tests = true #j2s.testing = null #j2s.compiler.nonqualified.packages = null diff --git a/utils/jalviewjs/test/src/jalview/bin/Jalview.java b/utils/jalviewjs/test/src/jalview/bin/Jalview.java new file mode 100644 index 0000000..4d7b59a --- /dev/null +++ b/utils/jalviewjs/test/src/jalview/bin/Jalview.java @@ -0,0 +1,11 @@ +package jalview.bin; + +public class Jalview { + + public static void main(String args[]) + { + System.out.println("Hello, java2script test src!"); + } +} + + diff --git a/utils/jalviewjs/test/test/jalview/bin/Test.java b/utils/jalviewjs/test/test/jalview/bin/Test.java new file mode 100644 index 0000000..77fc2de --- /dev/null +++ b/utils/jalviewjs/test/test/jalview/bin/Test.java @@ -0,0 +1,11 @@ +package jalview.bin; + +public class Test { + + public static void main(String args[]) + { + System.out.println("Hello, java2script test test!"); + } +} + + -- 1.7.10.2