JAL-3210 small fix for jalviewjsBuildDir

diff --git a/.classpath.all b/.classpath.all
deleted file mode 100644 (file)
index 8a4a050..0000000
--- a/.classpath.all
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <classpathentry kind="src" path="src"/>
-       <classpathentry kind="src" path="src2"/>
-       <classpathentry kind="src" path="utils"/>
-       <classpathentry kind="src" path="test"/>
-       <classpathentry kind="lib" path="lib/activation.jar"/>
-       <classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
-       <classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-       <classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-       <classpathentry kind="lib" path="lib/jhall.jar"/>
-       <classpathentry kind="lib" path="lib/mail.jar"/>
-       <classpathentry kind="lib" path="lib/regex.jar"/>
-       <classpathentry kind="lib" path="lib/saaj.jar"/>
-       <classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-       <classpathentry kind="lib" path="lib/xercesImpl.jar"/>
-       <classpathentry kind="lib" path="lib/castor-1.1-cycle-xml.jar" sourcepath="C:/Documents and Settings/JimP/workspace-3.3/castor/src/main/java"/>
-       <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
-       <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
-       <classpathentry kind="lib" path="lib/apache-mime4j-0.6.jar" sourcepath="G:/InstallsDir/Sources for Development/apache-mime4j-0.6-src.zip"/>
-       <classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/httpcore-4.0.1.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/httpmime-4.0.3.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
-       <classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
-       <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-       <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
-       <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
-       <classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
-       <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
-       <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
-       <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
-       <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
-       <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
-       <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
-       <classpathentry kind="lib" path="lib/VAqua4.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
-       <classpathentry kind="lib" path="lib/xml-apis.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-server-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/servlet-api-3.1.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-util-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/java-json.jar"/>
-       <classpathentry kind="lib" path="lib/Jmol-14.6.4_2016.10.26.jar"/>
-       <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
-       <classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
-       <classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
-       <classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
-       <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
-       <classpathentry kind="output" path="classes"/>
-</classpath>

diff --git a/.classpath.js b/.classpath.js
deleted file mode 100644 (file)
index 1a6df64..0000000
--- a/.classpath.js
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-       <classpathentry kind="src" path="src"/>
-       <!-- Not needed for java2script build
-        <classpathentry kind="src" path="utils"/>
-       <classpathentry kind="src" path="test"/>
-       -->
-        <classpathentry kind="lib" path="lib/activation.jar"/>
-       <classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
-       <classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-       <classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-       <classpathentry kind="lib" path="lib/jhall.jar"/>
-       <classpathentry kind="lib" path="lib/mail.jar"/>
-       <classpathentry kind="lib" path="lib/regex.jar"/>
-       <classpathentry kind="lib" path="lib/saaj.jar"/>
-       <classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-       <classpathentry kind="lib" path="lib/xercesImpl.jar"/>
-       <classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
-       <classpathentry kind="lib" path="lib/vamsas-client.jar"/>
-       <classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
-       <classpathentry kind="lib" path="lib/apache-mime4j-0.6.jar" sourcepath="G:/InstallsDir/Sources for Development/apache-mime4j-0.6-src.zip"/>
-       <classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/httpcore-4.0.1.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/httpmime-4.0.3.jar">
-               <attributes>
-                       <attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-               </attributes>
-       </classpathentry>
-       <classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
-       <classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
-       <classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-       <classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
-       <classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
-       <classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
-       <classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
-       <classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
-       <classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
-       <classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
-       <classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
-       <classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
-       <classpathentry kind="lib" path="utils/classgraph-4.1.6.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
-       <classpathentry kind="lib" path="lib/xml-apis.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
-       <classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-server-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/servlet-api-3.1.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-util-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
-       <classpathentry kind="lib" path="lib/java-json.jar"/>
-       <classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
-       <classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
-       <classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
-       <classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
-       <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
-       <classpathentry kind="lib" path="lib/intervalstore-v1.0.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
-        <classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
-       <classpathentry kind="output" path="classes"/>
-</classpath>

diff --git a/build.gradle b/build.gradle
index d575f18..9b7b171 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1266,11 +1266,11 @@ def jalviewjsBuildDir
 def jalviewjsSiteDir
 def jalviewjsTransferSiteDir
 task jalviewjsSitePath {
+  def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+  jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
   if (jalviewjs_site_dir.startsWith("/")) {
     jalviewjsSiteDir = jalviewjs_site_dir
   } else {
-    def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
-    jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
     jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
   }
   jalviewjsTransferSiteDir = jalviewjsBuildDir + "/tmp/site"