import org.apache.tools.ant.filters.ReplaceTokens
import org.gradle.internal.os.OperatingSystem
-
buildscript {
dependencies {
- //classpath files("$gradlePluginsDir/gradle-macappbundle-2.3.0-patched-2.3.0.jar")
+ classpath 'org.openclover:clover:4.3.1'
+ classpath 'org.apache.commons:commons-compress:1.18'
}
}
repositories {
jcenter()
mavenCentral()
+ mavenLocal()
flatDir {
dirs gradlePluginsDir
}
}
mainClassName = launcherClass
+def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
+def classes = "$jalviewDir/$classesDir"
+if (clover.equals("true")) {
+ use_clover = true
+ classes = "$buildDir/$cloverClassesDir"
+} else {
+ use_clover = false
+ classes = "$jalviewDir/$classesDir"
+}
+
+// configure classpath/args for j8/j11 compilation
+
+def libDir
+def libDistDir
+def compile_source_compatibility
+def compile_target_compatibility
+def additional_compiler_args = []
+def getdown_alt_java_min_version
+if (JAVA_VERSION.equals("1.8")) {
+ libDir = j11libDir
+ libDistDir = j8libDir
+ compile_source_compatibility = 1.8
+ compile_target_compatibility = 1.8
+ getdown_alt_java_min_version = getdown_alt_java8_min_version
+} else if (JAVA_VERSION.equals("11")) {
+ libDir = j11libDir
+ libDistDir = j11libDir
+ compile_source_compatibility = 11
+ compile_target_compatibility = 11
+ getdown_alt_java_min_version = getdown_alt_java11_min_version
+ additional_compiler_args += [
+ '--module-path', file("$jalviewDir/$j11modDir").getAbsolutePath(),
+ '--add-modules', j11modules
+ ]
+} else {
+ throw new GradleException("JAVA_VERSION=$JAVA_VERSION not currently supported by Jalview")
+}
sourceSets {
main {
java {
srcDirs "$jalviewDir/$sourceDir"
- outputDir = file("$jalviewDir/$classesDir")
+ outputDir = file("$classes")
}
resources {
srcDirs "$jalviewDir/$resourceDir"
- srcDirs "$jalviewDir/$libDir"
+ srcDirs "$jalviewDir/$libDistDir"
}
jar.destinationDir = file("$jalviewDir/$packageDir")
compileClasspath = files(sourceSets.main.java.outputDir)
compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
- if (JAVA_VERSION.equals("1.8")) {
- print("ADDING J11LIBS TO CLASSPATH")
- compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
- }
runtimeClasspath = compileClasspath
}
+
+ clover {
+ java {
+ srcDirs = [ cloverInstrDir ]
+ outputDir = file("${buildDir}/${cloverClassesDir}")
+ }
+
+ resources {
+ srcDirs = sourceSets.main.resources.srcDirs
+ }
+ compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
+ compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
+ runtimeClasspath = compileClasspath
+ }
+
test {
java {
srcDirs "$jalviewDir/$testSourceDir"
srcDirs = sourceSets.main.resources.srcDirs
}
- compileClasspath = sourceSets.main.compileClasspath
- compileClasspath += files( sourceSets.test.java.outputDir )
+ compileClasspath = files( sourceSets.test.java.outputDir )
+ if (use_clover) {
+ compileClasspath += sourceSets.clover.compileClasspath
+ } else {
+ compileClasspath += sourceSets.main.compileClasspath
+ compileClasspath += files(sourceSets.main.java.outputDir)
+ }
+ compileClasspath += files( sourceSets.main.resources.srcDirs)
compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
+ compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
runtimeClasspath = compileClasspath
}
+}
- modules {
- compileClasspath = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
-
- runtimeClasspath = compileClasspath
+// clover bits
+dependencies {
+ if (use_clover) {
+ cloverCompile 'org.openclover:clover:4.3.1'
+ testCompile 'org.openclover:clover:4.3.1'
}
+}
+
+configurations {
+ cloverRuntime
+ cloverRuntime.extendsFrom cloverCompile
+}
+
+task cloverInstr() {
+ // only instrument source, we build test classes as normal
+ inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+ outputs.dir cloverInstrDir
+
+ doFirst {
+ delete cloverInstrDir
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-d", "${buildDir}/${cloverSourcesInstrDir}"]
+ argsList.addAll(inputs.files.files.collect({ file ->
+ file.absolutePath
+ }))
+ String[] args = argsList.toArray()
+ println("About to instrument "+args.length +" files")
+ com.atlassian.clover.CloverInstr.mainImpl(args)
+ }
+}
+
+task cloverReport {
+ inputs.dir "${buildDir}/clover"
+ outputs.dir "${reportsDir}/clover"
+ onlyIf {
+ file("${buildDir}/clover/clover.db").exists()
+ }
+ doFirst {
+ def argsList = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover"]
+ String[] args = argsList.toArray()
+ com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
+
+ // and generate ${reportsDir}/clover/clover.xml
+ args = ["--initstring", "${buildDir}/clover/clover.db",
+ "-o", "${reportsDir}/clover/clover.xml"].toArray()
+ com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+ }
}
+// end clover bits
+
+
compileJava {
doFirst {
- if (JAVA_VERSION.equals("1.8")) {
- sourceCompatibility = 1.8
- targetCompatibility = 1.8
- } else if (JAVA_VERSION.equals("11")) {
- sourceCompatibility = 11
- targetCompatibility = 11
-
- options.compilerArgs = [
- '--module-path', sourceSets.modules.compileClasspath.asPath,
- '--add-modules', j11modules
- ]
- }
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
print ("Setting target compatibility to "+targetCompatibility+"\n")
}
}
+compileTestJava {
+
+ if (use_clover) {
+ dependsOn compileCloverJava
+ classpath += configurations.cloverRuntime
+ } else {
+ classpath += sourceSets.main.runtimeClasspath
+ }
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs = additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+}
+
+
+compileCloverJava {
+
+ doFirst {
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ options.compilerArgs += additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
+ }
+ classpath += configurations.cloverRuntime
+}
+
clean {
delete sourceSets.main.java.outputDir
}
cleanTest {
delete sourceSets.test.java.outputDir
+ delete cloverInstrDir
}
def getDate(format) {
task createBuildProperties(type: WriteProperties) {
inputs.dir("$jalviewDir/$sourceDir")
inputs.dir("$jalviewDir/$resourceDir")
- outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
+ outputFile "$classes/$buildPropertiesFile"
/* taking time/date specific comment out to allow better incremental builds */
//comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
property "VERSION", JALVIEW_VERSION
property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
outputs.file(outputFile)
- outputs.dir("$jalviewDir/$classesDir")
+ outputs.dir("$classes")
}
task syncDocs(type: Sync) {
- def syncDir = "$jalviewDir/$classesDir/$docDir"
+ def syncDir = "$classes/$docDir"
from fileTree("$jalviewDir/$docDir")
into syncDir
}
-def helpFile = "$jalviewDir/$classesDir/$helpDir/help.jhm"
+def helpFile = "$classes/$helpDir/help.jhm"
task syncHelp(type: Sync) {
inputs.files("$jalviewDir/$helpDir")
outputs.files(helpFile)
- def syncDir = "$jalviewDir/$classesDir/$helpDir"
+ def syncDir = "$classes/$helpDir"
from fileTree("$jalviewDir/$helpDir")
into syncDir
}
task copyHelp(type: Copy) {
def inputDir = "$jalviewDir/$helpDir"
- def outputDir = "$jalviewDir/$classesDir/$helpDir"
+ def outputDir = "$classes/$helpDir"
from inputDir
into outputDir
filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
}
task syncLib(type: Sync) {
- def syncDir = "$jalviewDir/$classesDir/$libDir"
- from fileTree("$jalviewDir/$libDir")
+ def syncDir = "$classes/$libDistDir"
+ from fileTree("$jalviewDir/$libDistDir")
into syncDir
}
task syncResources(type: Sync) {
from "$jalviewDir/$resourceDir"
include "**/*.*"
- into "$jalviewDir/$classesDir"
+ exclude "install4j"
+ into "$classes"
preserve {
include "**"
}
dependsOn copyHelp
}
+
//testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
test {
dependsOn prepare
dependsOn compileJava
- useTestNG {
+ if (use_clover) {
+ dependsOn cloverInstr
+ }
+ print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+
+ useTestNG() {
includeGroups testngGroups
+ preserveOrder true
+ useDefaultListeners=true
}
+
workingDir = jalviewDir
//systemProperties 'clover.jar' System.properties.clover.jar
+ sourceCompatibility = compile_source_compatibility
+ targetCompatibility = compile_target_compatibility
+ jvmArgs += additional_compiler_args
+ print ("Setting target compatibility to "+targetCompatibility+"\n")
}
task buildIndices(type: JavaExec) {
dependsOn copyHelp
classpath = sourceSets.main.compileClasspath
main = "com.sun.java.help.search.Indexer"
- workingDir = "$jalviewDir/$classesDir/$helpDir"
+ workingDir = "$classes/$helpDir"
def argDir = "html"
args = [ argDir ]
inputs.dir("$workingDir/$argDir")
- outputs.dir("$jalviewDir/$classesDir/doc")
- outputs.dir("$jalviewDir/$classesDir/help")
+ outputs.dir("$classes/doc")
+ outputs.dir("$classes/help")
outputs.file("$workingDir/JavaHelpSearch/DOCS")
outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB")
outputs.file("$workingDir/JavaHelpSearch/OFFSETS")
dependsOn prepare, compileLinkCheck
classpath = files("$jalviewDir/$utilsDir")
main = "HelpLinksChecker"
- workingDir = "$jalviewDir"
- args = [ "$classesDir/$helpDir", "-nointernet" ]
+ workingDir = jalviewDir
+ def help = "$classes/$helpDir"
+ args = [ "$classes/$helpDir", "-nointernet" ]
+ //args = [ "$classesDir/$helpDir", "-nointernet" ]
doFirst {
standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
exclude "**/*.jar"
exclude "**/*.jar.*"
- inputs.dir("$jalviewDir/$classesDir")
+ inputs.dir("$classes")
outputs.file("$jalviewDir/$packageDir/$archiveName")
}
task copyJars(type: Copy) {
- from fileTree("$jalviewDir/$classesDir").include("**/*.jar").include("*.jar").files
+ from fileTree("$classes").include("**/*.jar").include("*.jar").files
into "$jalviewDir/$packageDir"
}
// doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
task syncJars(type: Sync) {
- from fileTree("$jalviewDir/$libDir").include("**/*.jar").include("*.jar").files
+ from fileTree("$jalviewDir/$libDistDir").include("**/*.jar").include("*.jar").files
into "$jalviewDir/$packageDir"
preserve {
include jar.archiveName
shadowJar {
dependsOn makeDist
- if (JAVA_VERSION.equals("11")) {
- from ("$jalviewDir/$j11libDir") {
+ from ("$jalviewDir/$libDistDir") {
include("*.jar")
- }
}
mainClassName = shadowJarMainClass
mergeServiceFiles()
}
ext {
- getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir
+ // where the getdown channel will be built.
+ // TODO: consider allowing this expression to be overrriden by -P arg
+ getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir + '/' + JAVA_VERSION + '/'
getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
getdownLauncher = jalviewDir + '/' + getdown_launcher
getdownFilesDir = jalviewDir + '/' + getdown_files_dir
+ getdownLib1 = jalviewDir + '/' + getdown_lib1
+ def getdownChannel = getdown_channel_name
+ if (getdown_channel_name.equals("COMMIT")) {
+ getdownChannel = getGitHash()
+ }
+ getdown_app_base = getdown_channel_base+"/"+getdownChannel+"/"+JAVA_VERSION+"/"
}
task getdownWebsite() {
doFirst {
// go through properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
- if (JAVA_VERSION.equals("11")) {
- props.put("getdown_txt_java_min_version", getdown_alt_java11_min_version)
- } else {
- props.put("getdown_txt_java_min_version", getdown_alt_java8_min_version)
- }
+ props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+ props.put("getdown_txt_appbase", getdown_app_base)
props.each{ prop, val ->
if (prop.startsWith("getdown_txt_") && val != null) {
if (prop.startsWith("getdown_txt_multi_")) {
}
copy {
+ from getdownLib1
+ into project.ext.getdownFilesDir
+ }
+
+ copy {
+ from getdownLib1
+ into project.ext.getdownWebsiteDir
+ }
+
+ copy {
from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
task getdownDigest(type: JavaExec) {
dependsOn getdownWebsite
classpath = files(jalviewDir + '/' + getdown_core)
+ classpath file(jalviewDir + '/' + getdown_lib1)
main = "com.threerings.getdown.tools.Digester"
args project.ext.getdownWebsiteDir
outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
}
installDir = file(install4jHomeDir)
+ mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
+}
+
+def install4jConf
+def macosJavaVMDir
+def windowsJavaVMDir
+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/macos-jre"+JAVA_VERSION+"/java_vm"
+ windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/windows-jre"+JAVA_VERSION+"/java_vm"
+ from (install4jDir) {
+ include install4jTemplate
+ rename (install4jTemplate, install4jConfFile)
+ filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
+ filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir])
+ }
+ into install4jDir
+ inputs.files("$install4jDir/$install4jTemplate")
+ outputs.files(install4jConf)
}
task installers(type: com.install4j.gradle.Install4jTask) {
dependsOn getdown
- projectFile = "$jalviewDir/$install4jResourceDir/$install4jConf"
+ dependsOn copyInstall4jTemplate
+ projectFile = file(install4jConf)
+ println("Using projectFile "+projectFile)
variables = [majorVersion: version.substring(2, 11), build: 001]
destination = "$jalviewDir/$install4jBuildDir"
buildSelected = true
inputs.dir(project.ext.getdownWebsiteDir)
+ inputs.file(install4jConf)
+ inputs.dir(macosJavaVMDir)
+ inputs.dir(windowsJavaVMDir)
outputs.dir("$jalviewDir/$install4jBuildDir")
}
+
+clean {
+ delete install4jConf
+}
git://source.jalview.org / jalview.git / blobdiff