X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=172f9bcf27d3f38f4de25e500a2a6e6801960ae0;hb=refs%2Fheads%2Fimprovement%2FJAL-3848_slivka_0.8_updated_jslib;hp=86e984cc8c834f2966f9779a5f651fe24d3d1fda;hpb=4cf38a596371d40f25a7fcc7e3127b79c412ba63;p=jalview.git

diff --git a/build.gradle b/build.gradle
index 86e984c..172f9bc 100644
--- a/build.gradle
+++ b/build.gradle
@@ -51,6 +51,7 @@ repositories {
 }
 
 
+
 // in ext the values are cast to Object. Ensure string values are cast as String (and not GStringImpl) for later use
 def string(Object o) {
   return o == null ? "" : o.toString()
@@ -110,7 +111,7 @@ ext {
   }
   ////
   // Set JALVIEW_VERSION if it is not already set
-  if (findProperty(JALVIEW_VERSION)==null || "".equals(JALVIEW_VERSION)) {
+  if (findProperty("JALVIEW_VERSION")==null || "".equals(JALVIEW_VERSION)) {
     JALVIEW_VERSION = releaseProps.get("jalview.version")
   }
   
@@ -460,6 +461,7 @@ ext {
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
   jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+  jalviewjsJ2sAltSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_alt_settings}")
   jalviewjsJ2sProps = null
   jalviewjsJ2sPlugin = jalviewjs_j2s_plugin
 
@@ -1298,13 +1300,12 @@ task linkCheck(type: JavaExec) {
   args = [ "${classesDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
-  def errFOS = outFOS
   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    standardOutput)
+    System.out)
   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    errorOutput)
+    System.err)
 
   inputs.dir("${classesDir}/${help_dir}")
   outputs.file(helpLinksCheckerOutFile)
@@ -1335,6 +1336,9 @@ jar {
     "Codebase": application_codebase
   }
 
+  duplicatesStrategy "EXCLUDE"
+
+
   destinationDir = file("${jalviewDir}/${package_dir}")
   archiveName = rootProject.name+".jar"
 
@@ -1396,6 +1400,9 @@ shadowJar {
   manifest {
     attributes 'Implementation-Version': JALVIEW_VERSION
   }
+
+  duplicatesStrategy "EXCLUDE"
+
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1975,6 +1982,33 @@ task j2sSetHeadlessBuild {
 }
 
 
+task jalviewjsEnableAltFileProperty(type: WriteProperties) {
+  group "jalviewjs"
+  description "Enable the alternative J2S Config file for headless build"
+
+  outputFile = jalviewjsJ2sSettingsFileName
+  def j2sPropsFile = file(jalviewjsJ2sSettingsFileName)
+  def j2sProps = new Properties()
+  if (j2sPropsFile.exists()) {
+    try {
+      def j2sPropsFileFIS = new FileInputStream(j2sPropsFile)
+      j2sProps.load(j2sPropsFileFIS)
+      j2sPropsFileFIS.close()
+
+      j2sProps.each { prop, val ->
+        property(prop, val)
+      }
+    } catch (Exception e) {
+      println("Exception reading ${jalviewjsJ2sSettingsFileName}")
+      e.printStackTrace()
+    }
+  }
+  if (! j2sProps.stringPropertyNames().contains(jalviewjs_j2s_alt_file_property_config)) {
+    property(jalviewjs_j2s_alt_file_property_config, jalviewjs_j2s_alt_file_property)
+  }
+}
+
+
 task jalviewjsSetEclipseWorkspace {
   def propKey = "jalviewjs_eclipse_workspace"
   def propVal = null
@@ -2187,7 +2221,7 @@ task jalviewjsTransferUnzipAllLibs {
 
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   group "JalviewJS"
-  description "Create the .j2s file from the j2s.* properties"
+  description "Create the alternative j2s file from the j2s.* properties"
 
   jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
   def siteDirProperty = "j2s.site.directory"
@@ -2206,11 +2240,11 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
       property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
     }
   }
-  outputFile = jalviewjsJ2sSettingsFileName
+  outputFile = jalviewjsJ2sAltSettingsFileName
 
   if (! IN_ECLIPSE) {
     inputs.properties(jalviewjsJ2sProps)
-    outputs.file(jalviewjsJ2sSettingsFileName)
+    outputs.file(jalviewjsJ2sAltSettingsFileName)
   }
 }
 
@@ -2326,6 +2360,7 @@ task jalviewjsProjectImport(type: Exec) {
   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
   if (!IN_ECLIPSE) {
     args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+    args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
   }
 
   inputs.file("${jalviewDir}/.project")
@@ -2339,6 +2374,9 @@ task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsEclipseSetup 
   dependsOn jalviewjsProjectImport
   dependsOn jalviewjsEclipsePaths
+  if (!IN_ECLIPSE) {
+    dependsOn jalviewjsEnableAltFileProperty
+  }
 
   doFirst {
     // do not run a headless transpile when we claim to be in Eclipse
@@ -2358,6 +2396,7 @@ task jalviewjsTranspile(type: Exec) {
   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
   if (!IN_ECLIPSE) {
     args += [ "-D${j2sHeadlessBuildProperty}=true" ]
+    args += [ "-D${jalviewjs_j2s_alt_file_property}=${jalviewjsJ2sAltSettingsFileName}" ]
   }
 
   def stdout
@@ -2385,12 +2424,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2825,7 +2864,7 @@ task cleanJalviewjsAll {
     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
     }
-    delete "${jalviewDir}/${jalviewjs_j2s_settings}"
+    delete jalviewjsJ2sAltSettingsFileName
   }
 
   outputs.upToDateWhen( { false } )
@@ -2843,10 +2882,25 @@ task jalviewjsIDE_checkJ2sPlugin {
     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 '${eclipseJ2sPlugin}')\nTry running task jalviewjsIDE_copyJ2sPlugin"
+    def eclipseJ2sPluginDirs = [ "${eclipseHome}/dropins" ]
+    def altPluginsDir = System.properties["org.eclipse.equinox.p2.reconciler.dropins.directory"]
+    if (altPluginsDir != null && file(altPluginsDir).exists()) {
+      eclipseJ2sPluginDirs += altPluginsDir
+    }
+    def foundPlugin = false
+    def j2sPluginFileName = j2sPluginFile.getName()
+    def eclipseJ2sPlugin
+    def eclipseJ2sPluginFile
+    eclipseJ2sPluginDirs.any { dir ->
+      eclipseJ2sPlugin = "${dir}/${j2sPluginFileName}"
+      eclipseJ2sPluginFile = file(eclipseJ2sPlugin)
+      if (eclipseJ2sPluginFile.exists()) {
+        foundPlugin = true
+        return true
+      }
+    }
+    if (!foundPlugin) {
+      def msg = "Eclipse J2S Plugin is not installed (could not find '${j2sPluginFileName}' in\n"+eclipseJ2sPluginDirs.join("\n")+"\n)\nTry running task jalviewjsIDE_copyJ2sPlugin"
       System.err.println(msg)
       throw new StopExecutionException(msg)
     }
@@ -2864,7 +2918,7 @@ task jalviewjsIDE_checkJ2sPlugin {
       System.err.println(msg)
       throw new StopExecutionException(msg)
     } else {
-      def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}' (this is good)"
+      def msg = "Eclipse J2S Plugin '${eclipseJ2sPlugin}' is the same as '${j2sPlugin}' (this is good)"
       println(msg)
     }
   }