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

[Alex R. <ale...@gm...>]

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