From 650bca3ef095d09a5354240e7d2bafb6fc524122 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 11 Jan 2021 21:30:56 +0000
Subject: [PATCH] JAL-3789 Use j2s.config.altfileproperty in .j2s for
 alternative temporary build/jalviewjs/config/j2s settings
 file when running a headless build in gradle

---
 build.gradle      |   41 +++++++++++++++++++++++++++++++++++++----
 gradle.properties |   15 ++++++++++++++-
 2 files changed, 51 insertions(+), 5 deletions(-)

diff --git a/build.gradle b/build.gradle
index 147c31a..180d4ad 100644
--- a/build.gradle
+++ b/build.gradle
@@ -460,6 +460,7 @@ 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
 
@@ -1975,6 +1976,33 @@ 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 +2215,7 @@ 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 +2234,11 @@ 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 +2354,7 @@ 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 +2368,9 @@ 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 +2390,7 @@ 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
@@ -2825,7 +2858,7 @@ 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 } )
diff --git a/gradle.properties b/gradle.properties
index 98c2201..cb25e71 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -151,6 +151,19 @@ eclipse_project_name = jalview
 eclipse_bin_dir = bin
 eclipse_debug = false
 
+## IMPORTANT for headless build
+# to enable `gradle jalviewjs` headless build you MUST set
+# j2s.config.altfileproperty = org.jalview.jalviewjsj2sfilename
+# (or set to whatever value jalviewjs_j2s_alt_file_property is set to)
+# in your ./.j2s file
+# OR run the task `gradle jalviewjsEnableAltFileProperty` to do that for you (before headless build task)
+jalviewjs_j2s_alt_file_property = org.jalview.jalviewjsj2sfilename
+jalviewjs_j2s_alt_settings = build/jalviewjs/config/j2s
+
+# these are used for actual .j2s file to pass on to alt j2s file
+jalviewjs_j2s_settings = .j2s
+jalviewjs_j2s_alt_file_property_config = j2s.config.altfileproperty
+
 # for developing in Eclipse as IDE, set this to automatically copy current swingjs/net.sf.j2s.core.jar to your dropins dir
 jalviewjs_eclipseIDE_auto_copy_j2s_plugin = false
 # Override this in a local.properties file
@@ -162,7 +175,7 @@ jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core-j11.jar
 jalviewjs_libjs_dir = utils/jalviewjs/libjs
 jalviewjs_site_resource_dir = utils/jalviewjs/site-resources
 jalviewjs_classlists_dir = utils/jalviewjs/classlists
-jalviewjs_j2s_settings = .j2s
+jalviewjs_classlist_jalview = utils/jalviewjs/_j2sclasslist.txt
 #jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace
 # these 3 files/dirs found in build/jalviewjs
 jalviewjs_eclipse_tmp_dropins_dir = eclipse_dropins
-- 
1.7.10.2