X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=ed3ace3a3c3238f6b19219677608cecc2f3b889b;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=8b77be8ef3367a1e3436eed2e79022238fc40f9b;hpb=df74daf9d2a0f8e5911311589002774c73fb6d1a;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 8b77be8..ed3ace3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -11,6 +11,7 @@ buildscript {
 plugins {
   id 'java'
   id 'application'
+  id 'eclipse'
   id 'com.github.johnrengelman.shadow' version '4.0.3'
   id 'com.install4j.gradle' version '7.0.9'
 }
@@ -27,6 +28,7 @@ repositories {
 mainClassName = launcherClass
 def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
 def classes = "$jalviewDir/$classesDir"
+
 if (clover.equals("true")) {
   use_clover = true
   classes = "$buildDir/$cloverClassesDir"
@@ -37,26 +39,55 @@ if (clover.equals("true")) {
 
 // configure classpath/args for j8/j11 compilation
 
+def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
 def libDir
 def libDistDir
 def compile_source_compatibility
 def compile_target_compatibility
+
+ext {
+  // 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 + '/' + JAVA_VERSION + '/'
+  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+"/"
+  modules_compileClasspath = fileTree(dir: "$jalviewDir/$j11modDir", include: ["*.jar"])
+  modules_runtimeClasspath = modules_compileClasspath
+}
+
+def JAVA_INTEGER_VERSION
 def additional_compiler_args = []
+// these are getdown.txt properties defined dependent on the JAVA_VERSION 
 def getdown_alt_java_min_version
+// this property is assigned below and expanded to multiple lines in the getdown task
+def getdown_alt_multi_java_location
 if (JAVA_VERSION.equals("1.8")) {
+  JAVA_INTEGER_VERSION = "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
+  getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
 } else if (JAVA_VERSION.equals("11")) {
+  JAVA_INTEGER_VERSION = "11"
   libDir = j11libDir
   libDistDir = j11libDir
   compile_source_compatibility = 11
   compile_target_compatibility = 11
   getdown_alt_java_min_version = getdown_alt_java11_min_version
+  getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
   additional_compiler_args += [
-    '--module-path', file("$jalviewDir/$j11modDir").getAbsolutePath(),
+    '--module-path', ext.modules_compileClasspath.asPath,
     '--add-modules', j11modules
   ]
 } else {
@@ -73,7 +104,7 @@ sourceSets {
 
     resources {
       srcDirs "$jalviewDir/$resourceDir"
-      srcDirs "$jalviewDir/$libDir"
+      srcDirs "$jalviewDir/$libDistDir"
     }
 
     jar.destinationDir = file("$jalviewDir/$packageDir")
@@ -83,7 +114,6 @@ sourceSets {
 
     runtimeClasspath = compileClasspath
   }
-  
   clover {
     java {
         srcDirs = [ cloverInstrDir ]
@@ -94,6 +124,8 @@ sourceSets {
       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 += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
 
@@ -111,12 +143,13 @@ sourceSets {
     }
 
     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 += sourceSets.main.compileClasspath
     compileClasspath += files( sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
@@ -137,7 +170,140 @@ configurations {
     cloverRuntime
     cloverRuntime.extendsFrom cloverCompile
 }
- 
+
+eclipse {
+  project {
+    name = "Jalview with gradle build"
+
+    natures 'org.eclipse.jdt.core.javanature',
+        'org.eclipse.jdt.groovy.core.groovyNature',
+        'org.eclipse.buildship.core.gradleprojectnature'
+
+    buildCommand 'org.eclipse.jdt.core.javabuilder'
+    buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
+  }
+
+  classpath {
+    //defaultOutputDir = sourceSets.main.java.outputDir
+    def removeThese = []
+    configurations.each{ if (it.isCanBeResolved()) {
+        removeThese += it
+      }
+    }
+    containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
+    
+    minusConfigurations += removeThese
+    plusConfigurations = [ ]
+    file {
+
+      whenMerged { cp ->
+        def removeTheseToo = []
+        HashMap<String, Boolean> addedSrcPath = new HashMap<>();
+        cp.entries.each { entry ->
+          if (entry.kind == 'src') {
+            if (addedSrcPath.getAt(entry.path) || !(entry.path == "src" || entry.path == "test" || entry.path == "resources")) {
+              removeTheseToo += entry
+            } else {
+              addedSrcPath.putAt(entry.path, true)
+            }
+          }
+        }
+        cp.entries.removeAll(removeTheseToo)
+      }
+      
+      withXml {
+        def node = it.asNode()
+        def srcTestAttributes
+        node.children().each{ cpe ->
+          def attributes = cpe.attributes()
+          if (attributes.get("kind") == "src" && attributes.get("path") == "test") {
+            srcTestAttributes = cpe.find { a -> a.name() == "attributes" }
+            return
+          }
+        }
+        def addTestAttribute = true
+        srcTestAttributes.each{a ->
+          if (a.name() == "attribute" && a.attributes().getAt("name") == "test") {
+            addTestAttribute = false
+          }
+        }
+        if (addTestAttribute) {
+          srcTestAttributes.append(new Node(null, "attribute", [name:"test", value:"true"]))
+        }
+        
+        node.appendNode('classpathentry', [kind:"output", path:"bin/main"])
+        HashMap<String, Boolean> addedLibPath = new HashMap<>();
+        def allPaths = sourceSets.test.compileClasspath + sourceSets.main.compileClasspath
+        sourceSets.main.compileClasspath.each{
+          //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+          if (it.isDirectory() || ! it.exists()) {
+            // don't add dirs to classpath
+            //println("Not adding directory "+it)
+            return
+          }
+          def itPath = it.toString()
+          if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+          }
+          if (addedLibPath.get(itPath)) {
+            //println("Not adding duplicate entry "+itPath)
+          } else {
+            //println("Adding entry "+itPath)
+            node.appendNode('classpathentry', [kind:"lib", path:itPath])
+            addedLibPath.put(itPath, true)
+          }
+        }
+        sourceSets.test.compileClasspath.each{
+          //if ((it.isDirectory() || ! it.exists()) && ! (it.equals(sourceSets.main.java.outputDir))) {
+          //no longer want to add outputDir as eclipse is using its own output dir in bin/main
+          if (it.isDirectory() || ! it.exists()) {
+            // don't add dirs to classpath
+            //println("Not adding directory "+it)
+            return
+          }
+          def itPath = it.toString()
+          if (itPath.startsWith(jalviewDirAbsolutePath+"/")) {
+            itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
+          }
+          if (addedLibPath.get(itPath)) {
+            //println("Not adding duplicate entry "+itPath)
+          } else {
+            //println("Adding entry "+itPath)
+            node.appendNode('classpathentry', [kind:"lib", path:itPath])
+              .appendNode('attributes')
+                .appendNode('attribute', [name:"test", value:"true"])
+            addedLibPath.put(itPath, true)
+          }
+        }
+      }
+
+    }
+  }
+
+  jdt {
+    // for the IDE, use java 11 compatibility
+    sourceCompatibility = 11
+    targetCompatibility = 11
+    javaRuntimeName = "JavaSE-11"
+
+    file {
+      withProperties { props ->
+        def jalview_prefs = new Properties()
+		def ins = new FileInputStream(eclipse_extra_jdt_prefs_file)
+		jalview_prefs.load(ins)
+		ins.close()
+		jalview_prefs.forEach { t, v ->
+			if (props.getAt(t) == null) {
+				props.putAt(t, v)
+			}
+		}
+      }
+    }
+  }
+
+}
+
 task cloverInstr() {
   // only instrument source, we build test classes as normal
     inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
@@ -158,6 +324,8 @@ task cloverInstr() {
 
  
 task cloverReport {
+	group = "Verification"
+	description = "Createst the Clover report"
     inputs.dir "${buildDir}/clover"
     outputs.dir "${reportsDir}/clover"
     onlyIf {
@@ -191,7 +359,6 @@ compileJava {
 }
 
 compileTestJava {
-
   if (use_clover) {
     dependsOn compileCloverJava
     classpath += configurations.cloverRuntime
@@ -296,8 +463,8 @@ task copyHelp(type: Copy) {
 }
 
 task syncLib(type: Sync) {
-  def syncDir = "$classes/$libDir"
-  from fileTree("$jalviewDir/$libDir")
+  def syncDir = "$classes/$libDistDir"
+  from fileTree("$jalviewDir/$libDistDir")
   into syncDir
 }
 
@@ -325,6 +492,7 @@ test {
   if (use_clover) {
     dependsOn cloverInstr
   }
+
   print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") 
   
   useTestNG() {
@@ -370,6 +538,7 @@ task compileLinkCheck(type: JavaCompile) {
   outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
 }
 
+def helplinkscheckeroutputfile = file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
   classpath = files("$jalviewDir/$utilsDir")
@@ -380,10 +549,11 @@ task linkCheck(type: JavaExec) {
   //args = [ "$classesDir/$helpDir", "-nointernet" ]
 
   doFirst {
-    standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+    helplinkscheckeroutputfile.createNewFile()
+    standardOutput new FileOutputStream(helplinkscheckeroutputfile, false)
   }
 
-  outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
+  outputs.file(helplinkscheckeroutputfile)
 }
 
 task cleanPackageDir(type: Delete) {
@@ -422,7 +592,7 @@ task copyJars(type: Copy) {
 
 // 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
@@ -430,6 +600,8 @@ task syncJars(type: Sync) {
 }
 
 task makeDist {
+  group = "build"
+  description = "Put all required libraries in dist"
   // order of "cleanPackageDir", "copyJars", "jar" important!
   jar.mustRunAfter cleanPackageDir
   syncJars.mustRunAfter cleanPackageDir
@@ -447,33 +619,18 @@ task cleanDist {
 
 shadowJar {
   dependsOn makeDist
-  if (JAVA_VERSION.equals("11")) {
-    from ("$jalviewDir/$j11libDir") {
+  from ("$jalviewDir/$libDistDir") {
       include("*.jar")
-    }
   }
   mainClassName = shadowJarMainClass
   mergeServiceFiles()
-  classifier = "all"
+  classifier = "all-"+JAVA_VERSION
   minimize()
 }
 
-ext {
-  getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir
-  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+"/"+JAVA_VERSION+"/"+getdownChannel+"/"
-}
-
 task getdownWebsite() {
+  group = "distribution"
+  description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
   dependsOn makeDist
   def getdownWebsiteResourceFilenames = []
   def getdownTextString = ""
@@ -484,6 +641,8 @@ task getdownWebsite() {
     // go through properties looking for getdown_txt_...
     def props = project.properties.sort { it.key }
     props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
+    props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
+    
     props.put("getdown_txt_appbase", getdown_app_base)
     props.each{ prop, val ->
       if (prop.startsWith("getdown_txt_") && val != null) {
@@ -544,6 +703,8 @@ task getdownWebsite() {
       }
     }
 
+    // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
+    /*
     if (JAVA_VERSION.equals("11")) {
       def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
       j11libFiles.sort().each{f ->
@@ -555,6 +716,7 @@ task getdownWebsite() {
         }
       }
     }
+    */
 
     getdownTextString += "code = " + file(getdownLauncher).getName() + "\n"
     getdownTextString += "class = " + mainClass + "\n"
@@ -569,22 +731,17 @@ task getdownWebsite() {
 
     copy {
       from getdownLauncher
-      into project.ext.getdownWebsiteDir
-    }
-
-    copy {
-      from getdownLauncher
       into project.ext.getdownFilesDir
     }
 
     copy {
-      from getdownLib1
-      into project.ext.getdownFilesDir
+      from getdownLauncher
+      into project.ext.getdownWebsiteDir
     }
 
     copy {
       from getdownLib1
-      into project.ext.getdownWebsiteDir
+      into project.ext.getdownFilesDir + '/' + packageDir
     }
 
     copy {
@@ -603,6 +760,8 @@ task getdownWebsite() {
 }
 
 task getdownDigest(type: JavaExec) {
+  group = "distribution"
+  description = "Digest the getdown website folder"
   dependsOn getdownWebsite
   classpath = files(jalviewDir + '/' + getdown_core)
   classpath file(jalviewDir + '/' + getdown_lib1)
@@ -612,6 +771,8 @@ task getdownDigest(type: JavaExec) {
 }
 
 task getdown() {
+  group = "distribution"
+  description = "Create the minimal and full getdown app folder for installers and website and create digest file"
   dependsOn getdownDigest
 }
 
@@ -639,19 +800,23 @@ install4j {
 
 def install4jConf
 def macosJavaVMDir
+def macosJavaVMTgz
 def windowsJavaVMDir
+def windowsJavaVMTgz
 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"
+  macosJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/macos-jre"+JAVA_VERSION+"/jre"
+  macosJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre"+JAVA_VERSION+".tar.gz"
+  windowsJavaVMDir = System.env.HOME+"/buildtools/jre/openjdk-java_vm/getdown/windows-jre"+JAVA_VERSION+"/jre"
+  windowsJavaVMTgz = System.env.HOME+"/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre"+JAVA_VERSION+".tar.gz"
   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])
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['JAVA_VERSION': JAVA_VERSION, 'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION, 'VERSION': JALVIEW_VERSION, 'MACOS_JAVA_VM_DIR': macosJavaVMDir, 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz, 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir, 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz])
   }
   into install4jDir
   inputs.files("$install4jDir/$install4jTemplate")
@@ -659,18 +824,20 @@ task copyInstall4jTemplate(type: Copy) {
 }
 
 task installers(type: com.install4j.gradle.Install4jTask) {
+  group = "distribution"
+  description = "Create the install4j installers"
   dependsOn getdown
   dependsOn copyInstall4jTemplate
   projectFile = file(install4jConf)
   println("Using projectFile "+projectFile)
   variables = [majorVersion: version.substring(2, 11), build: 001]
-  destination = "$jalviewDir/$install4jBuildDir"
+  destination = "$jalviewDir/$install4jBuildDir/$JAVA_VERSION"
   buildSelected = true
   inputs.dir(project.ext.getdownWebsiteDir)
   inputs.file(install4jConf)
   inputs.dir(macosJavaVMDir)
   inputs.dir(windowsJavaVMDir)
-  outputs.dir("$jalviewDir/$install4jBuildDir")
+  outputs.dir("$jalviewDir/$install4jBuildDir/$JAVA_VERSION")
 }
 
 clean {