X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=8b77be8ef3367a1e3436eed2e79022238fc40f9b;hb=df74daf9d2a0f8e5911311589002774c73fb6d1a;hp=d4140bd46904d86e74226c38f01c92ac301abe08;hpb=e861a8212e4e459be8cc90c27b0e91dc5e081c59;p=jalview.git

diff --git a/build.gradle b/build.gradle
index d4140bd..8b77be8 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,10 +1,10 @@
 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'
   }
 }
 
@@ -18,19 +18,57 @@ plugins {
 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 {
@@ -42,14 +80,26 @@ sourceSets {
 
     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"
@@ -60,36 +110,81 @@ sourceSets {
       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")
   }
 
@@ -97,22 +192,30 @@ compileJava {
 
 compileTestJava {
 
+  if (use_clover) {
+    dependsOn compileCloverJava
+    classpath += configurations.cloverRuntime
+  } else {
+    classpath += sourceSets.main.runtimeClasspath
+  }
   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")
   }
+}
+
 
+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 {
@@ -121,6 +224,7 @@ clean {
 
 cleanTest {
   delete sourceSets.test.java.outputDir
+  delete cloverInstrDir
 }
 
 def getDate(format) {
@@ -152,7 +256,7 @@ def getGitBranch() {
 task createBuildProperties(type: WriteProperties) {
   inputs.dir("$jalviewDir/$sourceDir")
   inputs.dir("$jalviewDir/$resourceDir")
-  outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
+  outputFile "$classes/$buildPropertiesFile"
   /* taking time/date specific comment out to allow better incremental builds */
   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
@@ -160,29 +264,29 @@ task createBuildProperties(type: WriteProperties) {
   property "VERSION", JALVIEW_VERSION
   property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
   outputs.file(outputFile)
-  outputs.dir("$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"])
@@ -192,7 +296,7 @@ task copyHelp(type: Copy) {
 }
 
 task syncLib(type: Sync) {
-  def syncDir = "$jalviewDir/$classesDir/$libDir"
+  def syncDir = "$classes/$libDir"
   from fileTree("$jalviewDir/$libDir")
   into syncDir
 }
@@ -201,7 +305,7 @@ task syncResources(type: Sync) {
   from "$jalviewDir/$resourceDir"
   include "**/*.*"
   exclude "install4j"
-  into "$jalviewDir/$classesDir"
+  into "$classes"
   preserve {
     include "**"
   }
@@ -213,32 +317,27 @@ task prepare {
   dependsOn copyHelp
 }
 
+
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
   dependsOn compileJava
-  dependsOn compileTestJava
-  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
-  if (JAVA_VERSION.equals("1.8")) {
-    sourceCompatibility = 1.8
-    targetCompatibility = 1.8
-  } else if (JAVA_VERSION.equals("11")) {
-    sourceCompatibility = 11
-    targetCompatibility = 11
-
-    jvmArgs += [
-      '--module-path',
-      sourceSets.modules.compileClasspath.asPath,
-      '--add-modules',
-      j11modules
-    ]
-  }
+  sourceCompatibility = compile_source_compatibility
+  targetCompatibility = compile_target_compatibility
+  jvmArgs += additional_compiler_args
   print ("Setting target compatibility to "+targetCompatibility+"\n")
 }
 
@@ -246,13 +345,13 @@ 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("$workingDir/JavaHelpSearch/OFFSETS")
@@ -275,8 +374,10 @@ task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
   classpath = files("$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")
@@ -310,12 +411,12 @@ jar {
   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"
 }
 
@@ -364,6 +465,12 @@ ext {
   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+"/"+JAVA_VERSION+"/"+getdownChannel+"/"
 }
 
 task getdownWebsite() {
@@ -376,11 +483,8 @@ 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_")) {
@@ -474,6 +578,16 @@ task getdownWebsite() {
     }
 
     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')
@@ -491,6 +605,7 @@ task getdownWebsite() {
 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")
@@ -519,14 +634,45 @@ install4j {
     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
+}