JAL-3829 open web page for 3d beacons structure by right-clicking and selecting pop...

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index e6c8fbd..8efe39d 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -52,6 +52,7 @@ 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()
@@ -370,6 +371,7 @@ ext {
                                     .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
 
+  getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
   getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
@@ -1368,13 +1370,12 @@ task linkCheck(type: JavaExec) {
   args = [ "${helpBuildDir}/${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(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
@@ -1409,6 +1410,8 @@ jar {
   def outputDir = "${jalviewDir}/${package_dir}"
   destinationDirectory = file(outputDir)
   archiveFileName = rootProject.name+".jar"
+  duplicatesStrategy "EXCLUDE"
+
 
   exclude "cache*/**"
   exclude "*.jar"
@@ -1474,6 +1477,9 @@ shadowJar {
     attributes "Implementation-Version": JALVIEW_VERSION,
     "Application-Name": install4jApplicationName
   }
+
+  duplicatesStrategy "INCLUDE"
+
   mainClassName = shadow_jar_main_class
   mergeServiceFiles()
   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
@@ -1573,7 +1579,7 @@ task getdownWebsite() {
       }
     }
     
-    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script ]
+    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
     getdownWrapperScripts.each{ script ->
       def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
       if (s.exists()) {
@@ -1912,7 +1918,7 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
     'MACOS_DMG_DS_STORE': install4jDMGDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
-    'WRAPPER_LINK': getdown_wrapper_link,
+    'WRAPPER_LINK': getdownWrapperLink,
     'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
     'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
     'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
@@ -2393,6 +2399,10 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
+
+  // should this be exclude really ?
+  duplicatesStrategy "INCLUDE"
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -2547,12 +2557,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2640,7 +2650,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
           new org.apache.tools.ant.util.TeeOutputStream(
             logErrFOS,
             stderr),
-          errorOutput)
+          System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,
@@ -2947,7 +2957,13 @@ task jalviewjsServer {
   def htmlFile = "${jalviewDirAbsolutePath}/${filename}"
   doLast {
 
-    SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
+    def factory
+    try {
+      def f = Class.forName("org.gradle.plugins.javascript.envjs.http.simple.SimpleHttpFileServerFactory")
+      factory = f.newInstance()
+    } catch (ClassNotFoundException e) {
+      throw new GradleException("Unable to create SimpleHttpFileServerFactory")
+    }
     def port = Integer.valueOf(jalviewjs_server_port)
     def start = port
     def running = false