From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 17 Sep 2021 15:38:49 +0000 (+0100)
Subject: JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo
X-Git-Tag: Release_2_11_2_0~33^2^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fpatch%2FJAL-3874_newJmolAndGradleDedup;p=jalview.git

JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo
---

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index fa922d9..c26858d 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -42,7 +42,7 @@ jetty-util-9.2.10.v20150310.jar
 jfreesvg-2.1.jar	GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
 JGoogleAnalytics_0.3.jar	APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
 jhall.jar
-Jmol-14.6.4_2016.10.26.jar	GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
+Jmol-14.31.53.jar	GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
 json_simple-1.1.jar	Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
 jsoup-1.8.1.jar
 jsr311-api-1.1.1.jar
diff --git a/build.gradle b/build.gradle
index ee7be0f..8efe39d 100644
--- 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()
@@ -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
@@ -2393,6 +2399,10 @@ task jalviewjsSyncAllLibs (type: Sync) {
   preserve {
     include "**"
   }
+
+  // should this be exclude really ?
+  duplicatesStrategy "INCLUDE"
+
   outputs.files outputFiles
   inputs.files inputFiles
 }
@@ -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,
diff --git a/j11lib/Jmol-14.31.53-dedup.jar b/j11lib/Jmol-14.31.53.jar
similarity index 63%
rename from j11lib/Jmol-14.31.53-dedup.jar
rename to j11lib/Jmol-14.31.53.jar
index dc352de..5c37cb0 100644
Binary files a/j11lib/Jmol-14.31.53-dedup.jar and b/j11lib/Jmol-14.31.53.jar differ
diff --git a/j8lib/Jmol-14.31.53-dedup.jar b/j8lib/Jmol-14.31.53.jar
similarity index 63%
rename from j8lib/Jmol-14.31.53-dedup.jar
rename to j8lib/Jmol-14.31.53.jar
index dc352de..5c37cb0 100644
Binary files a/j8lib/Jmol-14.31.53-dedup.jar and b/j8lib/Jmol-14.31.53.jar differ