[Cdk-user] Problems runnint CDK 'ant run' & running CDK-taverna

[nikolaus . stiefl]

Hi,

I am new to CDK as well as java. After installing Java 1.5, ant 1.6.5, taverna, CDK (release 20050826), cdk-taverna (release 20051018) on my RedHat box (Enterprise 3.0), I have the following problems:


1. When running 'ant run' I get the follwing error message:

        ______________
       
        dist.init:

        compile-needed-test:

        compile-module:

        run:
                [java] Exception in thread "main" java.lang.NoClassDefFoundError: org/openscience/cdk/applications/FileConvertor

        ______________

I don't know if this is something serious but I woudl have expected this script to work ...



2. After installing taverna (no proxys enabled) and copying the cdk-taverna.jar and cdk.jar to the lib directory I am not able to start a simple 'parse smile' workflow. I get the following error

        __________________________

        ERROR                                      2005-11-23 16:50:31,433 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfDefinition
        ERROR                                      2005-11-23 16:50:31,443 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfDefinition
        ERROR                                      2005-11-23 16:50:31,444 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfDefinition
        ERROR                                      2005-11-23 16:50:31,449 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfInstance
        ERROR                                      2005-11-23 16:50:31,450 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfDefinition
        ERROR                                      2005-11-23 16:50:31,453 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfDefinition
        ERROR                                      2005-11-23 16:50:31,453 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type wfDefinition
        [EMAIL PROTECTED] :: Event reporting re-enabled, forcing update
        [EMAIL PROTECTED] :: Event reporting re-enabled, forcing update
        ERROR                                      2005-11-23 16:50:31,516 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type dataItem
        ERROR                                      2005-11-23 16:50:31,516 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type dataItem
        ERROR                                      2005-11-23 16:50:31,517 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type dataItem
        ERROR                                      2005-11-23 16:50:31,518 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type dataItem
        ERROR                                      2005-11-23 16:50:31,518 (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping found for namespace type dataItem
        uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException
                at org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerTask.execute(APIConsumerTask.java:192)
                at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:462)
                at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:407)
                at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:329)
                at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:521)
                at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:261)
                at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:199)
                at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
        Caused by: 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.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerTask.execute(APIConsumerTask.java:189)
                ... 7 more
        Caused by: java.lang.NoSuchMethodError: org.openscience.cdk.AtomContainer.addAtom(Lorg/openscience/cdk/interfaces/Atom;)V
                at org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules(ConnectivityChecker.java:117)
                at org.openscience.cdk.tools.HydrogenAdder.addImplicitHydrogensToSatisfyValency(HydrogenAdder.java:280)
                at org.openscience.cdk.smiles.SmilesParser.parseSmiles(SmilesParser.java:326)
                at org.openscience.cdk.applications.taverna.smiles.SmilesTools.parseSMILES(SmilesTools.java:46)
                ... 12 more
        ERROR                                      2005-11-23 16:50:31,520 (uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask:222)                                                                                                 -uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException
        Getting results...

        ___________________________

Now, I don't if this is due to my settings (environment variables etc.) since I am still new to the java world. It seems a bit like it since it deosn't find very simple functionalities (addAtom). Probably it's just some kind of environment variable that I am missing here :-(

Any comments on this will be greatly appreciated.

Thanks a lot in advance,
Nik