removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also

removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -83,11 +83,7 @@
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
-
-        <!-- Remove the reflections cache as the local dependency settings have changed. -->
-        <!-- Ok to remove after reflections goes back to a stable release. -->
-        <delete dir="${ivy.home}/cache/org.reflections/reflections"/>
-
+  
       <mkdir dir="${ivy.jar.dir}"/>
       <!-- Remove old versions of ivy. -->
       <delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
@@ -471,7 +467,7 @@
             <echo message="Sting: Running @{testtype} test cases!"/>
             <junit printsummary="yes" showoutput="yes" maxmemory="${test.maxmemory}" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
                 <formatter type="brief" usefile="false" />
-                <formatter type="xml"/> 
+                <formatter type="xml"/>
                 <classpath>
                     <path refid="runtime.dependencies"/>
                     <pathelement location="${java.classes}"/>

ivy.xml

@@ -19,7 +19,7 @@
     <dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
 
     <!-- Dependencies for reflections mvn repository -->
-    <dependency org="org.reflections" name="reflections" rev="0.9.5-svnversion79M_mod2"/>
+    <dependency org="org.reflections" name="reflections" rev="0.9.5-RC2"/>
 
     <!-- Matrix package from math.nist.gov -->
     <dependency org="gov.nist" name="Jama" rev="1.0.2"/>

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -25,12 +25,15 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
-import org.reflections.Reflections;
-import org.reflections.scanners.ResourcesScanner;
-import org.reflections.scanners.SubTypesScanner;
-import org.reflections.util.ConfigurationBuilder;
-import org.reflections.util.ManifestAwareClasspathHelper;
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.LoggerContext;
 import org.broadinstitute.sting.utils.StingException;
+import org.reflections.Reflections;
+import org.reflections.scanners.SubTypesScanner;
+import org.reflections.util.ClasspathHelper;
+import org.reflections.util.ConfigurationBuilder;
+import org.slf4j.LoggerFactory;
 
 import java.net.URL;
 import java.util.Set;
@@ -41,18 +44,21 @@ import java.util.List;
  * PackageUtils contains some useful methods for package introspection.
  */
 public class PackageUtils {
-    
+
     /**
      * A reference into our introspection utility.
      */
     private static Reflections reflections = null;
 
     static {
-        List<URL> urls = ManifestAwareClasspathHelper.getUrlsForManifestCurrentClasspath();
+        // turn off logging in the reflections library - they talk too much (to the wrong logger factory as well, logback)
+        Logger logger = (ch.qos.logback.classic.Logger)LoggerFactory.getLogger(Reflections.class);
+        logger.setLevel(Level.OFF);
+
         // Initialize general-purpose source tree reflector.
         reflections = new Reflections( new ConfigurationBuilder()
-                .setUrls(urls)
-                .setScanners(new SubTypesScanner(),new ResourcesScanner()));
+            .setUrls(getClassPathURLs())
+            .setScanners(new SubTypesScanner()));
     }
 
     /**
@@ -115,4 +121,8 @@ public class PackageUtils {
 
         return nonConcreteTypes;
     }
+
+    public static Set<URL> getClassPathURLs() {
+        return ClasspathHelper.getUrlsForCurrentClasspath();
+    }
 }

scala/src/org/broadinstitute/sting/queue/util/ClasspathUtils.scala

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.queue.util
 
 import collection.JavaConversions._
-import org.reflections.util.ManifestAwareClasspathHelper
+import org.broadinstitute.sting.utils.classloader.PackageUtils
 import java.io.File
 import javax.print.URIException
 import java.net.{URL, URLClassLoader}
@@ -16,7 +16,7 @@ object ClasspathUtils {
    * @return List[File] that build up the current classpath.
    */
   def manifestAwareClassPath = {
-    var urls = ManifestAwareClasspathHelper.getUrlsForManifestCurrentClasspath
+    var urls = PackageUtils.getClassPathURLs
     urls.map(url => try {new File(url.toURI)} catch {case urie: URIException => new File(url.getPath)})
   }
 
@@ -33,3 +33,4 @@ object ClasspathUtils {
     method.invoke(ClassLoader.getSystemClassLoader(), url);
   }
 }
+

settings/ivysettings.xml

@@ -9,12 +9,13 @@
     <ibiblio name="libraries" m2compatible="true" />
     <ibiblio name="libraries_with_inconsistent_poms" checkconsistency="false" m2compatible="true" />
     <ibiblio name="ukcomrobust-it" m2compatible="true" root="http://oss.sonatype.org/service/local/repositories/ukcomrobust-it-049/content" />
+    <ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
   </resolvers>
   <modules>
     <module organisation="edu.mit.broad" resolver="projects" />
     <module organisation="net.sf" module="functionalj" resolver="projects" />
     <module organisation="net.sf" module="samtools" resolver="projects" />
-    <module organisation="org.reflections" module="reflections" resolver="projects" />
+    <module organisation="org.reflections" module="reflections" resolver="reflections-repo" />
     <module organisation="org.broad" module="tribble" resolver="projects" />
     <module organisation="gov.nist" module="Jama" resolver="projects" />
     <module organisation="uk.com.robust-it" module="cloning" resolver="ukcomrobust-it" />

settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.xml

@@ -1,12 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.reflections" module="reflections" revision="0.9.5-svnversion79M_mod2" status="release" />
-    <dependencies defaultconf="default">
-        <dependency org="javassist" name="javassist" rev="3.8.0.GA"/>
-        <dependency org="ch.qos.logback" name="logback-core" rev="0.9.9"/>
-        <dependency org="ch.qos.logback" name="logback-classic" rev="0.9.9"/>
-        <dependency org="org.slf4j" name="slf4j-api" rev="1.5.6"/>
-        <dependency org="xml-apis" name="xml-apis" rev="1.0.b2"/>
-        <dependency org="com.google.collections" name="google-collections" rev="1.0"/>
-        <dependency org="dom4j" name="dom4j" rev="1.6"/>
-    </dependencies>
-</ivy-module>