X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=1f1bc2f6d9ba7c01880c10075b5f210955af0fad;hb=8e6e5eba1f8130dad6c2b697bf7671cb7036c1c0;hp=21a4c81056a60c515957e814586fac298713a1bf;hpb=e8a974af046e0ee231b09743c4299c89d3a95d87;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 21a4c81..1f1bc2f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -2,6 +2,7 @@ import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.internal.os.OperatingSystem
 import org.gradle.plugins.ide.eclipse.model.Output
 import org.gradle.plugins.ide.eclipse.model.Library
+import java.security.MessageDigest
 
 import groovy.transform.ExternalizeMethods
 
@@ -82,10 +83,17 @@ ext {
   } else {
     println("HEADLESS BUILD")
   }
-  /*
+  
+  J2S_ENABLED = (project.hasProperty('j2s.compiler.status') && project['j2s.compiler.status'] != null && project['j2s.compiler.status'] == "enable")
+  if (J2S_ENABLED) {
+    println("J2S ENABLED")
+  }
+  
+  /* *-/
   System.properties.sort { it.key }.each {
     key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
   }
+  /-* *-/
   if (false && IN_ECLIPSE) {
     jalviewDir = jalviewDirAbsolutePath
   }
@@ -115,7 +123,7 @@ ext {
   getdownDir = string("")
   reportRsyncCmd = false
   buildDist = true
-  buildProperties = build_properties_file
+  buildProperties = string("${resourceDir}/${build_properties_file}")
   getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}")
   switch (CHANNEL) {
 
@@ -125,7 +133,7 @@ ext {
     getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
     getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${classesDir}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     break
 
     case "RELEASE":
@@ -133,8 +141,13 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_release
-    buildProperties = string("${classesDir}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
+    // Don't ignore transpile errors for release build
+    if (jalviewjs_ignore_transpile_errors.equals("true")) {
+      jalviewjs_ignore_transpile_errors = "false"
+      println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+    }
     break
 
     case "ARCHIVE":
@@ -147,7 +160,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${resource_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -163,7 +176,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${resource_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -175,7 +188,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${classesDir}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -184,8 +197,13 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${classesDir}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
+    // Don't ignore transpile errors for release build
+    if (jalviewjs_ignore_transpile_errors.equals("true")) {
+      jalviewjs_ignore_transpile_errors = "false"
+      println("Setting jalviewjs_ignore_transpile_errors to 'false'")
+    }
     break
 
     case ~/^SCRATCH(|-[-\w]*)$/:
@@ -193,14 +211,14 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${classesDir}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
     case "LOCAL":
     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${classesDir}/${build_properties_file}")
+    buildProperties = string("${resourceDir}/${build_properties_file}")
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     break
 
@@ -314,10 +332,19 @@ ext {
   jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
   jalviewjsJ2sProps = null
 
+  eclipseJavaVersion = "55"
+  jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
+  if (IN_ECLIPSE) {
+    //def eclipseJavaVersion = System.property["java.class.version"]
+    if (Float.parseFloat(eclipseJavaVersion) >= 55 && file(jalviewjs_j2s_plugin_j11).exists()) { // 55 is Java 11
+      jalviewjsJ2sPlugin = jalviewjs_j2s_plugin_j11
+    }
+  }
   eclipseWorkspace = null
   eclipseBinary = string("")
   eclipseVersion = string("")
   eclipseDebug = false
+  eclipseJavaVersion = string("")
   // ENDEXT
 }
 
@@ -429,6 +456,9 @@ eclipse {
         def removeTheseToo = []
         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
         cp.entries.each { entry ->
+          // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+          // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+          // we add the resources and help/help dirs in as libs afterwards (see below)
           if (entry.kind == 'src') {
             if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
               removeTheseToo += entry
@@ -436,6 +466,7 @@ eclipse {
               alreadyAddedSrcPath.putAt(entry.path, true)
             }
           }
+
         }
         cp.entries.removeAll(removeTheseToo)
 
@@ -452,8 +483,8 @@ eclipse {
         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
           //don't 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
-            return
+            // don't add dirs to classpath, especially if they don't exist
+            return false // groovy "continue" in .any closure
           }
           def itPath = it.toString()
           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
@@ -506,6 +537,7 @@ eclipse {
     javaRuntimeName = eclipse_java_runtime_name
 
     // add in jalview project specific properties/preferences into eclipse core preferences
+    // and also the codestyle XML file
     file {
       withProperties { props ->
         def jalview_prefs = new Properties()
@@ -517,6 +549,22 @@ eclipse {
             props.putAt(t, v)
           }
         }
+        // codestyle file -- overrides previous formatter prefs
+        def csFile = file("${jalviewDirAbsolutePath}/${eclipse_codestyle_file}")
+        if (csFile.exists()) {
+          XmlParser parser = new XmlParser()
+          def profiles = parser.parse(csFile)
+          def profile = profiles.'profile'.find { p -> (p.'@kind' == "CodeFormatterProfile" && p.'@name' == "Jalview") }
+          if (profile != null) {
+            profile.'setting'.each { s ->
+              def id = s.'@id'
+              def value = s.'@value'
+              if (id != null && value != null) {
+                props.putAt(id, value)
+              }
+            }
+          }
+        }
       }
     }
 
@@ -525,7 +573,8 @@ eclipse {
   if (IN_ECLIPSE) {
     // Don't want these to be activated if in headless build
     synchronizationTasks "eclipseSynchronizationTask"
-    autoBuildTasks "eclipseAutoBuildTask"
+    //autoBuildTasks "eclipseAutoBuildTask"
+
   }
 }
 
@@ -657,6 +706,8 @@ task setGitVals {
 
 
 task createBuildProperties(type: WriteProperties) {
+  group = "build"
+  description = "Create the ${buildProperties} file"
   dependsOn setGitVals
   inputs.dir(sourceDir)
   inputs.dir(resourceDir)
@@ -672,6 +723,13 @@ task createBuildProperties(type: WriteProperties) {
 }
 
 
+clean {
+  doFirst {
+    delete buildProperties
+  }
+}
+
+
 task cleanBuildingHTML(type: Delete) {
   doFirst {
     delete buildingHTML
@@ -702,7 +760,7 @@ task convertBuildingMD(type: Exec) {
         commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
     } else {
         println("Cannot find pandoc. Skipping convert building.md to HTML")
-        throw new StopExecutionException()
+        throw new StopExecutionException("Cannot find pandoc. Skipping convert building.md to HTML")
     }
   }
 
@@ -767,6 +825,7 @@ task syncLib(type: Sync) {
 
 
 task syncResources(type: Sync) {
+  dependsOn createBuildProperties
   from resourceDir
   include "**/*.*"
   into "${classesDir}"
@@ -878,6 +937,7 @@ task cleanPackageDir(type: Delete) {
   }
 }
 
+
 jar {
   dependsOn linkCheck
   dependsOn buildIndices
@@ -1524,6 +1584,15 @@ task jalviewjsEclipsePaths {
 }
 
 
+task printProperties {
+  group "Debug"
+  description "Output to console all System.properties"
+  doFirst {
+    System.properties.each { key, val -> System.out.println("Property: ${key}=${val}") }
+  }
+}
+
+
 task eclipseSetup {
   dependsOn eclipseProject
   dependsOn eclipseClasspath
@@ -1536,7 +1605,7 @@ task jalviewjsEclipseCopyDropins(type: Copy) {
   dependsOn jalviewjsEclipsePaths
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
-  inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
+  inputFiles += file("${jalviewDir}/${jalviewjsJ2sPlugin}")
   def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
   from inputFiles
@@ -1827,7 +1896,12 @@ DEBUG: ${eclipseDebug}
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
       //throw new TaskExecutionException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
-      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      if (jalviewjs_ignore_transpile_errors.equals("true")) {
+        println("IGNORING TRANSPILE ERRORS")
+        println("See eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      } else {
+        throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
+      }
     }
   }
 
@@ -1877,6 +1951,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
   javaexec {
     classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
     args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+    maxHeapSize = "2g"
 
     msg = "\nRunning '"+commandLine.join(' ')+"'\n"
     println(msg)
@@ -1947,7 +2022,7 @@ task jalviewjsBuildAllCores {
 
     def file = hash['file']
     if (! file.exists()) {
-      println("...classlist file '"+file.getPath()+"' does not exist, skipping")
+      //println("...classlist file '"+file.getPath()+"' does not exist, skipping")
       return false // this is a "continue" in groovy .each closure
     }
     def name = hash['name']
@@ -2020,7 +2095,8 @@ task jalviewjsBuildAllCores {
     'list': allJsFiles,
     'name': allClasslistName
   ]
-  jalviewjsCoreClasslists += allClasslist
+  // not including this version of "all" core at the moment
+  //jalviewjsCoreClasslists += allClasslist
   inputs.files(allClasslist['list'])
   outputs.file(allClasslist['jsfile'])
   outputs.file(allClasslist['zjsfile'])
@@ -2157,12 +2233,19 @@ task jalviewjsBuildSite {
 }
 
 
-task cleanJalviewjsSite {
+task cleanJalviewjsTransferSite {
   doFirst {
     delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
     delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
     delete "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
     delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
+  }
+}
+
+
+task cleanJalviewjsSite {
+  dependsOn cleanJalviewjsTransferSite
+  doFirst {
     delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
@@ -2255,6 +2338,67 @@ task cleanJalviewjsAll {
 }
 
 
+task jalviewjsIDE_checkJ2sPlugin {
+  group "00 JalviewJS in Eclipse"
+  description "Compare the swingjs/net.sf.j2s.core(-j11)?.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
+
+  doFirst {
+    def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+    def j2sPluginFile = file(j2sPlugin)
+    def eclipseHome = System.properties["eclipse.home.location"]
+    if (eclipseHome == null || ! IN_ECLIPSE) {
+      throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
+    }
+    def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+    def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+    if (!eclipseJ2sPluginFile.exists()) {
+      def msg = "Eclipse J2S Plugin is not installed (could not find '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+      System.err.println(msg)
+      throw new StopExecutionException(msg)
+    }
+
+    def digest = MessageDigest.getInstance("MD5")
+
+    digest.update(j2sPluginFile.text.bytes)
+    def j2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+
+    //digest.update(eclipseJ2sPluginFile.text.bytes)
+    def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
+     
+    if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
+      def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
+      System.err.println(msg)
+      throw new StopExecutionException(msg)
+    } else {
+      def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+      println(msg)
+    }
+  }
+}
+
+task jalviewjsIDE_copyJ2sPlugin {
+  group "00 JalviewJS in Eclipse"
+  description "Copy the swingjs/net.sf.j2s.core(-j11)?.jar file into the Eclipse IDE's 'dropins' dir"
+
+  doFirst {
+    def j2sPlugin = string("${jalviewDir}/${jalviewjsJ2sPlugin}")
+    def j2sPluginFile = file(j2sPlugin)
+    def eclipseHome = System.properties["eclipse.home.location"]
+    if (eclipseHome == null || ! IN_ECLIPSE) {
+      throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. NOT copying J2S Plugin.")
+    }
+    def eclipseJ2sPlugin = "${eclipseHome}/dropins/${j2sPluginFile.getName()}"
+    def eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+    def msg = "WARNING! Copying this commit's j2s plugin '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n* May require an Eclipse restart"
+    System.err.println(msg)
+    copy {
+      from j2sPlugin
+      eclipseJ2sPluginFile.getParentFile().mkdirs()
+      into eclipseJ2sPluginFile.getParent()
+    }
+  }
+}
+
 
 task jalviewjsIDE_j2sFile {
   group "00 JalviewJS in Eclipse"
@@ -2270,9 +2414,7 @@ task jalviewjsIDE_SyncCore {
 }
 
 
-task jalviewjsIDE_PrepareSite {
-  group "00 JalviewJS in Eclipse"
-  description "Sync libs and resources to site dir, but not closure cores"
+task jalviewjsIDE_SyncSiteAll {
   dependsOn jalviewjsSyncAllLibs
   dependsOn jalviewjsSyncResources
   dependsOn jalviewjsSyncSiteResources
@@ -2280,6 +2422,18 @@ task jalviewjsIDE_PrepareSite {
 }
 
 
+cleanJalviewjsTransferSite.mustRunAfter jalviewjsIDE_SyncSiteAll
+
+
+task jalviewjsIDE_PrepareSite {
+  group "00 JalviewJS in Eclipse"
+  description "Sync libs and resources to site dir, but not closure cores"
+
+  dependsOn jalviewjsIDE_SyncSiteAll
+  dependsOn cleanJalviewjsTransferSite
+}
+
+
 task jalviewjsIDE_AssembleSite {
   group "00 JalviewJS in Eclipse"
   description "Assembles unzipped supporting zipfiles, resources, site resources and closure cores into the Eclipse transpiled site"
@@ -2301,16 +2455,22 @@ task jalviewjsIDE_Server {
 }
 
 
-// buildship runs this at import
+// buildship runs this at import or gradle refresh
 task eclipseSynchronizationTask {
   //dependsOn eclipseSetup
-  dependsOn jalviewjsIDE_j2sFile
+  dependsOn createBuildProperties
+  if (J2S_ENABLED) {
+    dependsOn jalviewjsIDE_j2sFile
+    dependsOn jalviewjsIDE_checkJ2sPlugin
+    dependsOn jalviewjsIDE_PrepareSite
+  }
 }
 
 
-// buildship runs this at build time
+// buildship runs this at build time or project refresh
 task eclipseAutoBuildTask {
-  dependsOn jalviewjsIDE_PrepareSite
+  //dependsOn jalviewjsIDE_checkJ2sPlugin
+  //dependsOn jalviewjsIDE_PrepareSite
 }