diff --git a/build.xml b/build.xml
index 6d9bc8f0790b52d9e65c7ee220e80a4ed4bd1fe3..b73ca87fcf4df6ff639bb40b46a8360343ae5a66 100644
--- a/build.xml
+++ b/build.xml
@@ -210,7 +210,7 @@
<onejar file="ontowrap"
group="fr.inrialpes.exmo"
desc="Ontology wrapper"
- path="jena/arq.jar jena/icu4j.jar jena/iri.jar jena/jena.jar skosapi/skosapi.jar owlapi10/api.jar owlapi10/impl.jar owlapi10/io.jar owlapi10/rdfapi.jar owlapi10/rdfparser.jar owlapi3/owlapi-bin.jar">
+ path="jena/arq.jar jena/iri.jar jena/jena.jar skosapi/skosapi.jar owlapi10/api.jar owlapi10/impl.jar owlapi10/io.jar owlapi10/rdfapi.jar owlapi10/rdfparser.jar owlapi3/owlapi-bin.jar">
<files>
<fileset dir="classes">
<include name="fr/inrialpes/exmo/ontowrap/**/*.class" />
@@ -224,7 +224,7 @@
group="fr.inrialpes.exmo.align"
desc="Alignment API implementation"
main="fr.inrialpes.exmo.align.cli.Procalign"
- path="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar cli/commons-cli.jar slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar jena/icu4j.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/hermit.jar align.jar ontowrap.jar procalign.jar">
+ path="skosapi/skosapi.jar owlapi30/owlapi-bin.jar ontosim/ontosim.jar cli/commons-cli.jar slf4j/jcl-over-slf4j.jar slf4j/log4j-over-slf4j.jar slf4j/slf4j-api.jar jwnl/jwnl.jar lucene/lucene-core.jar jena/jena.jar jena/iri.jar iddl/iddl.jar xerces/xercesImpl.jar xerces/resolver.jar xerces/xml-apis.jar hermit/hermit.jar align.jar ontowrap.jar procalign.jar">
<files>
<fileset dir="classes">
<include name="fr/inrialpes/exmo/align/impl/**/*.class"/>
@@ -527,7 +527,6 @@
<onepom file="jdbc/mysql-connector-java" />
<onepom file="jdbc/postgresql-jdbc4" />
<onepom file="jena/arq" />
- <onepom file="jena/icu4j" />
<onepom file="jena/iri" />
<onepom file="jena/jena" />
<onepom file="jetty/jetty-util" />
diff --git a/html/relnotes.html b/html/relnotes.html
index eb504151cec7f0ea48b6c52ce01606571386ed0b..5599154e4feeb4eba8f95dddb2458cd265ec9a11 100644
--- a/html/relnotes.html
+++ b/html/relnotes.html
@@ -73,7 +73,7 @@ with a warning:
<!--h2>Version 4.9 (1xxx): ??/??/201X - Al pesto</h2-->
<!--h2>Version 4.8 (1xxx): ??/??/201x - Antésine</h2-->
<!--h2>Version 4.7 (1xxx): ??/??/201x - Letraset</h2-->
-<!--h2>Version 4.6 (1xxx): ??/01/2014 - Da lec'h all</h2-->
+<!--h2>Version 4.6 (18xx): ??/01/2014 - Da lec'h all</h2-->
<p><ul compact="1">
<li>Fixed a bug in <tt>EDOALAlignment.init()</tt> which would prohibit rendering (edoal)</li>
<li>Fixed a bug in <tt>OWLAxiomsRendererVisitor</tt>, <tt>SWRLRendererVisitor</tt>, <tt>SEKTMappingRendererVisitor</tt>, <tt>COWLMappingRendererVisitor</tt> <tt>SPARQLConstructRendererVisitor</tt>, and <tt>SPARQLSelectRendererVisitor</tt> which sometimes rendered alignments empty (impl)</li>
@@ -90,6 +90,12 @@ with a warning:
<li>Updated tutorial2 with deprecated <tt>BasicParameters</tt> (tutorial)</li>
<li>Added complete command line option tests in <tt>tests/clitest.sh</tt> (cli)</li>
<li>Upgraded to <span style="color: green">SLF4J</span> to 1.7.5 (lib)</li>
+<li>Upgraded to <span style="color: green">xercesImpl</span> to 2.11.0 (lib)</li>
+<!--li>Upgraded to <span style="color: green">Lucene</span> to 4.6.0 (lib)</li-->
+<li>Upgraded to <span style="color: green">mysql</span> to 5.1.28 and <span style="color: green">postgres</span> to 9.3-1100 (lib)</li>
+<li>Upgraded to <span style="color: green">Jena</span> to 2.9.0 (lib)</li>
+<li>Upgraded to <span style="color: green">OWL API</span> to 3.4.8 (lib)</li>
+<li>Upgraded to <span style="color: green">HermiT</span> to 1.3.8 (lib)</li>
</ul></p>
<h2>Version 4.5 (1847): 25/03/2013 - Building 16</h2>
diff --git a/lib/hermit/hermit.jar b/lib/hermit/hermit.jar
index 2043a963a705ae900c0808969199deaf95621a13..408886017cb07f855f1b1affce059040a4c5b037 100644
Binary files a/lib/hermit/hermit.jar and b/lib/hermit/hermit.jar differ
diff --git a/lib/hermit/hermit.pom b/lib/hermit/hermit.pom
index 3f665d244b82528efbac03cb9b17fee58a939a16..df93b593f88e43605e1aeebd597d22287a703db1 100644
--- a/lib/hermit/hermit.pom
+++ b/lib/hermit/hermit.pom
@@ -3,7 +3,7 @@
<groupId>org.semanticweb.HermiT</groupId>
<artifactId>HermiT</artifactId>
- <version>1.3.6</version>
+ <version>1.3.8</version>
<!-- This is a stripped down version of HermiT with suppressed:
getopt, owl-api, common-loggins -->
<name>HermiT</name>
diff --git a/lib/jdbc/mysql-connector-java.jar b/lib/jdbc/mysql-connector-java.jar
index af5847eed4ccfd139427aaadbf3e9f3fbcef020d..2f1b7ab5fb924a6e637a6b605721ea85f0af7884 100644
Binary files a/lib/jdbc/mysql-connector-java.jar and b/lib/jdbc/mysql-connector-java.jar differ
diff --git a/lib/jdbc/mysql-connector-java.pom b/lib/jdbc/mysql-connector-java.pom
index a975c9a7f785c313213ac2a9b6d4101f3e41b8e7..f9be14a8db5eca32122766f15c38ad4cb5ba1151 100644
--- a/lib/jdbc/mysql-connector-java.pom
+++ b/lib/jdbc/mysql-connector-java.pom
@@ -3,7 +3,7 @@
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
- <version>5.1.12</version>
+ <version>5.1.28</version>
<name>Java Database connector (JDBC) for MySQL</name>
<licenses>
<license>
diff --git a/lib/jdbc/postgresql-jdbc4.jar b/lib/jdbc/postgresql-jdbc4.jar
index e21beec54882a8f5b27fe277055859dd2c33fe01..04a86ad7a67a96c37fa4fc1e71fec951d220dda5 100644
Binary files a/lib/jdbc/postgresql-jdbc4.jar and b/lib/jdbc/postgresql-jdbc4.jar differ
diff --git a/lib/jdbc/postgresql-jdbc4.pom b/lib/jdbc/postgresql-jdbc4.pom
index 1c611703beb913994ba699b7512069357ef50c27..39db5e83be61153847c87c08d6d6c4dc58491300 100644
--- a/lib/jdbc/postgresql-jdbc4.pom
+++ b/lib/jdbc/postgresql-jdbc4.pom
@@ -3,7 +3,7 @@
<groupId>org.postgresql</groupId>
<artifactId>postgresql-jdbc4</artifactId>
- <version>8.4-701</version>
+ <version>9.3-1100</version>
<name>Java Database connector (JDBC) for Postgres</name>
<licenses>
<license>
diff --git a/lib/jena/arq.jar b/lib/jena/arq.jar
index d4ac9a3fd4c2fb4358f1d328dd2cbcc1d4679387..0d3c9a7763f1bbc591ddf9e3892e400838963424 100644
Binary files a/lib/jena/arq.jar and b/lib/jena/arq.jar differ
diff --git a/lib/jena/arq.pom b/lib/jena/arq.pom
index aae2725b412a7ee44304f6a56847173f2cb264b4..702ea8f24a0e433d3bac13b3298f212178beff0d 100644
--- a/lib/jena/arq.pom
+++ b/lib/jena/arq.pom
@@ -3,7 +3,7 @@
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
- <version>2.9.0-incubating q</version>
+ <version>2.11.0</version>
<name>ARQ</name>
<description>ARQ is a SPARQL 1.1 query engine for Jena</description>
<packaging>jar</packaging>
diff --git a/lib/jena/icu4j.jar b/lib/jena/icu4j.jar
deleted file mode 100644
index f5e8c167e7f7f3d078407859cb50b8abf23c697e..0000000000000000000000000000000000000000
Binary files a/lib/jena/icu4j.jar and /dev/null differ
diff --git a/lib/jena/icu4j.pom b/lib/jena/icu4j.pom
deleted file mode 100644
index 3fbc948c537e1cbae613c343be570e74507c20c3..0000000000000000000000000000000000000000
--- a/lib/jena/icu4j.pom
+++ /dev/null
@@ -1,126 +0,0 @@
-<project>
- <modelVersion>4.0.0</modelVersion>
-
- <groupId>com.ibm.icu</groupId>
- <artifactId>icu4j</artifactId>
- <version>3.4.4</version>
- <name>ICU4J</name>
- <description>International Component for Unicode for Java (ICU4J) is a mature, widely used Java library providing Unicode and Globalization support</description>
- <licenses>
- <license>
- <name>ICU License</name>
- <url>http://source.icu-project.org/repos/icu/icu/trunk/license.html</url>
- <distribution>repo</distribution>
- </license>
- </licenses>
-
- <url>http://icu-project.org/</url>
-
-
- <developers>
- <developer>
- <id>mark</id>
- <name>Mark Davis</name>
- <organization>Google</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- <developer>
- <id>emmons</id>
- <name>John Emmons</name>
- <organization>IBM Corporation</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- <developer>
- <id>doug</id>
- <name>Doug Felt</name>
- <organization>Google</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- <developer>
- <id>deborah</id>
- <name>Deborah Goldsmith</name>
- <organization>Apple</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- <developer>
- <id>srl</id>
- <name>Steven Loomis</name>
- <organization>IBM Corporation</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- <developer>
- <id>markus</id>
- <name>Markus Scherer</name>
- <organization>Google</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- <developer>
- <id>yoshito</id>
- <name>Yoshito Umaoka</name>
- <organization>IBM Corporation</organization>
- <roles>
- <role>PMC Member</role>
- </roles>
- </developer>
- </developers>
-
- <mailingLists>
- <mailingList>
- <name>icu-support</name>
- <subscribe>https://lists.sourceforge.net/lists/listinfo/icu-support</subscribe>
- <unsubscribe>https://lists.sourceforge.net/lists/listinfo/icu-support</unsubscribe>
- <post>icu-support@lists.sourceforge.net</post>
- <archive>http://sourceforge.net/mailarchive/forum.php?forum_name=icu-support</archive>
- </mailingList>
- <mailingList>
- <name>icu-announce</name>
- <subscribe>https://lists.sourceforge.net/lists/listinfo/icu-announce</subscribe>
- <unsubscribe>https://lists.sourceforge.net/lists/listinfo/icu-announce</unsubscribe>
- <post>icu-announce@lists.sourceforge.net</post>
- <archive>http://sourceforge.net/mailarchive/forum.php?forum_name=icu-announce</archive>
- </mailingList>
- <mailingList>
- <name>icu-design</name>
- <subscribe>https://lists.sourceforge.net/lists/listinfo/icu-design</subscribe>
- <unsubscribe>https://lists.sourceforge.net/lists/listinfo/icu-design</unsubscribe>
- <post>icu-design@lists.sourceforge.net</post>
- <archive>http://sourceforge.net/mailarchive/forum.php?forum_name=icu-design</archive>
- </mailingList>
- </mailingLists>
-
- <scm>
- <connection>scm:svn:http://source.icu-project.org/repos/icu/icu4j/trunk/</connection>
- <developerConnection>scm:svn:http://source.icu-project.org/repos/icu/icu4j/trunk/</developerConnection>
- <url>http://source.icu-project.org/repos/icu/icu4j/trunk/</url>
- </scm>
- <issueManagement>
- <system>Trac</system>
- <url>http://bugs.icu-project.org/trac/</url>
- </issueManagement>
-
- <distributionManagement>
- <repository>
- <id>icu4j-releases</id>
- <name>ICU4J Central Repository</name>
- <url>http://oss.sonatype.org/service/local/staging/deploy/maven2</url>
- </repository>
- <snapshotRepository>
- <id>icu4j-snapshots</id>
- <name>ICU4J Central Development Repository</name>
- <url>http://oss.sonatype.org/content/repositories/snapshots</url>
- </snapshotRepository>
- </distributionManagement>
-
-</project>
diff --git a/lib/jena/iri.jar b/lib/jena/iri.jar
index 23830b7f7d57af33a71aef84d0c94d9a26111041..ef0ff7edb4132510f0afbec659f2b7792680a826 100644
Binary files a/lib/jena/iri.jar and b/lib/jena/iri.jar differ
diff --git a/lib/jena/iri.pom b/lib/jena/iri.pom
index 9430db55a86763f9ee96589148a538da73889111..0af55190b4a461f942d5faa5b4089b3ca323f453 100644
--- a/lib/jena/iri.pom
+++ b/lib/jena/iri.pom
@@ -3,7 +3,7 @@
<groupId>org.apache.jena</groupId>
<artifactId>jena-iri</artifactId>
- <version>0.9.0-incubating</version>
+ <version>1.0.0</version>
<name>IRI</name>
<packaging>jar</packaging>
<licenses>
diff --git a/lib/jena/jena.jar b/lib/jena/jena.jar
index b0068f30d92ad592f330c3e8fbc3080e1cfb36a4..c646971ecea3b2904376796706d485d4ea3d8141 100644
Binary files a/lib/jena/jena.jar and b/lib/jena/jena.jar differ
diff --git a/lib/jena/jena.pom b/lib/jena/jena.pom
index f644348c0d8b3d10669920dd4064d4420e9d5486..3ac98467764673ec6f3084916239c00b039fdc50 100644
--- a/lib/jena/jena.pom
+++ b/lib/jena/jena.pom
@@ -3,7 +3,7 @@
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
- <version>2.7.0-incubating</version>
+ <version>2.11.0</version>
<name>Jena core</name>
<description>Jena is a Java framework for building Semantic Web applications. It provides a programmatic environment for RDF, RDFS and OWL, SPARQL and includes a rule-based inference engine.</description>
<packaging>jar</packaging>
@@ -21,10 +21,6 @@
<!-- There is a decent pom in the Jar-file -->
<!--dependencies>
- <dependency>
- <groupId>com.ibm.icu</groupId>
- <artifactId>icu4j</artifactId>
- </dependency>
<dependency>
<groupId>org.apache.xml</groupId>
<artifactId>xml-apis</artifactId>
diff --git a/lib/owlapi30/owlapi-bin.jar b/lib/owlapi30/owlapi-bin.jar
index 700b27f724d6391dbfbc48043bc8c1fb30aa1062..ee93ec2e38a907bdc9efdd0524d081a32e2932b7 100644
Binary files a/lib/owlapi30/owlapi-bin.jar and b/lib/owlapi30/owlapi-bin.jar differ
diff --git a/lib/owlapi30/owlapi-bin.pom b/lib/owlapi30/owlapi-bin.pom
index f2aa49a5931b2c426773a5f3189d72b2ce0612e0..3595b352cb9e0c0c2ffb1358b2404bebfa80cdf1 100644
--- a/lib/owlapi30/owlapi-bin.pom
+++ b/lib/owlapi30/owlapi-bin.pom
@@ -3,7 +3,8 @@
<groupId>org.semanticweb</groupId>
<artifactId>owlapi</artifactId>
- <version>3.4.2</version>
+ <version>3.4.8</version>
+ <!-- version 3.4.9 is incomplete: jump to 3.4.10 -->
<name>OWL API</name>
<description>API and implementation for OWL</description>
<licenses>
diff --git a/lib/xerces/xercesImpl.jar b/lib/xerces/xercesImpl.jar
index 9dcd8c38196b24e51f78d8e1b0a42d1ffef60acb..0aaa990f3ecadf60d28b5395dc87bbe49da0cdd7 100644
Binary files a/lib/xerces/xercesImpl.jar and b/lib/xerces/xercesImpl.jar differ
diff --git a/lib/xerces/xercesImpl.pom b/lib/xerces/xercesImpl.pom
index 7044e16d25ee69af07961befdaf3df8192f9c1c7..3c765b93ef21a07595503a81caabddd95a99710a 100644
--- a/lib/xerces/xercesImpl.pom
+++ b/lib/xerces/xercesImpl.pom
@@ -3,7 +3,7 @@
<groupId>org.apache</groupId>
<artifactId>xerces</artifactId>
- <version>2.10.0</version>
+ <version>2.11.0</version>
<name></name>
<description></description>
<!-- Copyright 1999-2010 The Apache Software Foundation -->
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 6bfa373535f4fe36b082888153aee413a8f3fbb2..a3401f3b06d7550cb6d10951d9201236962f8748 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2006-2013
+ * Copyright (C) INRIA, 2006-2014
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -61,6 +61,9 @@ import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.AlignmentException;
import org.semanticweb.owl.align.Evaluator;
+import org.reflections.Reflections;
+import org.reflections.util.ConfigurationBuilder;
+
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -73,6 +76,7 @@ import java.lang.IllegalAccessException;
import java.lang.NullPointerException;
import java.lang.UnsatisfiedLinkError;
import java.lang.ExceptionInInitializerError;
+import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.io.ByteArrayOutputStream;
import java.io.InputStream;
@@ -104,7 +108,7 @@ import java.util.jar.JarEntry;
import java.util.zip.ZipEntry;
/**
- * This is the main class that control the behaviour of the Alignment Server
+ * This is the main class which controls the behaviour of the Alignment Server
* It is as independent from the OWL API as possible.
* However, it is still necessary to test for the reachability of an ontology and moreover to resolve its URI for that of its source.
* For these reasons we still need a parser of OWL files here.
@@ -461,11 +465,10 @@ public class AServProtocolManager implements Service {
new OutputStreamWriter( result, "UTF-8" )), true);
AlignmentVisitor renderer = null;
try {
- Object[] mparams = {(Object) writer };
- java.lang.reflect.Constructor[] rendererConstructors =
- Class.forName(method).getConstructors();
- renderer =
- (AlignmentVisitor) rendererConstructors[0].newInstance(mparams);
+ Class[] cparams = { PrintWriter.class };
+ Constructor rendererConstructor = Class.forName( method ).getConstructor( cparams );
+ Object[] mparams = { (Object)writer };
+ renderer = (AlignmentVisitor) rendererConstructor.newInstance( mparams );
} catch ( ClassNotFoundException cnfex ) {
// should return the message
logger.error( "Unknown method", cnfex );
@@ -684,12 +687,11 @@ public class AServProtocolManager implements Service {
if ( classname == null ) classname = "fr.inrialpes.exmo.align.impl.eval.PRecEvaluator";
Evaluator eval = null;
try {
- Object [] mparams = {(Object)ref, (Object)al};
- Class<?> oClass = Class.forName("org.semanticweb.owl.align.Alignment");
- Class[] cparams = { oClass, oClass };
- Class<?> evaluatorClass = Class.forName(classname);
- java.lang.reflect.Constructor evaluatorConstructor = evaluatorClass.getConstructor(cparams);
- eval = (Evaluator)evaluatorConstructor.newInstance(mparams);
+ Class[] cparams = { Alignment.class, Alignment.class };
+ Class<?> evaluatorClass = Class.forName( classname );
+ Constructor evaluatorConstructor = evaluatorClass.getConstructor( cparams );
+ Object [] mparams = { (Object)ref, (Object)al };
+ eval = (Evaluator)evaluatorConstructor.newInstance( mparams );
} catch ( ClassNotFoundException cnfex ) {
logger.error( "Unknown method", cnfex );
return new UnknownMethod(newId(),mess,serverId,mess.getSender(),classname,(Properties)null);
@@ -856,10 +858,51 @@ public class AServProtocolManager implements Service {
/*********************************************************************
* Utilities: Finding the implementation of an interface
+ *
+ * This is starting causing "java.lang.OutOfMemoryError: PermGen space"
+ * (when it was in static)
+ * Remedied (for the moment by improving the visited cache)
+ * This may also benefit by first filling the visited by the path of the
+ * libraries we know.
+ *
+ * May be replaced by org.reflections (see reflectiveImplementations)
+ * JE: Was unable to set it properly
*********************************************************************/
- public static void implementations( Class tosubclass, Set<String> list ){
+ /*
+ public Set<Class<?>> reflectiveImplementations( String interfaceName ) {
+ Set<Class<?>> classes = null;
+ try {
+ Class toclass = Class.forName( interfaceName );
+ //Reflections reflections = new Reflections("com.mycompany");
+ Reflections reflections = new Reflections( new ConfigurationBuilder() );
+ //Set<Class<? extends MyInterface>>
+ classes = reflections.getSubTypesOf(toclass);
+ } catch (ClassNotFoundException ex) {
+ logger.debug( "IGNORED Class {} not found!", interfaceName );
+ }
+ return classes;
+ }*/
+
+ /**
+ * Display all the classes inheriting or implementing a given
+ * interface in the currently loaded packages.
+ * @param interfaceName the name of the interface to implement
+ */
+ public Set<String> implementations( String interfaceName ) {
+ Set<String> list = new HashSet<String>();
+ try {
+ Class toclass = Class.forName(interfaceName);
+ implementations( toclass, list );
+ } catch (ClassNotFoundException ex) {
+ logger.debug( "IGNORED Class {} not found!", interfaceName );
+ }
+ return list;
+ }
+
+ public void implementations( Class tosubclass, Set<String> list ){
Set<String> visited = new HashSet<String>();
+ //visited.add();
String classPath = System.getProperty("java.class.path",".");
// Hack: this is not necessary
//classPath = classPath.substring(0,classPath.lastIndexOf(File.pathSeparatorChar));
@@ -889,32 +932,41 @@ public class AServProtocolManager implements Service {
}
}
}
- } else if ( file.toString().endsWith(".jar") &&
- !visited.contains( file.toString() ) &&
- file.exists() ) {
- //logger.trace("JAR {}", file);
- visited.add( file.toString() );
- JarFile jar = null;
+ } else {
+ String canon = null;
try {
- jar = new JarFile( file );
- exploreJar( list, visited, tosubclass, jar );
- // Iterate on needed Jarfiles
- // JE(caveat): this deals naively with Jar files,
- // in particular it does not deal with section'ed MANISFESTs
- Attributes mainAttributes = jar.getManifest().getMainAttributes();
- String path = mainAttributes.getValue( Name.CLASS_PATH );
- //logger.trace(" >CP> {}", path);
- if ( path != null && !path.equals("") ) {
- // JE: Not sure where to find the other Jars:
- // in the path or at the local place?
- //classPath += File.pathSeparator+file.getParent()+File.separator + path.replaceAll("[ \t]+",File.pathSeparator+file.getParent()+File.separator);
- // This replaces the replaceAll which is not tolerant on Windows in having "\" as a separator
- // Is there a way to make it iterable???
- for( StringTokenizer token = new StringTokenizer(path," \t"); token.hasMoreTokens(); )
- classPath += File.pathSeparator+file.getParent()+File.separator+token.nextToken();
+ canon = file.getCanonicalPath();
+ } catch ( IOException ioex ) {
+ canon = file.toString();
+ logger.warn( "IGNORED Invalid Jar path", ioex );
+ }
+ if ( canon.endsWith(".jar") &&
+ !visited.contains( canon ) &&
+ file.exists() ) {
+ //logger.trace("JAR {}", file);
+ visited.add( canon );
+ JarFile jar = null;
+ try {
+ jar = new JarFile( file );
+ exploreJar( list, visited, tosubclass, jar );
+ // Iterate on needed Jarfiles
+ // JE(caveat): this deals naively with Jar files,
+ // in particular it does not deal with section'ed MANISFESTs
+ Attributes mainAttributes = jar.getManifest().getMainAttributes();
+ String path = mainAttributes.getValue( Name.CLASS_PATH );
+ //logger.trace(" >CP> {}", path);
+ if ( path != null && !path.equals("") ) {
+ // JE: Not sure where to find the other Jars:
+ // in the path or at the local place?
+ //classPath += File.pathSeparator+file.getParent()+File.separator + path.replaceAll("[ \t]+",File.pathSeparator+file.getParent()+File.separator);
+ // This replaces the replaceAll which is not tolerant on Windows in having "\" as a separator
+ // Is there a way to make it iterable???
+ for( StringTokenizer token = new StringTokenizer(path," \t"); token.hasMoreTokens(); )
+ classPath += File.pathSeparator+file.getParent()+File.separator+token.nextToken();
+ }
+ } catch (NullPointerException nullexp) { //Raised by JarFile
+ //logger.trace( "JarFile, file {} unavailable", file );
}
- } catch (NullPointerException nullexp) { //Raised by JarFile
- //logger.trace( "JarFile, file {} unavailable", file );
}
}
} catch( IOException e ) {
@@ -928,7 +980,7 @@ public class AServProtocolManager implements Service {
}
}
- public static void exploreJar( Set<String> list, Set<String> visited, Class tosubclass, JarFile jar ) {
+ public void exploreJar( Set<String> list, Set<String> visited, Class tosubclass, JarFile jar ) {
Enumeration enumeration = jar.entries();
while( enumeration != null && enumeration.hasMoreElements() ){
JarEntry entry = (JarEntry)enumeration.nextElement();
@@ -944,38 +996,46 @@ public class AServProtocolManager implements Service {
if ( implementsInterface( entryName, tosubclass ) ) {
list.add( entryName );
}
- } else if( entryName.endsWith(".jar") &&
- !visited.contains( entryName ) ) { // a jar in a jar
- //logger.trace("JAR {}", entryName);
- visited.add( entryName );
- //logger.trace( "jarEntry is a jarfile={}", je.getName() );
- InputStream jarSt = null;
- OutputStream out = null;
- File f = null;
+ } else {
+ String canon = entryName;
try {
- jarSt = jar.getInputStream( (ZipEntry)entry );
- f = File.createTempFile( "aservTmpFile"+visited.size(), "jar" );
- out = new FileOutputStream( f );
- byte buf[]=new byte[1024];
- int len1 ;
- while( (len1 = jarSt.read(buf))>0 )
- out.write(buf,0,len1);
- JarFile inJar = new JarFile( f );
- exploreJar( list, visited, tosubclass, inJar );
- } catch (IOException ioex) {
- logger.warn( "IGNORED Cannot read embedded jar", ioex );
- } finally {
+ canon = new File( entryName ).getCanonicalPath();
+ } catch ( IOException ioex ) {
+ logger.warn( "IGNORED Invalid Jar path", ioex );
+ }
+ if( canon.endsWith(".jar") &&
+ !visited.contains( canon ) ) { // a jar in a jar
+ //logger.trace("JAR {}", entryName);
+ visited.add( canon );
+ //logger.trace( "jarEntry is a jarfile={}", je.getName() );
+ InputStream jarSt = null;
+ OutputStream out = null;
+ File f = null;
try {
- jarSt.close();
- out.close();
- f.delete();
- } catch (Exception ex) {};
+ jarSt = jar.getInputStream( (ZipEntry)entry );
+ f = File.createTempFile( "aservTmpFile"+visited.size(), "jar" );
+ out = new FileOutputStream( f );
+ byte buf[]=new byte[1024];
+ int len1 ;
+ while( (len1 = jarSt.read(buf))>0 )
+ out.write(buf,0,len1);
+ JarFile inJar = new JarFile( f );
+ exploreJar( list, visited, tosubclass, inJar );
+ } catch (IOException ioex) {
+ logger.warn( "IGNORED Cannot read embedded jar", ioex );
+ } finally {
+ try {
+ jarSt.close();
+ out.close();
+ f.delete();
+ } catch (Exception ex) {};
+ }
}
}
}
}
- public static boolean implementsInterface( String classname, Class tosubclass ) {
+ public boolean implementsInterface( String classname, Class tosubclass ) {
try {
if ( classname.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ||
classname.equals("org.apache.log4j.net.ZeroConfSupport")
@@ -1006,27 +1066,6 @@ public class AServProtocolManager implements Service {
return false;
}
- /**
- * Display all the classes inheriting or implementing a given
- * interface in the currently loaded packages.
- * @param interfaceName the name of the interface to implement
- */
- public static Set<String> implementations( String interfaceName ) {
- Set<String> list = new HashSet<String>();
- try {
- Class toclass = Class.forName(interfaceName);
- //Package [] pcks = Package.getPackages();
- //for (int i=0;i<pcks.length;i++) {
- //logger.trace(interfaceName+ ">> "+pcks[i].getName() );
- //implementations( pcks[i].getName(), toclass, list );
- //}
- implementations( toclass, list );
- } catch (ClassNotFoundException ex) {
- logger.debug( "IGNORED Class {} not found!", interfaceName );
- }
- return list;
- }
-
protected class Aligner implements Runnable {
private Message mess = null;
private Message result = null;
@@ -1075,13 +1114,13 @@ public class AServProtocolManager implements Service {
// Create alignment object
try {
- Object[] mparams = {};
if ( method == null )
method = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
Class<?> alignmentClass = Class.forName(method);
Class[] cparams = {};
- java.lang.reflect.Constructor alignmentConstructor = alignmentClass.getConstructor(cparams);
- AlignmentProcess aresult = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
+ Constructor alignmentConstructor = alignmentClass.getConstructor( cparams );
+ Object[] mparams = {};
+ AlignmentProcess aresult = (AlignmentProcess)alignmentConstructor.newInstance( mparams );
try {
aresult.init( uri1, uri2 );
long time = System.currentTimeMillis();
diff --git a/test/clitest.sh b/test/clitest.sh
index eed6d1ce69f53391b52c2e5b73bcb71c9a20894e..e4cdd098476d2a80bdbfec1ba81ffabd068d6b13 100644
--- a/test/clitest.sh
+++ b/test/clitest.sh
@@ -993,12 +993,13 @@ kill -TERM $!
#-------------------
echo "\t-A,--jade <PORT>"
-java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -A 5555 &> $RESDIR/err.txt &
+echo "\tOnly works with increased PermGenSize"
+java -XX:PermSize=128m -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -A 5555 &> $RESDIR/err.txt &
sleep 20;
if [ -s $RESDIR/err.txt ]; then grep "is ready" $RESDIR/err.txt > $RESDIR/jerr.txt; else echo error with ASERV-JADE1; fi
if [ ! -s $RESDIR/jerr.txt ]; then echo error with ASERV-JADE2; fi
kill -TERM $!
-java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --jade 5555 &> $RESDIR/err.txt &
+java -XX:PermSize=128m -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --jade 5555 &> $RESDIR/err.txt &
sleep 20;
if [ -s $RESDIR/err.txt ]; then grep "is ready" $RESDIR/err.txt > $RESDIR/jerr.txt; else echo error with ASERV-JADE3; fi
if [ ! -s $RESDIR/jerr.txt ]; then echo error with ASERV-JADE4; fi