JAL-4059 fix not merging html files to the final site from libs

diff --git a/build.gradle b/build.gradle
index 751e6c3..fb1a83b 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -3401,8 +3401,6 @@ task jalviewjsTransferUnzipSwingJs {
     copy {
       from zipTree(file_zip)
       into "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}"
-      exclude "**.html"
-      exclude "**.htm"
     }
   }
 
@@ -3419,8 +3417,6 @@ task jalviewjsTransferUnzipLib {
       copy {
         from zipTree(file_zip)
         into "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
-        exclude "**.html"
-        exclude "**.htm"
 
         // The following replace() is needed due to a mismatch in Jmol calls to
         // colorPtToFFRGB$javajs_util_T3d when only colorPtToFFRGB$javajs_util_T3 is defined
@@ -3696,7 +3692,7 @@ DEBUG: ${eclipseDebug}
 }
 
 
-task jalviewjsTranserSiteMergeDirs (type: Sync) {
+task jalviewjsTranserSiteMergeLibDirs (type: Sync) {
   dependsOn jalviewjsTransferUnzipAllLibs
   dependsOn jalviewjsTransferUnzipSwingJs
   dependsOn jalviewjsTranspile
@@ -3704,8 +3700,35 @@ task jalviewjsTranserSiteMergeDirs (type: Sync) {
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
   // merge swingjs lib last
   inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}")
+
+  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
+
+  from inputFiles
+  into outputDir
+  def outputFiles = []
+  rename { filename ->
+    outputFiles += "${outputDir}/${filename}"
+    null
+  }
+
+  exclude "**/*.html"
+  exclude "**/*.htm"
+
+  // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
+  duplicatesStrategy "INCLUDE"
+
+  outputs.files outputFiles
+  inputs.files inputFiles
+}
+
+
+task jalviewjsTranserSiteMergeSwingDir (type: Sync) {
+  dependsOn jalviewjsTransferUnzipAllLibs
+  dependsOn jalviewjsTransferUnzipSwingJs
+  dependsOn jalviewjsTranspile
+
   // merge jalview files very last
-  inputFiles += fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteJsDir}")
 
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
 
@@ -3720,7 +3743,7 @@ task jalviewjsTranserSiteMergeDirs (type: Sync) {
     include "**"
   }
 
-  // should this be exclude really ? No, swingjs dir should be transferred last (and overwrite)
+  // should this be exclude really ? No, jalview dir should be transferred last (and overwrite)
   duplicatesStrategy "INCLUDE"
 
   outputs.files outputFiles
@@ -3728,6 +3751,12 @@ task jalviewjsTranserSiteMergeDirs (type: Sync) {
 }
 
 
+task jalviewjsTranserSiteMergeDirs {
+  dependsOn jalviewjsTranserSiteMergeLibDirs
+  dependsOn jalviewjsTranserSiteMergeSwingDir
+}
+
+
 def jalviewjsCallCore(String name, FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
 
   def stdout = new ByteArrayOutputStream()