From 85cf5584182fa3327888d6c617a278b5ef6b6b83 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 13 Nov 2019 17:01:32 +0000 Subject: [PATCH] JAL-3210 Improved dirs in build.gradle. Fixed _all core (added exclusions). Possibly fixed eclipse_workspace_location disappearances --- build.gradle | 152 +++++++++++++++++++++++++++++++++-------------------- gradle.properties | 21 ++++---- 2 files changed, 105 insertions(+), 68 deletions(-) diff --git a/build.gradle b/build.gradle index ae93e40..2612fdb 100644 --- a/build.gradle +++ b/build.gradle @@ -42,6 +42,7 @@ def string(Object o) { ext { jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath() + jalviewDirRelativePath = jalviewDir // local build environment properties def localProps = "${jalviewDirAbsolutePath}/local.properties" @@ -64,7 +65,6 @@ ext { } } - // this property set when running Eclipse headlessly j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild") // this property set by Eclipse @@ -86,18 +86,31 @@ ext { System.properties.sort { it.key }.each { key, val -> println("SYSTEM PROPERTY ${key}='${val}'") } + if (false && IN_ECLIPSE) { + jalviewDir = jalviewDirAbsolutePath + } */ + // essentials + bareSourceDir = string(source_dir) + sourceDir = string("${jalviewDir}/${bareSourceDir}") + resourceDir = string("${jalviewDir}/${resource_dir}") + bareTestSourceDir = string(test_source_dir) + testSourceDir = string("${jalviewDir}/${bareTestSourceDir}") + + // clover cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}") - classes = string("${jalviewDir}/${classesDir}") + classesDir = string("${jalviewDir}/${classes_dir}") if (clover.equals("true")) { use_clover = true - classes = string("${buildDir}/${cloverClassesDir}") + classesDir = string("${buildDir}/${cloverClassesDir}") } else { use_clover = false - classes = string("${jalviewDir}/${classesDir}") + classesDir = string("${jalviewDir}/${classes_dir}") } + classes = classesDir + getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}") getdownDir = string("") reportRsyncCmd = false @@ -112,7 +125,7 @@ ext { getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}") getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}") getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + buildProperties = string("${classesDir}/${build_properties_file}") break case "RELEASE": @@ -120,7 +133,7 @@ ext { getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_release - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + buildProperties = string("${classesDir}/${build_properties_file}") reportRsyncCommand = true break @@ -134,7 +147,7 @@ ext { exit } else { packageDir = string("${ARCHIVEDIR}/${packageDir}") - buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}") + buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true @@ -150,7 +163,7 @@ ext { exit } else { packageDir = string("${ARCHIVEDIR}/${packageDir}") - buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}") + buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}") buildDist = false } reportRsyncCommand = true @@ -162,7 +175,7 @@ ext { getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + buildProperties = string("${classesDir}/${build_properties_file}") reportRsyncCommand = true break @@ -171,7 +184,7 @@ ext { getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + buildProperties = string("${classesDir}/${build_properties_file}") reportRsyncCommand = true break @@ -180,14 +193,14 @@ ext { getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}") getdown_app_base = string("${getdown_channel_base}/${getdownDir}") getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + buildProperties = string("${classesDir}/${build_properties_file}") reportRsyncCommand = true break case "LOCAL": getdown_app_base = file(getdownWebsiteDir).toURI().toString() getdown_app_dir = getdown_app_dir_alt - buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}") + buildProperties = string("${classesDir}/${build_properties_file}") getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}") break @@ -277,7 +290,10 @@ ext { buildingHTML = string("${jalviewDir}/${docDir}/building.html") - helpFile = string("${classes}/${helpDir}/help.jhm") + helpFile = string("${classesDir}/${help_dir}/help.jhm") + helpParentDir = string("${jalviewDir}/${help_parent_dir}") + helpDir = string("${help_dir}") + helpSourceDir = string("${helpParentDir}/${helpDir}") relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) @@ -295,6 +311,8 @@ ext { jalviewjsJalviewCoreName = string(jalviewjs_core_name) jalviewjsCoreClasslists = [] jalviewjsJalviewTemplateName = string(jalviewjs_name) + jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}") + jalviewjsJ2sProps = null eclipseWorkspace = null eclipseBinary = string("") @@ -307,12 +325,12 @@ ext { sourceSets { main { java { - srcDirs "${jalviewDir}/${sourceDir}" - outputDir = file(project.classes) + srcDirs sourceDir + outputDir = file(classesDir) } resources { - srcDirs "${jalviewDir}/${resourceDir}" + srcDirs resourceDir } jar.destinationDir = file("${jalviewDir}/${packageDir}") @@ -343,7 +361,7 @@ sourceSets { test { java { - srcDirs "${jalviewDir}/${testSourceDir}" + srcDirs testSourceDir outputDir = file("${jalviewDir}/${testOutputDir}") } @@ -412,7 +430,7 @@ eclipse { HashMap alreadyAddedSrcPath = new HashMap<>(); cp.entries.each { entry -> if (entry.kind == 'src') { - if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) { + if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) { removeTheseToo += entry } else { alreadyAddedSrcPath.putAt(entry.path, true) @@ -421,11 +439,9 @@ eclipse { } cp.entries.removeAll(removeTheseToo) - if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) { - cp.entries += new Output("${eclipse_bin_dir}/main") - } - if (file(helpParentDir).isDirectory()) { - cp.entries += new Library(fileReference(helpParentDir)) + cp.entries += new Output("${eclipse_bin_dir}/main") + if (file(helpSourceDir).isDirectory()) { + cp.entries += new Library(fileReference(helpSourceDir)) } if (file(resourceDir).isDirectory()) { cp.entries += new Library(fileReference(resourceDir)) @@ -508,7 +524,7 @@ eclipse { if (IN_ECLIPSE) { // Don't want these to be activated if in headless build - //synchronizationTasks "eclipseConfiguration" + synchronizationTasks "eclipseSynchronizationTask" autoBuildTasks "eclipseAutoBuildTask" } } @@ -516,7 +532,7 @@ eclipse { task cloverInstr() { // only instrument source, we build test classes as normal - inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"])) + inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"])) outputs.dir cloverInstrDir doFirst { @@ -642,8 +658,8 @@ task setGitVals { task createBuildProperties(type: WriteProperties) { dependsOn setGitVals - inputs.dir("${jalviewDir}/${sourceDir}") - inputs.dir("${jalviewDir}/${resourceDir}") + inputs.dir(sourceDir) + inputs.dir(resourceDir) file(buildProperties).getParentFile().mkdirs() outputFile (buildProperties) // taking time specific comment out to allow better incremental builds @@ -707,7 +723,7 @@ clean { task syncDocs(type: Sync) { dependsOn convertBuildingMD - def syncDir = "${classes}/${docDir}" + def syncDir = "${classesDir}/${docDir}" from fileTree("${jalviewDir}/${docDir}") into syncDir @@ -715,8 +731,8 @@ task syncDocs(type: Sync) { task copyHelp(type: Copy) { - def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}" - def outputDir = "${classes}/${helpDir}" + def inputDir = helpSourceDir + def outputDir = "${classesDir}/${helpDir}" from(inputDir) { exclude '**/*.gif' exclude '**/*.jpg' @@ -744,16 +760,16 @@ task copyHelp(type: Copy) { task syncLib(type: Sync) { - def syncDir = "${classes}/${libDistDir}" + def syncDir = "${classesDir}/${libDistDir}" from fileTree("${jalviewDir}/${libDistDir}") into syncDir } task syncResources(type: Sync) { - from "${jalviewDir}/${resourceDir}" + from resourceDir include "**/*.*" - into "${classes}" + into "${classesDir}" preserve { include "**" } @@ -798,13 +814,13 @@ task buildIndices(type: JavaExec) { dependsOn copyHelp classpath = sourceSets.main.compileClasspath main = "com.sun.java.help.search.Indexer" - workingDir = "${classes}/${helpDir}" + workingDir = "${classesDir}/${helpDir}" def argDir = "html" args = [ argDir ] inputs.dir("${workingDir}/${argDir}") - outputs.dir("${classes}/doc") - outputs.dir("${classes}/help") + outputs.dir("${classesDir}/doc") + outputs.dir("${classesDir}/help") outputs.file("${workingDir}/JavaHelpSearch/DOCS") outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB") outputs.file("${workingDir}/JavaHelpSearch/OFFSETS") @@ -834,8 +850,8 @@ task linkCheck(type: JavaExec) { classpath = files("${jalviewDir}/${utilsDir}") main = "HelpLinksChecker" workingDir = jalviewDir - def help = "${classes}/${helpDir}" - args = [ "${classes}/${helpDir}", "-nointernet" ] + def help = "${classesDir}/${helpDir}" + args = [ "${classesDir}/${helpDir}", "-nointernet" ] def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append def errFOS = outFOS @@ -846,13 +862,13 @@ task linkCheck(type: JavaExec) { outFOS, errorOutput) - inputs.dir("${classes}/${helpDir}") + inputs.dir("${classesDir}/${helpDir}") outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target ant.properties.basedir = "${jalviewDir}" -ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}" +ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}" ant.importBuild "${utilsDir}/publishHelp.xml" @@ -883,13 +899,13 @@ jar { exclude "**/*.jar" exclude "**/*.jar.*" - inputs.dir("${classes}") + inputs.dir(classesDir) outputs.file("${jalviewDir}/${packageDir}/${archiveName}") } task copyJars(type: Copy) { - from fileTree(dir: "${classes}", include: "**/*.jar").files + from fileTree(dir: classesDir, include: "**/*.jar").files into "${jalviewDir}/${packageDir}" } @@ -1379,8 +1395,8 @@ task helppages { dependsOn copyHelp dependsOn pubhtmlhelp - inputs.dir("${classes}/${helpDir}") - outputs.dir("${helpOutputDir}") + inputs.dir("${classesDir}/${helpDir}") + outputs.dir("${buildDir}/distributions/${helpDir}") } @@ -1448,7 +1464,7 @@ task jalviewjsSetEclipseWorkspace { //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date outputs.file(propsFileName) - outputs.upToDateWhen { eclipseWorkspace.exists() } + outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() } } @@ -1594,11 +1610,10 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { group "JalviewJS" description "Create the .j2s file from the j2s.* properties" - outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}") - def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } + jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key } def siteDirProperty = "j2s.site.directory" def setSiteDir = false - j2s_props.each { prop, val -> + jalviewjsJ2sProps.each { prop, val -> if (val != null) { if (prop == siteDirProperty) { if (!(val.startsWith('/') || val.startsWith("file://") )) { @@ -1609,11 +1624,15 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { property(prop,val) } if (!setSiteDir) { // default site location, don't override specifically set property - property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}") + property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}") } } - inputs.properties(j2s_props) - outputs.file(outputFile) + outputFile = jalviewjsJ2sSettingsFileName + + if (! IN_ECLIPSE) { + inputs.properties(jalviewjsJ2sProps) + outputs.file(jalviewjsJ2sSettingsFileName) + } } @@ -1646,7 +1665,7 @@ task jalviewjsSyncAllLibs (type: Sync) { task jalviewjsSyncResources (type: Sync) { - def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}") + def inputFiles = fileTree(dir: resourceDir) def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}" from inputFiles @@ -1974,8 +1993,26 @@ task jalviewjsBuildAllCores { // _all core def allClasslistName = "_all" def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js") - //allJsFiles += fileTree(dir: libJ2sDir, include: "**/*.js") - //allJsFiles += fileTree(dir: swingJ2sDir, include: "**/*.js") + allJsFiles += fileTree( + dir: libJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js", + "**/org/jmol/export/JSExporter.js" + ] + ) + allJsFiles += fileTree( + dir: swingJ2sDir, + include: "**/*.js", + excludes: [ + // these exlusions are files that the closure-compiler produces errors for. Should fix them + "**/sun/misc/Unsafe.js", + "**/swingjs/jquery/jquery-editable-select.js", + "**/swingjs/jquery/j2sComboBox.js", + "**/sun/misc/FloatingDecimal.js" + ] + ) def allClasslist = [ 'jsfile': "${outputDir}/core${allClasslistName}.js", 'zjsfile': "${outputDir}/core${allClasslistName}.z.js", @@ -2179,7 +2216,8 @@ task jalviewjsServer { } def htmlText = """

JalviewJS Test. <${url}>

-

JalviewJS Test with debug. <${url}?j2sdebug<

+

JalviewJS Test with debug. <${url}?j2sdebug>

+

JalviewJS Test with verbose. <${url}?j2sdebug>

""" jalviewjsCoreClasslists.each { cl -> def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName()) @@ -2263,8 +2301,8 @@ task jalviewjsIDE_Server { // buildship runs this at import -task eclipseConfiguration { - dependsOn eclipseSetup +task eclipseSynchronizationTask { + //dependsOn eclipseSetup dependsOn jalviewjsIDE_j2sFile } diff --git a/gradle.properties b/gradle.properties index 784970c..7389cbe 100644 --- a/gradle.properties +++ b/gradle.properties @@ -3,11 +3,11 @@ jalviewDir = . #JAVA_VERSION = 1.8 JAVA_VERSION = 11 -sourceDir = src -#sourceDir = utils/jalviewjs/test/src +source_dir = src +#source_dir = utils/jalviewjs/test/src -testSourceDir = test -#testSourceDir = utils/jalviewjs/test/test +test_source_dir = test +#test_source_dir = utils/jalviewjs/test/test JALVIEW_VERSION = DEVELOPMENT INSTALLATION = Source @@ -25,13 +25,12 @@ testngGroups = Functional j8libDir = j8lib j11libDir = j11lib -resourceDir = resources -helpParentDir = help -helpDir = help -helpOutputDir = build/distributions/help +resource_dir = resources +help_parent_dir = help +help_dir = help docDir = doc schemaDir = schemas -classesDir = classes +classes_dir = classes examplesDir = examples clover = false use_clover = false @@ -174,8 +173,8 @@ jalviewjs_server_wait = 30 jalviewjs_server_resource = /jalview_bin_Jalview.html jalviewjs_core_name = _jalview jalviewjs_name = JalviewJS -#jalviewjs_core_key = core -jalviewjs_core_key = preloadCore +jalviewjs_core_key = core +#jalviewjs_core_key = preloadCore j2s.compiler.status = enable #j2s.site.directory = null ## site defined from buildDir+'/jalviewjs/'+jalviewjs_site_dir -- 1.7.10.2