From: Ben Soares <bsoares@dundee.ac.uk>
Date: Tue, 12 May 2020 22:05:14 +0000 (+0100)
Subject: JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspa... 
X-Git-Tag: Release_2_11_1_1~13^2~26^2^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ef3fcd7746645316925b66c36cd56dd68b4a38b7;p=jalview.git

JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.
---

diff --git a/build.gradle b/build.gradle
index 2c7f138..431c67b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -13,9 +13,6 @@ buildscript {
     mavenCentral()
     mavenLocal()
   }
-  dependencies {
-    classpath 'org.openclover:clover:4.4.1'
-  }
 }
 
 
@@ -132,19 +129,16 @@ ext {
   bareTestSourceDir = string(test_source_dir)
   testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
 
+  classesDir = string("${jalviewDir}/${classes_dir}")
+
   // clover
-  cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
+  useClover = clover.equals("true")
+  cloverInstrDir = file("${buildDir}/clover/${clover_sources_instr_dir}")
+  cloverClassesDir = file("${buildDir}/clover/${clover_classes_dir}")
+  cloverReportDir = file("${buildDir}/clover/${clover_report_dir}")
   cloverDb = string("${buildDir}/clover/clover.db")
-  classesDir = string("${jalviewDir}/${classes_dir}")
-  if (clover.equals("true")) {
-    use_clover = true
-    classesDir = string("${buildDir}/${cloverClassesDir}")
-  } else {
-    use_clover = false
-    classesDir = string("${jalviewDir}/${classes_dir}")
-  }
 
-  classes = classesDir
+  resourceClassesDir = useClover ? cloverClassesDir : classesDir
 
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   buildDist = true
@@ -173,8 +167,8 @@ ext {
     getdownAppBase = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
     jvlChannelName += "_${getdownChannelName}"
     // automatically add the test group Not-bamboo for exclusion 
-    if ("".equals(testngExcludedGroups)) { 
-      testngExcludedGroups = "Not-bamboo"
+    if ("".equals(testng_excluded_groups)) { 
+      testng_excluded_groups = "Not-bamboo"
     }
     install4jExtraScheme = "jalviewb"
     break
@@ -409,8 +403,8 @@ ext {
 
 
 
-  buildingHTML = string("${jalviewDir}/${docDir}/building.html")
-  helpFile = string("${classesDir}/${help_dir}/help.jhm")
+  buildingHTML = string("${jalviewDir}/${doc_dir}/building.html")
+  helpFile = string("${resourceClassesDir}/${help_dir}/help.jhm")
   helpParentDir = string("${jalviewDir}/${help_parent_dir}")
   helpSourceDir = string("${helpParentDir}/${help_dir}")
 
@@ -456,7 +450,6 @@ sourceSets {
     jar.destinationDir = file("${jalviewDir}/${packageDir}")
 
     compileClasspath = files(sourceSets.main.java.outputDir)
-    //compileClasspath += files(sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
@@ -464,18 +457,17 @@ sourceSets {
 
   clover {
     java {
-      srcDirs = [ cloverInstrDir ]
-      outputDir = file("${buildDir}/${cloverClassesDir}")
+      srcDirs cloverInstrDir
+      outputDir = cloverClassesDir
     }
 
     resources {
       srcDirs = sourceSets.main.resources.srcDirs
     }
-    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 = files( sourceSets.clover.java.outputDir )
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+    compileClasspath += fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
   }
@@ -483,44 +475,22 @@ sourceSets {
   test {
     java {
       srcDirs testSourceDir
-      outputDir = file("${jalviewDir}/${testOutputDir}")
+      outputDir = file("${jalviewDir}/${test_output_dir}")
     }
 
     resources {
-      srcDirs = sourceSets.main.resources.srcDirs
+      srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir )
-
-    if (use_clover) {
-      compileClasspath = sourceSets.clover.compileClasspath
-    } else {
-      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 += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
   }
 }
 
 
-// clover bits
-dependencies {
-  if (use_clover) {
-    cloverCompile 'org.openclover:clover:4.4.1'
-    testCompile 'org.openclover:clover:4.4.1'
-  }
-}
-
-configurations {
-  cloverRuntime
-  cloverRuntime.extendsFrom cloverCompile
-}
-
-
 // eclipse project and settings files creation, also used by buildship
 eclipse {
   project {
@@ -656,27 +626,40 @@ eclipse {
 }
 
 
-task cloverInstr {
-  // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava,sourceSets.test.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
-  outputs.dir cloverInstrDir
+// clover bits
+
+
+task cloverInstr(type: JavaExec) {
+  group = "Verification"
+  description = "Create clover instrumented source files"
+
+  inputs.files(sourceSets.main.allJava)
+  outputs.dir(cloverInstrDir)
+
+  //classpath = fileTree(dir: "${jalviewDir}/${clover_lib_dir}", include: ["*.jar"])
+  classpath = sourceSets.clover.compileClasspath
+  main = "com.atlassian.clover.CloverInstr"
+
+  def argsList = [
+    "--encoding",
+    "UTF-8",
+    "--initstring",
+    cloverDb,
+    "--destdir",
+    cloverInstrDir.getPath(),
+  ]
+  def srcFiles = sourceSets.main.allJava.files
+  argsList.addAll(
+    srcFiles.collect(
+      { file -> file.absolutePath }
+    )
+  )
+  args argsList.toArray()
 
   doFirst {
     delete cloverInstrDir
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-d",
-      cloverInstrDir.getPath(),
-    ]
-    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)
+    delete cloverDb
+    println("Clover: About to instrument "+srcFiles.size() +" files")
   }
 }
 
@@ -684,33 +667,62 @@ task cloverInstr {
 cloverClasses.dependsOn cloverInstr
 
 
-task cloverReport {
+task cloverXmlReport(type: JavaExec) {
   group = "Verification"
-  description = "Creates the Clover report"
-  inputs.dir "${buildDir}/clover"
-  outputs.dir "${reportsDir}/clover"
+  description = "Creates clover XML report"
+
+  inputs.dir cloverClassesDir
+  outputs.dir cloverReportDir
   onlyIf {
     file(cloverDb).exists()
   }
-  doFirst {
-    def argsList = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover"
-    ]
-    String[] args = argsList.toArray()
-    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
-
-    // and generate ${reportsDir}/clover/clover.xml
-    args = [
-      "--initstring",
-      cloverDb,
-      "-o",
-      "${reportsDir}/clover/clover.xml"
-    ].toArray()
-    com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.xml.XMLReporter"
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outfile",
+    "${cloverReportDir}/clover.xml"
+  ]
+
+  args argsList.toArray()
+}
+
+
+task cloverHtmlReport(type: JavaExec) {
+  group = "Verification"
+  description = "Creates clover HTML report"
+
+  inputs.dir cloverClassesDir
+  outputs.dir cloverReportDir
+  onlyIf {
+    file(cloverDb).exists()
   }
+
+  classpath = sourceSets.clover.runtimeClasspath
+  main = "com.atlassian.clover.reporters.html.HtmlReporter"
+
+  def argsList = [
+    "--alwaysreport",
+    "--initstring",
+    cloverDb,
+    "--outputdir",
+    "${cloverReportDir}/clover"
+  ]
+
+  args argsList.toArray()
+}
+
+
+task cloverReport {
+  group = "Verification"
+  description = "Creates clover reports"
+
+  dependsOn cloverXmlReport
+  dependsOn cloverHtmlReport
 }
 
 
@@ -728,8 +740,7 @@ compileCloverJava {
 
 task cleanClover {
   doFirst {
-    delete cloverInstrDir
-    delete cloverDb
+    delete "${buildDir/clover}"
   }
 }
 // end clover bits
@@ -748,12 +759,6 @@ compileJava {
 
 
 compileTestJava {
-  if (use_clover) {
-    dependsOn compileCloverJava
-    classpath += configurations.cloverRuntime
-  } else {
-    classpath += sourceSets.main.runtimeClasspath
-  }
   doFirst {
     sourceCompatibility = compile_source_compatibility
     targetCompatibility = compile_target_compatibility
@@ -832,8 +837,8 @@ task cleanBuildingHTML(type: Delete) {
 
 task convertBuildingMD(type: Exec) {
   dependsOn cleanBuildingHTML
-  def buildingMD = "${jalviewDir}/${docDir}/building.md"
-  def css = "${jalviewDir}/${docDir}/github.css"
+  def buildingMD = "${jalviewDir}/${doc_dir}/building.md"
+  def css = "${jalviewDir}/${doc_dir}/github.css"
 
   def pandoc = null
   pandoc_exec.split(",").each {
@@ -875,8 +880,8 @@ clean {
 
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
-  def syncDir = "${classesDir}/${docDir}"
-  from fileTree("${jalviewDir}/${docDir}")
+  def syncDir = "${resourceClassesDir}/${doc_dir}"
+  from fileTree("${jalviewDir}/${doc_dir}")
   into syncDir
 
 }
@@ -884,7 +889,7 @@ task syncDocs(type: Sync) {
 
 task copyHelp(type: Copy) {
   def inputDir = helpSourceDir
-  def outputDir = "${classesDir}/${help_dir}"
+  def outputDir = "${resourceClassesDir}/${help_dir}"
   from(inputDir) {
     exclude '**/*.gif'
     exclude '**/*.jpg'
@@ -912,7 +917,7 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classesDir}/${libDistDir}"
+  def syncDir = "${resourceClassesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
@@ -921,7 +926,7 @@ task syncLib(type: Sync) {
 task syncResources(type: Sync) {
   from resourceDir
   include "**/*.*"
-  into "${classesDir}"
+  into "${resourceClassesDir}"
   preserve {
     include "**"
   }
@@ -938,18 +943,16 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  dependsOn compileJava
-  if (use_clover) {
-    dependsOn cloverInstr
-  }
 
-  if (use_clover) {
-    print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
+  if (useClover) {
+    dependsOn cloverClasses
+  } else {
+    dependsOn compileJava
   }
 
   useTestNG() {
-    includeGroups testngGroups
-    excludeGroups testngExcludedGroups
+    includeGroups testng_groups
+    excludeGroups testng_excluded_groups
     preserveOrder true
     useDefaultListeners=true
   }
@@ -972,6 +975,11 @@ test {
   targetCompatibility = compile_target_compatibility
   jvmArgs += additional_compiler_args
 
+  doFirst {
+    if (useClover) {
+      print("Running tests " + (useClover?"WITH":"WITHOUT") + " clover [clover="+useClover+"]\n")
+    }
+  }
 }
 
 
@@ -997,22 +1005,22 @@ task buildIndices(type: JavaExec) {
 
 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"])
-
-  inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
-  inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
-  outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
-  outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
+  classpath = files("${jalviewDir}/${utils_dir}")
+  destinationDir = file("${jalviewDir}/${utils_dir}")
+  source = fileTree(dir: "${jalviewDir}/${utils_dir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
+
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  inputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.java")
+  outputs.file("${jalviewDir}/${utils_dir}/HelpLinksChecker.class")
+  outputs.file("${jalviewDir}/${utils_dir}/BufferedLineReader.class")
 }
 
 
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
 
-  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
-  classpath = files("${jalviewDir}/${utilsDir}")
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utils_dir}/HelpLinksChecker.out")
+  classpath = files("${jalviewDir}/${utils_dir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
   args = [ "${classesDir}/${help_dir}", "-nointernet" ]
@@ -1033,7 +1041,7 @@ task linkCheck(type: JavaExec) {
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${help_dir}"
-ant.importBuild "${utilsDir}/publishHelp.xml"
+ant.importBuild "${utils_dir}/publishHelp.xml"
 
 
 task cleanPackageDir(type: Delete) {
@@ -1048,7 +1056,7 @@ jar {
   dependsOn createBuildProperties
 
   manifest {
-    attributes "Main-Class": mainClass,
+    attributes "Main-Class": main_class,
     "Permissions": "all-permissions",
     "Application-Name": "Jalview Desktop",
     "Codebase": application_codebase
@@ -1114,7 +1122,7 @@ shadowJar {
   manifest {
     attributes 'Implementation-Version': JALVIEW_VERSION
   }
-  mainClassName = shadowJarMainClass
+  mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
   minimize()
diff --git a/gradle.properties b/gradle.properties
index 782a495..5b80dae 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -23,38 +23,35 @@ proxyHost = sqid
 jalview_keyalg = SHA1withRSA
 jalview_keydig = SHA1
 
-testngGroups = Functional
-testngExcludedGroups = 
+testng_groups = Functional
+testng_excluded_groups = 
 
 j8libDir = j8lib
 j11libDir = j11lib
 resource_dir = resources
 help_parent_dir = help
 help_dir = help
-docDir = doc
-schemaDir = schemas
+doc_dir = doc
 classes_dir = classes
-examplesDir = examples
 clover = false
-use_clover = false
+clover_classes_dir = clover-classes
+clover_sources_instr_dir = clover-instr
+clover_report_dir = clover-report
+clover_lib_dir = utils/clover/lib
 cloverReportJVMHeap = 2g
 cloverReportJVMArgs = -Dfile.encoding=UTF-8
 cloverReportHTMLOptions = 
 cloverReportXMLOptions =
-cloverClassesDir = clover-classes
-cloverSourcesInstrDir = sources-instr
 packageDir = dist
 ARCHIVEDIR =
-outputJar = jalview.jar
 
-testOutputDir = tests
-utilsDir = utils
+test_output_dir = tests
+utils_dir = utils
 
 build_properties_file = .build_properties
 application_codebase = *.jalview.org
-mainClass = jalview.bin.Jalview
-shadowJarMainClass = jalview.bin.Launcher
-launcherClass = jalview.bin.Jalview
+main_class = jalview.bin.Jalview
+shadow_jar_main_class = jalview.bin.Launcher
 
 jalview_name = Jalview
 
diff --git a/utils/clover/lib/clover-ant-4.4.1.jar b/utils/clover/lib/clover-ant-4.4.1.jar
new file mode 100644
index 0000000..4f92395
Binary files /dev/null and b/utils/clover/lib/clover-ant-4.4.1.jar differ