JAL-3130 some clover fixes for helplinks. Use 'gradle test -Pclover=true'

diff --git a/build.gradle b/build.gradle
index 5f33b20..291d718 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -25,14 +25,22 @@ repositories {
 }
 
 mainClassName = launcherClass
-def cloverInstrDir = file("$buildDir/sources-instr")
+def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
+def classes = "$jalviewDir/$classesDir"
+if (clover.equals("true")) {
+  clover = true
+  classes = "$buildDir/$cloverClassesDir"
+} else {
+  clover = false
+  classes = "$jalviewDir/$classesDir"
+}
 
 sourceSets {
 
   main {
     java {
       srcDirs "$jalviewDir/$sourceDir"
-      outputDir = file("$jalviewDir/$classesDir")
+      outputDir = file("$classes")
     }
 
     resources {
@@ -45,7 +53,7 @@ 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")
+      print("ADDING J11LIBS TO CLASSPATH\n")
       compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
     }
 
@@ -61,7 +69,7 @@ sourceSets {
   clover {
     java {
         srcDirs = [ cloverInstrDir ]
-        outputDir = file("${buildDir}/clover-classes")
+        outputDir = file("${buildDir}/${cloverClassesDir}")
     }
     
     resources {
@@ -71,7 +79,7 @@ sourceSets {
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
     if (JAVA_VERSION.equals("1.8")) {
-      print("ADDING J11LIBS TO CLASSPATH")
+      print("ADDING J11LIBS TO CLASSPATH\n")
       compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
     }
 
@@ -88,15 +96,17 @@ sourceSets {
       srcDirs = sourceSets.main.resources.srcDirs
     }
 
-
-    compileClasspath = configurations.cloverRuntime 
-    compileClasspath += files( sourceSets.test.java.outputDir ) 
-    compileClasspath += files( sourceSets.clover.java.outputDir )
+    compileClasspath = files( sourceSets.test.java.outputDir ) 
+    if (clover) {
+      compileClasspath += sourceSets.clover.compileClasspath
+    } else {
+      compileClasspath += sourceSets.main.compileClasspath
+    }
     compileClasspath += files( sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
     if (JAVA_VERSION.equals("1.8")) {
-      print("ADDING J11LIBS TO CLASSPATH")
+      print("ADDING J11LIBS TO CLASSPATH\n")
       compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
     }
 
@@ -106,8 +116,10 @@ sourceSets {
 
 // clover bits
 dependencies {
-  cloverCompile 'org.openclover:clover:4.3.1'
-  testCompile 'org.openclover:clover:4.3.1'
+  if (clover) {
+    cloverCompile 'org.openclover:clover:4.3.1'
+    testCompile 'org.openclover:clover:4.3.1'
+  }
 }
 
 configurations {
@@ -123,7 +135,7 @@ task cloverInstr() {
     doFirst {
         delete cloverInstrDir
         def argsList = ["--initstring", "${buildDir}/clover/clover.db",
-                        "-d", "${buildDir}/sources-instr"]
+                        "-d", "${buildDir}/${cloverSourcesInstrDir}"]
         argsList.addAll(inputs.files.files.collect({ file ->
             file.absolutePath
         }))
@@ -133,8 +145,6 @@ task cloverInstr() {
     }
 }
 
-test.dependsOn cloverInstr
-
  
 task cloverReport {
     inputs.dir "${buildDir}/clover"
@@ -179,7 +189,10 @@ compileJava {
 }
 
 compileTestJava {
-  dependsOn compileCloverJava
+  if (clover) {
+    dependsOn compileCloverJava
+    classpath += configurations.cloverRuntime
+  }
   doFirst {
     if (JAVA_VERSION.equals("1.8")) {
       sourceCompatibility = 1.8
@@ -195,7 +208,6 @@ compileTestJava {
     }
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
-  classpath += configurations.cloverRuntime
 }
 
 
@@ -257,7 +269,7 @@ def getGitBranch() {
 task createBuildProperties(type: WriteProperties) {
   inputs.dir("$jalviewDir/$sourceDir")
   inputs.dir("$jalviewDir/$resourceDir")
-  outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
+  outputFile "$classes/$buildPropertiesFile"
   /* taking time/date specific comment out to allow better incremental builds */
   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
@@ -265,29 +277,29 @@ task createBuildProperties(type: WriteProperties) {
   property "VERSION", JALVIEW_VERSION
   property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
   outputs.file(outputFile)
-  outputs.dir("$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"])
@@ -297,7 +309,7 @@ task copyHelp(type: Copy) {
 }
 
 task syncLib(type: Sync) {
-  def syncDir = "$jalviewDir/$classesDir/$libDir"
+  def syncDir = "$classes/$libDir"
   from fileTree("$jalviewDir/$libDir")
   into syncDir
 }
@@ -306,7 +318,7 @@ task syncResources(type: Sync) {
   from "$jalviewDir/$resourceDir"
   include "**/*.*"
   exclude "install4j"
-  into "$jalviewDir/$classesDir"
+  into "$classes"
   preserve {
     include "**"
   }
@@ -322,7 +334,10 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  
+  if (clover) {
+    dependsOn cloverInstr
+  }
+  print("Running tests " + (clover?"WITH":"WITHOUT") + " clover [clover="+clover+"]\n") 
   
   useTestNG() {
     includeGroups testngGroups
@@ -353,13 +368,13 @@ 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("$workingDir/JavaHelpSearch/OFFSETS")
@@ -382,8 +397,10 @@ task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
   classpath = files("$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")
@@ -417,12 +434,12 @@ 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"
 }
 

diff --git a/gradle.properties b/gradle.properties
index cb335d6..6533899 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,7 +1,7 @@
 #org.gradle.java.home = /Users/bsoares/Java/installs/OpenJDK8U-jdk_x64_mac_hotspot_8u192b12/jdk8u192-b12/Contents/Home
 jalviewDir = .
 
-JAVA_VERSION = 11
+JAVA_VERSION = 1.8
 JALVIEW_VERSION = DEVELOPMENT
 INSTALLATION = Source
 jalview_keystore = keys/.keystore
@@ -26,7 +26,9 @@ docDir = doc
 sourceDir = src
 schemaDir = schemas
 classesDir = classes
-clover.classesDir = cloverclasses
+clover = false
+cloverClassesDir = clover-classes
+cloverSourcesInstrDir = sources-instr
 packageDir = dist
 outputJar = jalview.jar