From 1fa42eb71e69ca42f3b20eb26b17de99b015c55a Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Wed, 30 Oct 2019 01:52:21 +0000
Subject: [PATCH 1/1] JAL-3210 firming up relative paths with jalviewDir. Some
 comments on possibility of using eclipse plugins
 differently

---
 build.gradle |   24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/build.gradle b/build.gradle
index 815c6d2..8378a28 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1463,13 +1463,13 @@ task jalviewjsUnzipFiles {
     zipFiles.each { file_zip -> 
       copy {
         from zipTree(file_zip)
-        into jalviewjsSiteDir
+        into "${jalviewDir}/${jalviewjsSiteDir}"
       }
     }
   }
 
   inputs.files zipFiles
-  outputs.dir jalviewjsSiteDir
+  outputs.dir "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
@@ -1504,8 +1504,8 @@ task jalviewjsEclipseSetup {
 
 task jalviewjsCopyResources (type: Sync) {
   dependsOn jalviewjsSitePath
-  def inputFiles = fileTree(dir: resourceDir)
-  def outputDir = "${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
+  def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
+  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
   into outputDir
@@ -1524,7 +1524,7 @@ task jalviewjsCopyResources (type: Sync) {
 task jalviewjsCopySiteResources (type: Sync) {
   dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
-  def outputDir = jalviewjsSiteDir
+  def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
 
   from inputFiles
   into outputDir
@@ -1551,6 +1551,7 @@ task jalviewjsProjectImport(type: Exec) {
   if (eclipseDebug) {
     args += "-debug"
   }
+  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=utils/jalviewjs/eclipse/dropins"] here? (instead of copying plugins to eclipse dropins dir)
 
   doFirst {
     println("IMPORT ECLIPSE_DEBUG=${eclipseDebug}")
@@ -1571,6 +1572,7 @@ task jalviewjsTranspile(type: Exec) {
   if (eclipseDebug) {
     args += "-debug"
   }
+  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=swingjs"] here? (instead of copying plugins to eclipse dropins dir)
 
   def stdout
   def stderr
@@ -1626,17 +1628,17 @@ DEBUG: ${eclipseDebug}
     println("TRANSPILE ECLIPSE_DEBUG=${eclipseDebug}")
   }
 
-  inputs.dir(sourceDir)
-  outputs.dir("${eclipse_bin_dir}/main")
-  outputs.dir(jalviewjsTransferSiteDir)
-  outputs.upToDateWhen { file("${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
+  inputs.dir("${jalviewDir}/${sourceDir}")
+  outputs.dir("${jalviewDir}/${eclipse_bin_dir}/main")
+  outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}")
+  outputs.upToDateWhen { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
 
 }
 
 task jalviewjsCopyTransferSite(type: Copy) {
   dependsOn jalviewjsTranspile
-  from jalviewjsTransferSiteDir
-  into jalviewjsSiteDir
+  from "${jalviewDir}/${jalviewjsTransferSiteDir}"
+  into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
 jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
-- 
1.7.10.2