From b8bbab1e3d858853b8d18087e0b94ac5deeaeff1 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 10 Nov 2023 14:43:29 +0000
Subject: [PATCH] JAL-4059 Checked through and fixed build tasks

---
 build.gradle |   23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/build.gradle b/build.gradle
index fe7e4e4..751e6c3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -3696,8 +3696,9 @@ DEBUG: ${eclipseDebug}
 }
 
 
-task jalviewjsMergeJs (type: Sync) {
+task jalviewjsTranserSiteMergeDirs (type: Sync) {
   dependsOn jalviewjsTransferUnzipAllLibs
+  dependsOn jalviewjsTransferUnzipSwingJs
   dependsOn jalviewjsTranspile
 
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteLibDir}")
@@ -3811,9 +3812,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
 task jalviewjsBuildAllCores {
   group "JalviewJS"
   description "Build the core js lib closures listed in the classlists dir"
-  dependsOn jalviewjsTranspile
-  dependsOn jalviewjsTransferUnzipSwingJs
-  dependsOn jalviewjsMergeJs
+  dependsOn jalviewjsTranserSiteMergeDirs
 
   def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
   def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteMergeDir}/${jalviewjs_j2s_subdir}"
@@ -3955,6 +3954,7 @@ def jalviewjsPublishCoreTemplate(String coreName, String templateName, File inpu
 
 task jalviewjsPublishCoreTemplates {
   dependsOn jalviewjsBuildAllCores
+
   def inputFileName = "${jalviewDir}/${j2s_coretemplate_html}"
   def inputFile = file(inputFileName)
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
@@ -3979,6 +3979,7 @@ task jalviewjsPublishCoreTemplates {
 task jalviewjsSyncCore (type: Sync) {
   dependsOn jalviewjsBuildAllCores
   dependsOn jalviewjsPublishCoreTemplates
+
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjsTransferSiteCoreDir}")
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
@@ -3998,8 +3999,18 @@ task jalviewjsSyncCore (type: Sync) {
 
 
 // this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteMergeDir(type: Copy) {
+  dependsOn jalviewjsTranserSiteMergeDirs
+
+  from "${jalviewDir}/${jalviewjsTransferSiteMergeDir}"
+  into "${jalviewDir}/${jalviewjsSiteDir}"
+}
+
+
+// this Copy version of TransferSiteJs will delete anything else in the target dir
 task jalviewjsCopyTransferSiteJs(type: Copy) {
   dependsOn jalviewjsTranspile
+
   from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
@@ -4030,7 +4041,7 @@ jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
 task jalviewjsPrepareSite {
   group "JalviewJS"
   description "Prepares the website folder including unzipping files and copying resources"
-  dependsOn jalviewjsSyncAllLibs
+  //dependsOn jalviewjsSyncAllLibs // now using jalviewjsCopyTransferSiteMergeDir
   dependsOn jalviewjsSyncResources
   dependsOn jalviewjsSyncSiteResources
   dependsOn jalviewjsSyncBuildProperties
@@ -4041,7 +4052,7 @@ task jalviewjsPrepareSite {
 task jalviewjsBuildSite {
   group "JalviewJS"
   description "Builds the whole website including transpiled code"
-  dependsOn jalviewjsCopyTransferSiteJs
+  dependsOn jalviewjsCopyTransferSiteMergeDir
   dependsOn jalviewjsPrepareSite
 }
 
-- 
1.7.10.2