Re: [Opaltoolkit-users] Cannot run date test service with Opal 2.5 (Error during database update: c

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

Hey,
You should try to look into the catalina.log file for more clues into why
it is throwing that error.

Luca

On Jun 14, 2017 2:56 PM, "Alex Reynolds" <ale...@gm...> wrote:

> Hello,
>
> My larger goal is to install MEME web services. However, I am having great
> difficulty getting Opal 2.5 working with the test services contained within
> Opal itself, which is also causing downstream problems with MEME.
>
> I'm hoping anyone might see this and would be able to help out.
>
> My host is a Centos 7 box.
>
> I am running JDK 1.8.0_131-b12:
>
> $ java -version
> openjdk version "1.8.0_131"
> OpenJDK Runtime Environment (build 1.8.0_131-b12)
> OpenJDK 64-Bit Server VM (build 25.131-b12, mixed mode)
>
> I have a Tomcat 7.0.69 installation running. This otherwise appears to
> work properly. I can start, stop and restart this service and view it in a
> web browser.
>
> I downloaded and compiled Opal 2.5 from here:
>
> https://sourceforge.net/projects/opaltoolkit/files/
>
> Specifically, opal-ws-2.5.tar.gz.
>
> I went through installation instructions here:
>
> http://rocce-vm0.ucsd.edu/data/docs/opal/docs/2.X/clientsetup.html#AEN305
>
> I copied the date_config.xml file from $OPAL_HOME/configs/date_config.xml
> to $CATALINA_HOME/deploy/date.xml
>
> Per documentation, I tried to run the date service to test that the Opal
> setup is working correctly. This is where things fail.
>
> This are the commands I used:
>
> $ source etc/classpath.sh
> ...
> $ java edu.sdsc.nbcr.opal.GenericServiceClient -l
> http://myhost:8080/opal2/services/date -r launchJob -a \""-v1d -v3m -v0y
> -v-1d -u"\"
>
> I get the following error from running this command:
>
> Reading command line arguments
> Service URL: http://myhost:8080/opal2/services/date
> Invoking operation: launchJob
>
> Command line arguments: -v1d -v3m -v0y -v-1d -u
> Making non-blocking invocation on Opal service -
> Exception in thread "main" AxisFault
>  faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.
> generalException
>  faultSubcode:
>  faultString:
>  faultActor:
>  faultNode:
>  faultDetail:
>         {http://nbcr.sdsc.edu/opal/types}opalFaultOutput:<message>Error
> during database update: could not insert: [edu.sdsc.nbcr.opal.state.
> JobInfo]</message>
>         {http://xml.apache.org/axis/}exceptionName:edu.sdsc.nbcr.
> opal.FaultType
>         {http://xml.apache.org/axis/}hostname:tools0.altiusinstitute.org
>
>
>         at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
>         at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> NativeConstructorAccessorImpl.java:62)
>         at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> DelegatingConstructorAccessorImpl.java:45)
>         at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
>         at java.lang.Class.newInstance(Class.java:442)
>         at org.apache.axis.encoding.ser.BeanDeserializer.<init>(
> BeanDeserializer.java:104)
>         at org.apache.axis.encoding.ser.BeanDeserializer.<init>(
> BeanDeserializer.java:90)
>         at edu.sdsc.nbcr.opal.FaultType.getDeserializer(FaultType.
> java:114)
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(
> NativeMethodAccessorImpl.java:62)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at org.apache.axis.encoding.ser.BaseDeserializerFactory.
> getSpecialized(BaseDeserializerFactory.java:154)
>         at org.apache.axis.encoding.ser.BaseDeserializerFactory.
> getDeserializerAs(BaseDeserializerFactory.java:84)
>         at org.apache.axis.encoding.DeserializationContext.
> getDeserializer(DeserializationContext.java:464)
>         at org.apache.axis.encoding.DeserializationContext.
> getDeserializerForType(DeserializationContext.java:547)
>         at org.apache.axis.message.SOAPFaultDetailsBuilder.onStartChild(
> SOAPFaultDetailsBuilder.java:157)
>         at org.apache.axis.encoding.DeserializationContext.startElement(
> DeserializationContext.java:1035)
>         at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
> Source)
>         at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown
> Source)
>         at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl
> $FragmentContentDispatcher.dispatch(Unknown Source)
>         at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
> Source)
>         at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
> Source)
>         at org.apache.xerces.parsers.XML11Configuration.parse(Unknown
> Source)
>         at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>         at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown
> Source)
>         at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
>         at org.apache.axis.encoding.DeserializationContext.parse(
> DeserializationContext.java:227)
>         at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
>         at org.apache.axis.Message.getSOAPEnvelope(Message.java:424)
>         at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(
> MustUnderstandChecker.java:62)
>         at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
>         at org.apache.axis.client.Call.invokeEngine(Call.java:2765)
>         at org.apache.axis.client.Call.invoke(Call.java:2748)
>         at org.apache.axis.client.Call.invoke(Call.java:2424)
>         at org.apache.axis.client.Call.invoke(Call.java:2347)
>         at org.apache.axis.client.Call.invoke(Call.java:1804)
>         at edu.sdsc.nbcr.opal.AppServicePortTypeSoapBindingStub.launchJob(
> AppServicePortTypeSoapBindingStub.java:624)
>         at edu.sdsc.nbcr.opal.GenericServiceClient.main(
> GenericServiceClient.java:359)
>
> I double-checked the permissions on the database folder here:
>
> $ ls -al $CATALINA_HOME/webapps/opal2/WEB-INF/data
>
> All "opaldb*" files are owned by the "tomcat" user and are read-write-able
> by this and all users.
>
> Is there a way to fix this?
>
> Thanks in advance for any guidance!
>
> Regards,
> Alex
>
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Re: [Opaltoolkit-users] Cannot run date test service with Opal 2.5 (Error during database update: c

Re: [Opaltoolkit-users] Cannot run date test service with Opal 2.5 (Error during database update: could not insert)