[Topaz-dev] serializing Article from Session.get()
Russell Uman
ruman at plos.org
Tue Mar 11 17:40:45 PDT 2008
tried it. patched fine.
i got new and interesting errors!
we're still only able to share a single key between caches (the
Annotation-info key) out of the 3 that are generated on
fetchArticle.action.
i noticed that you added a logger to Session.java. i upped logging for
org.topazproject to debug, but i did not see its log message after
fetchArticle.
[root at topaz01-multi ~]# grep "Serializable replacement"
/var/log/topaz/plosone.log
[root at topaz01-multi ~]#
here's what i did get:
2008-03-11 17:29:08,013 WARN RMIAsynchronousCacheReplicator()> Unable
to send message to remote peer. Message was: error performing query:
select $s $p $o\
subquery (select $t from <local:///topazproject#filter:model=profiles>
where $o <rdf:type> $t) from <local:///topazproject#filter:model=ri>
where $s $p $o \
and $s <mulgara:is>
<info:doi/10.1371/journal.pone.0000581/bibliographicCitation>; select $s
$p $o subquery (select $t from <local:///topazproject#filter:mo\
del=ri> where $s <rdf:type> $t) from
<local:///topazproject#filter:model=ri> where $s $p $o and $o
<mulgara:is> <info:doi/10.1371/journal.pone.0000581/bibli\
ographicCitation>; [Replication Thread
net.sf.ehcache.distribution.RMIAsynchronousCacheReplicator]
org.topazproject.otm.OtmException: error performing query: select $s $p
$o subquery (select $t from
<local:///topazproject#filter:model=profiles> where $o <\
rdf:type> $t) from <local:///topazproject#filter:model=ri> where $s $p
$o and $s <mulgara:is>
<info:doi/10.1371/journal.pone.0000581/bibliographicCitation>;\
select $s $p $o subquery (select $t from
<local:///topazproject#filter:model=ri> where $s <rdf:type> $t) from
<local:///topazproject#filter:model=ri> where\
$s $p $o and $o <mulgara:is>
<info:doi/10.1371/journal.pone.0000581/bibliographicCitation>;
at org.topazproject.otm.stores.ItqlStore.get(ItqlStore.java:333)
at org.topazproject.otm.Session.getFromStore(Session.java:596)
at org.topazproject.otm.Session.access$100(Session.java:45)
at org.topazproject.otm.Session$1.invoke(Session.java:736)
at
org.plos.models.Citation_$$_javassist_6.writeReplace(Citation_$$_javassi
st_6.java)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at
java.io.ObjectStreamClass.invokeWriteReplace(ObjectStreamClass.java:1004
)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1036)
at
java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:13
75)
at
java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1347)
at
java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1
290)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1079)
at
java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:13
75)
at
java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1347)
at
java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1
290)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1079)
at
java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:13
75)
at
java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1347)
at
java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1
290)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1079)
at
java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:302)
at
net.sf.ehcache.distribution.EventMessage.writeObject(EventMessage.java:1
35)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.jav
a:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at
java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:917)
at
java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1339)
at
java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1
290)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1079)
at
java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:302)
at java.util.ArrayList.writeObject(ArrayList.java:569)
at sun.reflect.GeneratedMethodAccessor62.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessor
Impl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at
java.io.ObjectStreamClass.invokeWriteObject(ObjectStreamClass.java:917)
at
java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1339)
at
java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1
290)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1079)
at
java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:302)
at sun.rmi.server.UnicastRef.marshalValue(UnicastRef.java:258)
at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:117)
at net.sf.ehcache.distribution.RMICachePeer_Stub.send(Unknown
Source)
at
net.sf.ehcache.distribution.RMIAsynchronousCacheReplicator.flushReplicat
ionQueue(RMIAsynchronousCacheReplicator.java:313)
at
net.sf.ehcache.distribution.RMIAsynchronousCacheReplicator.replicationTh
readMain(RMIAsynchronousCacheReplicator.java:122)
at
net.sf.ehcache.distribution.RMIAsynchronousCacheReplicator.access$100(RM
IAsynchronousCacheReplicator.java:55)
at
net.sf.ehcache.distribution.RMIAsynchronousCacheReplicator$ReplicationTh
read.run(RMIAsynchronousCacheReplicator.java:372)
Caused by: javax.xml.soap.SOAPException: ItqlInterpreter error -
java.lang.IllegalStateException: Attempt to resume unsuspended
transaction
Caused by: (IllegalStateException) Attempt to resume unsuspended
transaction
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.ja
va:222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.jav
a:129)
at
org.apache.axis.encoding.DeserializationContext.endElement(Deserializati
onContext.java:1087)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(
AbstractSAXParser.java:633)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanEnd
Element(XMLNSDocumentScannerImpl.java:719)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$F
ragmentContentDispatcher.dispatch(XMLDocumentFragmentScannerImpl.java:16
8\
5)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.s
canDocument(XMLDocumentFragmentScannerImpl.java:368)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML1
1Configuration.java:834)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML1
1Configuration.java:764)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.jav
a:148)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Abstr
actSAXParser.java:1242)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:375)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationCon
text.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(MustUnderstan
dChecker.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:1812)
at
org.topazproject.mulgara.itql.service.ItqlInterpreterBeanServicePortSoap
BindingStub.executeQueryToString(ItqlInterpreterBeanServicePortSoapBindi
n\
gStub.java:358)
at
org.topazproject.mulgara.itql.ItqlHelper.doQuery(ItqlHelper.java:225)
at org.topazproject.otm.stores.ItqlStore.get(ItqlStore.java:331)
... 49 more
> -----Original Message-----
> From: topaz-dev-bounces at topazproject.org
> [mailto:topaz-dev-bounces at topazproject.org] On Behalf Of
> Pradeep Krishnan
> Sent: Tuesday, March 11, 2008 5:02 PM
> To: topaz-dev
> Subject: Re: [Topaz-dev] serializing Article from Session.get()
>
> Hi Russ,
>
> Would you be kind enough to try the attached patch (patch -p0 <
> ser.patch) against 0.8.2.1/topaz/core and see if that fixes
> the problem?
>
> I'll port this over to head in the mean time and test it.
> (Don't have a test set-up for 0.8.2.1 - sorry)
>
> Cheers,
> Pradeep
>
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