NoSuchMehodError in Reactor.setReaction()

I got this error while trying to run Reactor.setReaction().  It is new since we started using JChem 5.2.1.

java.lang.NoSuchMethodError: org.w3c.dom.Node.getTextContent()Ljava/lang/String;

        at chemaxon.jep.EvaluatorConfiguration.getTextContentsOfNodes(EvaluatorConfiguration.java:636)

        at chemaxon.jep.EvaluatorConfiguration.getFuntab(EvaluatorConfiguration.java:276)

        at chemaxon.jep.Evaluator.compile(Evaluator.java:775)

        at chemaxon.jep.Evaluator.compile(Evaluator.java:743)

        at chemaxon.reaction.Reaction.setReactivityRule(Reaction.java:587)

        at chemaxon.reaction.Reactor.createReactionObject(Reactor.java:1301)

        at chemaxon.reaction.Reactor.createReactionObject(Reactor.java:1245)

        at chemaxon.reaction.Reactor.createReactionObject(Reactor.java:1201)

        at chemaxon.reaction.Reactor.setReaction(Reactor.java:1026)

        at chemaxon.reaction.Reactor.setReaction(Reactor.java:1008)

        at com.prenhall.epoch.synthesis.SingleReactionSolver.calcProducts(SingleReactionSolver.java:164)

Bob, please update your Java Virtual Machine to 1.5 version or later.

Zsolt

We are already running Java 1.5.

[bob@epoch synthesis]$ java -version

java version "1.5.0_02"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_02-b09)

Java HotSpot(TM) Client VM (build 1.5.0_02-b09, mixed mode, sharing)

Refoyl wrote:

Neither of these two jars are required by chemaxon.jep.EvaluatorConfiguration class. org.w3c.dom.Node is part of JDK, and it contains the org.w3c.dom.Node.getTextContent() method since Java 1.5.

Please post your

- operating system version
- content of your classpath (result of "echo $CLASSPATH")

It seems to be a classpath problem.

Zsolt

Any insights here?  Reactor is completely inoperable until this problems is solved.

We did not have this problem until we upgraded to JChem 5.2.1 (from JChem 5.1.5).

/usr/local/java/jre/lib/rt.jar should contain org.w3c.dom.Node.

Please run the Evaluator command line tool:

evaluate -e "mass()" "CCCCC"

If the same exception is thrown as before, then try the following:

1. Delete batik-core.jar and xerces.jar, and run the reactor again. Let us know what happens.

2. Uninstall the JChem package, install MarvinBeans 5.2.1.1, run Evaluator again, and let us know the result.

Zsolt

Not exactly the same exception, but an exception nonetheless:

[bob@epoch bob]$ evaluate -e "mass()" "CCCCC"

Exception in thread "main" chemaxon.nfunk.jep.ParseException: chemaxon.jep.function.TotalCharge

	at chemaxon.jep.EvaluatorConfiguration.getFuntab(EvaluatorConfiguration.java:297)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:779)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:743)

	at chemaxon.jep.Evaluator.main(Evaluator.java:1047)

Caused by:

java.lang.ClassNotFoundException: chemaxon.jep.function.TotalCharge

	at java.net.URLClassLoader$1.run(URLClassLoader.java:200)

	at java.security.AccessController.doPrivileged(Native Method)

	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)

	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)

	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)

	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

	at java.lang.Class.forName0(Native Method)

	at java.lang.Class.forName(Class.java:164)

	at chemaxon.jep.EvaluatorConfiguration.getFuntab(EvaluatorConfiguration.java:278)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:779)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:743)

	at chemaxon.jep.Evaluator.main(Evaluator.java:1047)

[bob@epoch aceorg]$ ~aceorg/aceorg/jchem5.1.05/bin/evaluate -e "mass()" "CCCCC"

72.15

evaluate in MarvinBeans 5.2.1.1 works properly.

[bob@epoch aceorg]$ /tmp/new/bin/evaluate -e "mass()" "CCCCC" 

72.15

[bob@epoch bob]$ evaluate -e "mass()" "CCCCC"

Exception in thread "main" chemaxon.nfunk.jep.ParseException: chemaxon.jep.function.TotalCharge

	at chemaxon.jep.EvaluatorConfiguration.getFuntab(EvaluatorConfiguration.java:297)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:779)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:743)

	at chemaxon.jep.Evaluator.main(Evaluator.java:1047)

Caused by:

java.lang.ClassNotFoundException: chemaxon.jep.function.TotalCharge

	at java.net.URLClassLoader$1.run(URLClassLoader.java:200)

	at java.security.AccessController.doPrivileged(Native Method)

	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)

	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)

	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)

	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

	at java.lang.Class.forName0(Native Method)

	at java.lang.Class.forName(Class.java:164)

	at chemaxon.jep.EvaluatorConfiguration.getFuntab(EvaluatorConfiguration.java:278)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:779)

	at chemaxon.jep.Evaluator.compile(Evaluator.java:743)

	at chemaxon.jep.Evaluator.main(Evaluator.java:1047)

This exception indicates a completely different error.

As I know you define your own Chemical Terms functions (like dynamicpKa()) in the evaluator.xml config file (see the Default function definitions, plugin definitions and matching conditions section in the Evaluator manual). From Marvin/JChem 5.1.1 version the exaluator.xml files defined by the users should only contain the functions defined by the users, and not all of the functions. I think there is a

<Function ID="totalCharge" Class="chemaxon.jep.function.TotalCharge"/>

line in one of your evaluator.xml config files, and it is causing this (the second) error. Please remove your evaluator.xml files from the marvin/config, jchem/config and .chemaxon/MARVIN_MAJOR_VERSION/ directories (MARVIN_MAJOR_VERSION is the major version of Marvin, e.g. "5.1") and run the reactor and evaluator again (with removed batik-core.jar and xerces.jar).

Do you get the original exception only on epoch.chem.uky.edu?

Zsolt

After removing the configuration files from JChem 5.2.1:

[bob@epoch aceorg]$ bin/evaluate -e "mass()" "CCCCC"

72.15

This is with batik-core.jar and xerces.jar in OR out of the lib directory.  

However, I am still getting the NoSuchMethodError when I use the API, regardless of whether batik-core.jar and xerces.jar are in or out of the lib directory.

What next?

bobgr wrote:

Do you get the exception when you run Reactor GUI, or Reactor command line application?

Do you get the original exception only on epoch.chem.uky.edu?

Zsolt

I get it when I run the Reactor GUI.  

From the command line, it appears to work fine, even when using an MRV file as the reaction definition.  (I created the MRV file by converting your example RDF file to MRV.)

[bob@epoch bin]$ react -r "[Cl:4][C:3]=O.[#7:2][H:1]>>[#7:2][C:3]=O.[Cl:4][H:1]..r:charge(ratom(4)) > -1.2" "CCCC(Cl)=O" "NCCC1CCCCC1" -x 1

CCCC(=O)NCCC1CCCCC1

[bob@epoch bin]$ react -r ../examples/reactor/acid-halide+nucleophile.rdf "CCCC(Cl)=O" "NCCC1CCCCC1"     

Cl

CCCC(=O)NCCC1CCCCC1

[bob@epoch bin]$ react -r ../examples/reactor/acid-halide+nucleophile.mrv "CCCC(Cl)=O" "NCCC1CCCCC1"

Cl

CCCC(=O)NCCC1CCCCC1

Oh, and I don't know what you mean by do we get the exception only on epoch.chem.uky.edu.  We don't have any other server that runs ACE with JChem 5.2.1.  We did not get the error when we ran ACE with JChem 5.1.5 on epoch.chem.uky.edu.  The problem is not in ACE or Tomcat per se, it's in a clash between some part of JChem new to 5.2.1 and some part of ACE or Tomcat.

Bob, please run your application from command line with java -verbose:class option.

Example:

$ java -verbose:class chemaxon.jep.Evaluator -e "logP()" "CCCCCC"
[Loaded java.lang.Object from shared objects file]
[Loaded java.io.Serializable from shared objects file]
[Loaded java.lang.Comparable from shared objects file]
[Loaded java.lang.CharSequence from shared objects file]
[Loaded java.lang.String from shared objects file]
...

It will display all java classes loaded by the JVM. My example runs the Evaluator class with its command line options. Maybe you have to modify your application before you can do this (add a main() method, etc.).

Filter the messages with grep:

$ java -verbose:class chemaxon.jep.Evaluator -e "logP()" "CCCCCC" | grep org.w3c.dom.Node
[Loaded org.w3c.dom.Node from shared objects file]
[Loaded org.w3c.dom.NodeList from shared objects file]

This will be a short list; loaded org.w3c.dom.Node* classes will be listed only.

Zsolt

From which directory do I run this application?  I tried it from jchem/bin and got this message:

[bob@epoch bin]$ java -verbose:class chemaxon.jep.Evaluator -e "logP()" "CCCCCC" | grep org.w3c.dom.Node

Exception in thread "main" java.lang.NoClassDefFoundError: chemaxon/jep/Evaluator

From the directory where jchem.jar is located. It is jchem/lib.

Zsolt

Houston, we have a problem.

[bob@epoch jchem5.2.1]$ cd lib

[bob@epoch lib]$ java -verbose:class chemaxon.jep.Evaluator -e "logP()" "CCCCCC" | grep org.w3c.dom.Node

Exception in thread "main" java.lang.NoClassDefFoundError: chemaxon/jep/Evaluator

[bob@epoch lib]$ ls

aloe.jar                          inchi-native-macosx-ppc-1_1.jar

backport-util-concurrent.jar      inchi-native-windows-1_1.jar

batik-core.jar                    izmcomjni.jar

castor-1.0.1-xml.jar              izmcom-natives.jar

chart.jar                         izmcomtlb.jar

commons-lang-2.4.jar              jar.properties

commons-logging-1.1.jar           jchem.jar

db2jcc.jar                        jextexp.jar

dom4j.jar                         jh.jar

forms-1.1.0.jar                   jnbtools.jar

freehep-export-2.1.1.jar          jogl_1.1.0-rc2

freehep-graphics2d-2.1.1.jar      jogl.jar

freehep-graphicsio-2.1.1.jar      looks-2.1.4.jar

freehep-graphicsio-emf-2.1.1.jar  marvinOLEServer.exe

freehep-graphicsio-pdf-2.1.1.jar  marvinOLEServer-native.jar

freehep-io-2.0.2.jar              mysql-connector-java-5.1.6-bin.jar

freehep-swing-2.0.3.jar           ojdbc5.jar

freehep-util-2.0.2.jar            openide-lookup-1.9-patched-1.0.jar

gluegen-rt.jar                    postgresql-8.3-603.jdbc3.jar

hsqldb.jar                        sqljdbc.jar

inchi-native-linux-1_1.jar        xerces.jar

inchi-native-macosx-1_1.jar

[bob@epoch lib]$ 

jchem.jar has to be in the CLASSPATH, or should be specified with the -classpath option.

$ java -classpath jchem.jar -verbose:class chemaxon.jep.Evaluator -e "logP()" "CCCCCC" | grep org.w3c.dom.Node
[Loaded org.w3c.dom.Node from shared objects file]
[Loaded org.w3c.dom.NodeList from shared objects file]

Zsolt

I'm a Linux novice, so you have to spell these things out for me.

[bob@epoch lib]$ java -classpath jchem.jar -verbose:class chemaxon.jep.Evaluator -e "logP()" "CCCCCC" | grep org.w3c.dom.Node

[Loaded org.w3c.dom.Node from shared objects file]

[Loaded org.w3c.dom.NodeList from shared objects file]

[bob@epoch lib]$ 

I also did the one without the grep option at the end, and I got a ridiculously large amount of output.  Do you want to see it also?

After our skype discussion I discussed this problem with one of my colleagues. He will send you the information how you can check the CLASSPATH used by your web application (this classpath is set by Tomcat), and will describe how Tomcat can be configured to log the loaded classes.

The browser thing will not work (I was wrong when I suggested this), web application runs on server.

Zsolt

Hi,

The Tomcat uses its own classloader and classpath to running a web application. In this case your system classpath will not be valid, you have to care about that your jar files are in the Tomcat's lib directory. The contents of the lib directory are got into the Tomcat's classpath automatically.

You can use two different lib directory; the fist one is a global for all web application (it is placed in <Tomcat home>/shared/lib in Tomcat 5.5. or <Tomcat home>/lib in Tomcat 6.0), the second one is relevant with the specified application. I recommend to take your library elements to the application's library (<Tomcat's root>/webapps/<appname>/WEB-INF/lib), elements in this directory will come before the global elements in the Tomcat's classpath.
I hope it can help you.

Regards, Evard

Tomcat also picks up jar files from two WEB-INF library directories. The first contains

LewisSketch.jar@ bb-persistence-layer.jar@ dom4j.jar jchem.jar@

The second contains only jchem.jar@. The symlinks point to jchem5.2.1/lib.

None of these jar files contains w3c code. Only batik.jar and xerces.jar contain w3c code.

Does this discussion help?

http://www.velocityreviews.com/forums/t144510-problems-with-jboss-an-xerces.html

Or this comment from http://nicklothian.com/blog/index.php?s=string ?

Getting this error in Tomcat?
java.lang.NoSuchMethodError: org.w3c.dom.Node.getTextContent()Ljava/lang/String;
There’s a good chance you installed Tomcat with the JDK 1.4 Compatibility package and are now running under JDK 5.
To fix it, delete xercesImpl.jar, xml-apis.jar and xalan.jar from $CATALINA_HOME\common\endorsed\

Yes, this helps. You should check your Tomcat installation.

Zsolt

What do you mean, "check your Tomcat installation"?  Please be more specific about what exactly we need to check.

And let me say this once more: We did not get any of these errors when we were running JChem 5.1.  These errors only started when we started running JChem 5.2.  All that changed in switching from JChem 5.1 to JChem 5.2 was moving a symlink to point to JChem 5.2 instead of JChem 5.1.  The unavoidable conclusion is that something new in JChem 5.2 is clashing with our installation.  It would be much appreciated if you tried to figure out what new feature in JChem 5.2 is clashing with our installation, instead of just trying to blame our installation for the problem.

JChem 5.1 was Java 1.4.2 compatible, but JChem 5.2 requires Java 1.5 or later.

We try to help. Please check your Tomcat installation, because "There’s a good chance you installed Tomcat with the JDK 1.4 Compatibility package and are now running under JDK 5.". I'm not too familiar with Tomcat, so Edvard will get back to you and will help to diagnose Tomcat related issues.

Zsolt

I believe we did indeed install Tomcat under Java 1.4 and later upgraded to Java 1.5.

I found xercesImpl.jar and xml-apis.jar in tomcat5/common/endorsed/ .  I moved them into tomcat5/common/oldEndorsed/ .  But then I was unable to shut down Tomcat cleanly; I got this error:

java.lang.reflect.InvocationTargetException

        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:585)

        at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:336)

        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:427)

Caused by: javax.xml.parsers.FactoryConfigurationError: Provider org.apache.xerces.jaxp.SAXParserFactoryImpl not found

        at javax.xml.parsers.SAXParserFactory.newInstance(SAXParserFactory.java:113)

        at org.apache.commons.digester.Digester.getFactory(Digester.java:512)

        at org.apache.commons.digester.Digester.getParser(Digester.java:686)

        at org.apache.commons.digester.Digester.getXMLReader(Digester.java:902)

        at org.apache.commons.digester.Digester.parse(Digester.java:1548)

        at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:399)

        ... 6 more

I downloaded newer versions of xercesImpl.jar (2.9.0 instead of 2.6.2) and xml-apis.jar from www.java2s.com and placed them in common/endorsed.  I restarted Tomcat, and everything appears to work now.