Pipeline problem when testing release xnat_1_4rc4

[Mélanie]

Dear all,

I've just installed Xnat Release 1_4rc4 on a fresh CentOS 5.4
distribution, in my $HOME directory.

I have
** java version "1.6.0"
OpenJDK Runtime Environment (build 1.6.0-b09)
OpenJDK Server VM (build 1.6.0-b09, mixed mode)

** Apache Tomcat/5.5.23

** PostgreSQL 8.1.18

Installation went OK thanks to the tutorial http://nrg.wikispaces.com/XNAT_Source
I've downloaded sample1.zip example dataset and tried to upload the
data in the database, that's where things went wrong.

Apparently I managed to upload the data in the prearchive location.
Then the transfer to archive starts but fails. I've looked in the
pipeline logs and here is what I got (any idea would be helpful)...

FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldnt
search for queued workflows
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}
Server.userException
faultSubcode:
faultString: java.lang.RuntimeException: No compiler found in your
classpath! (you may need to add 'tools.jar')
faultActor:
faultNode:
faultDetail:
{http://xml.apache.org/axis/}hostname:MY.HOST.NAME

java.lang.RuntimeException: No compiler found in your classpath! (you
may need to add 'tools.jar')
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:
222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:
129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:
1087)
at
org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
at
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(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.DTDConfiguration.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(Unknown Source)
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:435)
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:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.apache.axis.client.Call.invoke(Call.java:1812)
at
org.nrg.xnattools.xml.AbsService.createServiceSession(AbsService.java:
100)
at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:
97)
at
org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:
120)
at
org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:
45)
at
org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:
264)
INFO main org.nrg.pipeline.utils.PipelineUtils - Loop Resolved
INFO main org.nrg.pipeline.utils.PipelineUtils - Parameter Resolved
INFO main org.nrg.pipeline.utils.PipelineUtils - Output resolved
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/ant-tools/AntCopy.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/ant-tools/AntCopy.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/images/resources/WebBasedQCImageCreator.xml
DEBUG main org.nrg.pipeline.task.StepManager - Couldnt resolve xpath
expression on base document. Will try on the internal rep ^/Pipeline/
paramete
rs/parameter[name='pwd']/values/unique/text()^
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/images/resources/WebBasedQCImageCreator.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/ant-tools/AntMove.xml
INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/notifications/Notifier.xml
INFO main org.nrg.pipeline.manager.ResourceManager - Loaded $HOME/xnat/
pipeline/catalog/notifications/Notifier.xml
INFO main org.nrg.pipeline.manager.ExecutionManager - Launching step 0
FATAL main org.nrg.pipeline.client.XNATPipelineLauncher -
java.lang.RuntimeException: No compiler found in your classpath! (you
may need to add '
tools.jar')

[Timothy Olsen]

Is the java version for this OS user account a JDK? Per WIKI instructions, XNAT requires the JDK version of java (rather than just the JRE).

Tim

Dear all,

** Apache Tomcat/5.5.23

** PostgreSQL 8.1.18

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[Mélanie]

The standard java for this OS is JRE 1.4, so I had to find an update
(jdk-6u18-linux-i586-rpm.bin) .
My JAVA_HOME is /usr/java/jdk1.6.0_18
But maybe I have something wrong with my java config anyway ???

I have checked through tomcat manager interface that I am indeed using
the 1.6.0-b09 version.

Melanie

[Mohana Ramaratnam]

Melanie,

Please check your PATH environment variable to see that the java executable points to jdk<version>/bin

Mohana

[Mélanie]

OK, my java executable was
/usr/lib/jvm/jre-1.6.0-openjdk/bin/java
So it was in fact just a JRE :-(

I think I found where the problem was... It's a mess with the default
installation of tomcat5.

My tomcat5 installation comes with the CentOS package. It uses by
default the java in /usr/lib/jvm (which I installed with the OS
package update yum system), which here is jre-1.6.0-openjdk (so, just
a JRE if I understand it correctly).

I then also installed separately a JDK package from jdk-6u18-linux-
i586-rpm.bin, which is in /usr/java/latest (jdk1.6.0_18)
java version "1.6.0_18"
Java(TM) SE Runtime Environment (build 1.6.0_18-b07)
Java HotSpot(TM) Server VM (build 16.0-b13, mixed mode)

I set my JAVA_HOME to /usr/java/latest/bin/java (so then I use a JDK).
But tomcat5 did not use it.
I linked /usr/lib/jvm/java to /usr/java/latest and restarted tomcat5.
I checked from Apache manager interface that tomcat5 was now using JDK
1.6.0_18-b07.

I uploaded again the sample data and now the transfer to the archive
directory was successful (I received a confirming email).
I can see the data (and the snapshots) in the archive directory.

Thanks for your help, I think my problem is solved for now :-D

Melanie