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IHE Bridge deserialization error (XDS.a) [message #40142] Fri, 11 January 2008 08:27 Go to next message
Takeo Satomi is currently offline Takeo Satomi
Messages: 32
Registered: July 2009
Member
Hello all,

Today I've been looking for a public XDS registry which has pdf-embedded
documents to see if my doc consumer works, and tried IBM registry
( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but the
latest IHE Bridge
(org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
deserialize the message returned from the server. The query was

<query:AdhocQueryRequest
xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
returnComposedObjects="true" returnType="LeafClass"
/><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
ExternalIdentifier patId WHERE doc.objectType =
'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND (patId.registryObject
= doc.id AND patId.identificationScheme =
'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
'139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>

and here's the stack trace excerpt.

index=0,
size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
index=0, size=0
at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
at
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
at
org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)

At first glance it looks some elements Bridge requires are not contained
in the returned query result, which seems to have a couple of documents.

Is it a bridge bug, or is the query result invalid?

Thanks,
Takeo
Re: IHE Bridge deserialization error (XDS.a) [message #40199 is a reply to message #40142] Fri, 11 January 2008 18:43 Go to previous messageGo to next message
Matthew Davis
Messages: 269
Registered: July 2009
Senior Member
Hi Takeo,

This is a bug in the Bridge and will be fixed in the next build.

Thanks,
-Matt

Takeo Satomi wrote:
> Hello all,
>
> Today I've been looking for a public XDS registry which has pdf-embedded
> documents to see if my doc consumer works, and tried IBM registry
> ( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but the
> latest IHE Bridge
> (org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
> deserialize the message returned from the server. The query was
>
> <query:AdhocQueryRequest
> xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
> returnComposedObjects="true" returnType="LeafClass"
> /><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
> ExternalIdentifier patId WHERE doc.objectType =
> 'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND
> (patId.registryObject = doc.id AND patId.identificationScheme =
> 'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
> '139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
> 'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>
>
> and here's the stack trace excerpt.
>
> index=0,
> size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
> index=0, size=0
> at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
>
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
>
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
>
> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
> at
> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>
> At first glance it looks some elements Bridge requires are not contained
> in the returned query result, which seems to have a couple of documents.
>
> Is it a bridge bug, or is the query result invalid?
>
> Thanks,
> Takeo
>
>
Re: IHE Bridge deserialization error (XDS.a) [message #40493 is a reply to message #40199] Thu, 24 January 2008 08:49 Go to previous messageGo to next message
Takeo Satomi is currently offline Takeo Satomi
Messages: 32
Registered: July 2009
Member
Hello Matt,

Thanks to your fix, I could successfully retrieve documents a couple of
days ago, but today I got different errors. When I made non-stored SQL
query for pid=139158 and aaid=1.3.6.1.4.1.21367.2005.3.7 the following
error returned.

ull/njava.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(Unknown Source)
at
org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extractExtrinsicObjectSlots(EbXML_2_1DocumentEn tryExtractor.java:486)
at
org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extract(EbXML_2_1DocumentEntryExtractor.java:20 8)
at
org.eclipse.ohf.ihe.xds.consumer.AbstractConsumer.processEbX ML_2_1QueryResults(AbstractConsumer.java:400)
at org.eclipse.ohf.ihe.xds.consumer.Consumer.query(Consumer.jav a:142)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:424)
at
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
at
org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)

And with the stored query, I got the error below.

Java heap space/njava.lang.OutOfMemoryError: Java heap space
at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
at java.lang.AbstractStringBuilder.append(Unknown Source)
at java.lang.StringBuffer.append(Unknown Source)
at
org.apache.log4j.helpers.PatternParser$LiteralPatternConvert er.format(PatternParser.java:412)
at org.apache.log4j.PatternLayout.format(PatternLayout.java:495 )
at org.apache.log4j.WriterAppender.subAppend(WriterAppender.jav a:293)
at
org.apache.log4j.RollingFileAppender.subAppend(RollingFileAp pender.java:249)
at org.apache.log4j.WriterAppender.append(WriterAppender.java:1 50)
at org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton. java:221)
at
org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOn Appenders(AppenderAttachableImpl.java:57)
at org.apache.log4j.Category.callAppenders(Category.java:187)
at org.apache.log4j.Category.forcedLog(Category.java:372)
at org.apache.log4j.Category.debug(Category.java:241)
at
org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:184)
at
org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:104)
at org.eclipse.ohf.ihe.xds.consumer.Consumer.sendQuery(Consumer .java:533)
at
org.eclipse.ohf.ihe.xds.consumer.Consumer.invokeStoredQuery( Consumer.java:314)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:410)
at
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
at
org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)

As for the latter it looks modifying log4j configuration would fix the
problem as suggested in
https://bugs.eclipse.org/bugs/show_bug.cgi?id=211941 - wouldn't it?

I wish it can be fixed easily or is not a showstopper.

Thanks,
Takeo

Matthew Davis wrote:

> Hi Takeo,

> This is a bug in the Bridge and will be fixed in the next build.

> Thanks,
> -Matt

> Takeo Satomi wrote:
>> Hello all,
>>
>> Today I've been looking for a public XDS registry which has pdf-embedded
>> documents to see if my doc consumer works, and tried IBM registry
>> ( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but the
>> latest IHE Bridge
>> (org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
>> deserialize the message returned from the server. The query was
>>
>> <query:AdhocQueryRequest
>>
xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
>> returnComposedObjects="true" returnType="LeafClass"
>> /><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
>> ExternalIdentifier patId WHERE doc.objectType =
>> 'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND
>> (patId.registryObject = doc.id AND patId.identificationScheme =
>> 'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
>> '139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
>> 'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>
>>
>> and here's the stack trace excerpt.
>>
>> index=0,
>>
size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
>> index=0, size=0
>> at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
>> at
>>
org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
>>
>> at
>>
org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
>>
>> at
>>
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
>>
>> at
>>
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>>
>> at
>> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>>
>> At first glance it looks some elements Bridge requires are not contained
>> in the returned query result, which seems to have a couple of documents.
>>
>> Is it a bridge bug, or is the query result invalid?
>>
>> Thanks,
>> Takeo
>>
>>
Re: IHE Bridge deserialization error (XDS.a) [message #40529 is a reply to message #40493] Thu, 24 January 2008 21:10 Go to previous message
Matthew Davis
Messages: 269
Registered: July 2009
Senior Member
Hi Takeo,

The logger issue - I think the only way you'll be able to resolve that
is to decrease the sensitivity in the log4j.xml configuration file.
We'll take a look at the ebXML 2.1 issue and get back to you on that.

Thanks,
-Matt


Takeo Satomi wrote:
> Hello Matt,
>
> Thanks to your fix, I could successfully retrieve documents a couple of
> days ago, but today I got different errors. When I made non-stored SQL
> query for pid=139158 and aaid=1.3.6.1.4.1.21367.2005.3.7 the following
> error returned.
>
> ull/njava.util.NoSuchElementException
> at java.util.StringTokenizer.nextToken(Unknown Source)
> at
> org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extractExtrinsicObjectSlots(EbXML_2_1DocumentEn tryExtractor.java:486)
>
> at
> org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extract(EbXML_2_1DocumentEntryExtractor.java:20 8)
>
> at
> org.eclipse.ohf.ihe.xds.consumer.AbstractConsumer.processEbX ML_2_1QueryResults(AbstractConsumer.java:400)
>
> at org.eclipse.ohf.ihe.xds.consumer.Consumer.query(Consumer.jav a:142)
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:424)
>
> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
> at
> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>
> And with the stored query, I got the error below.
>
> Java heap space/njava.lang.OutOfMemoryError: Java heap space
> at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
> at java.lang.AbstractStringBuilder.append(Unknown Source)
> at java.lang.StringBuffer.append(Unknown Source)
> at
> org.apache.log4j.helpers.PatternParser$LiteralPatternConvert er.format(PatternParser.java:412)
>
> at org.apache.log4j.PatternLayout.format(PatternLayout.java:495 )
> at org.apache.log4j.WriterAppender.subAppend(WriterAppender.jav a:293)
> at
> org.apache.log4j.RollingFileAppender.subAppend(RollingFileAp pender.java:249)
>
> at org.apache.log4j.WriterAppender.append(WriterAppender.java:1 50)
> at
> org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton. java:221)
> at
> org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOn Appenders(AppenderAttachableImpl.java:57)
>
> at org.apache.log4j.Category.callAppenders(Category.java:187)
> at org.apache.log4j.Category.forcedLog(Category.java:372)
> at org.apache.log4j.Category.debug(Category.java:241)
> at
> org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:184)
>
> at
> org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:104)
>
> at
> org.eclipse.ohf.ihe.xds.consumer.Consumer.sendQuery(Consumer .java:533)
> at
> org.eclipse.ohf.ihe.xds.consumer.Consumer.invokeStoredQuery( Consumer.java:314)
>
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:410)
>
> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
> at
> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>
> As for the latter it looks modifying log4j configuration would fix the
> problem as suggested in
> https://bugs.eclipse.org/bugs/show_bug.cgi?id=211941 - wouldn't it?
>
> I wish it can be fixed easily or is not a showstopper.
>
> Thanks,
> Takeo
>
> Matthew Davis wrote:
>
>> Hi Takeo,
>
>> This is a bug in the Bridge and will be fixed in the next build.
>
>> Thanks,
>> -Matt
>
>> Takeo Satomi wrote:
>>> Hello all,
>>>
>>> Today I've been looking for a public XDS registry which has
>>> pdf-embedded documents to see if my doc consumer works, and tried IBM
>>> registry
>>> ( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but
>>> the latest IHE Bridge
>>> (org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
>>> deserialize the message returned from the server. The query was
>>>
>>> <query:AdhocQueryRequest
> xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
>
>>> returnComposedObjects="true" returnType="LeafClass"
>>> /><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
>>> ExternalIdentifier patId WHERE doc.objectType =
>>> 'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND
>>> (patId.registryObject = doc.id AND patId.identificationScheme =
>>> 'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
>>> '139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
>>> 'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>
>>>
>>> and here's the stack trace excerpt.
>>>
>>> index=0,
> size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
>
>>> index=0, size=0
>>> at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
>>> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
>
>>>
>>> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
>
>>>
>>> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
>
>>>
>>> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
>>>
>>> at
>>> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>>>
>>>
>>> At first glance it looks some elements Bridge requires are not
>>> contained in the returned query result, which seems to have a couple
>>> of documents.
>>>
>>> Is it a bridge bug, or is the query result invalid?
>>>
>>> Thanks,
>>> Takeo
>>>
>>>
>
>
Re: IHE Bridge deserialization error (XDS.a) [message #584356 is a reply to message #40142] Fri, 11 January 2008 18:43 Go to previous message
Matthew Davis
Messages: 269
Registered: July 2009
Senior Member
Hi Takeo,

This is a bug in the Bridge and will be fixed in the next build.

Thanks,
-Matt

Takeo Satomi wrote:
> Hello all,
>
> Today I've been looking for a public XDS registry which has pdf-embedded
> documents to see if my doc consumer works, and tried IBM registry
> ( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but the
> latest IHE Bridge
> (org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
> deserialize the message returned from the server. The query was
>
> <query:AdhocQueryRequest
> xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
> returnComposedObjects="true" returnType="LeafClass"
> /><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
> ExternalIdentifier patId WHERE doc.objectType =
> 'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND
> (patId.registryObject = doc.id AND patId.identificationScheme =
> 'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
> '139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
> 'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>
>
> and here's the stack trace excerpt.
>
> index=0,
> size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
> index=0, size=0
> at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
>
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
>
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
>
> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
> at
> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>
> At first glance it looks some elements Bridge requires are not contained
> in the returned query result, which seems to have a couple of documents.
>
> Is it a bridge bug, or is the query result invalid?
>
> Thanks,
> Takeo
>
>
Re: IHE Bridge deserialization error (XDS.a) [message #584484 is a reply to message #40199] Thu, 24 January 2008 08:49 Go to previous message
Takeo Satomi is currently offline Takeo Satomi
Messages: 32
Registered: July 2009
Member
Hello Matt,

Thanks to your fix, I could successfully retrieve documents a couple of
days ago, but today I got different errors. When I made non-stored SQL
query for pid=139158 and aaid=1.3.6.1.4.1.21367.2005.3.7 the following
error returned.

ull/njava.util.NoSuchElementException
at java.util.StringTokenizer.nextToken(Unknown Source)
at
org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extractExtrinsicObjectSlots(EbXML_2_1DocumentEn tryExtractor.java:486)
at
org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extract(EbXML_2_1DocumentEntryExtractor.java:20 8)
at
org.eclipse.ohf.ihe.xds.consumer.AbstractConsumer.processEbX ML_2_1QueryResults(AbstractConsumer.java:400)
at org.eclipse.ohf.ihe.xds.consumer.Consumer.query(Consumer.jav a:142)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:424)
at
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
at
org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)

And with the stored query, I got the error below.

Java heap space/njava.lang.OutOfMemoryError: Java heap space
at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
at java.lang.AbstractStringBuilder.append(Unknown Source)
at java.lang.StringBuffer.append(Unknown Source)
at
org.apache.log4j.helpers.PatternParser$LiteralPatternConvert er.format(PatternParser.java:412)
at org.apache.log4j.PatternLayout.format(PatternLayout.java:495 )
at org.apache.log4j.WriterAppender.subAppend(WriterAppender.jav a:293)
at
org.apache.log4j.RollingFileAppender.subAppend(RollingFileAp pender.java:249)
at org.apache.log4j.WriterAppender.append(WriterAppender.java:1 50)
at org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton. java:221)
at
org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOn Appenders(AppenderAttachableImpl.java:57)
at org.apache.log4j.Category.callAppenders(Category.java:187)
at org.apache.log4j.Category.forcedLog(Category.java:372)
at org.apache.log4j.Category.debug(Category.java:241)
at
org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:184)
at
org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:104)
at org.eclipse.ohf.ihe.xds.consumer.Consumer.sendQuery(Consumer .java:533)
at
org.eclipse.ohf.ihe.xds.consumer.Consumer.invokeStoredQuery( Consumer.java:314)
at
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:410)
at
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
at
org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)

As for the latter it looks modifying log4j configuration would fix the
problem as suggested in
https://bugs.eclipse.org/bugs/show_bug.cgi?id=211941 - wouldn't it?

I wish it can be fixed easily or is not a showstopper.

Thanks,
Takeo

Matthew Davis wrote:

> Hi Takeo,

> This is a bug in the Bridge and will be fixed in the next build.

> Thanks,
> -Matt

> Takeo Satomi wrote:
>> Hello all,
>>
>> Today I've been looking for a public XDS registry which has pdf-embedded
>> documents to see if my doc consumer works, and tried IBM registry
>> ( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but the
>> latest IHE Bridge
>> (org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
>> deserialize the message returned from the server. The query was
>>
>> <query:AdhocQueryRequest
>>
xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
>> returnComposedObjects="true" returnType="LeafClass"
>> /><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
>> ExternalIdentifier patId WHERE doc.objectType =
>> 'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND
>> (patId.registryObject = doc.id AND patId.identificationScheme =
>> 'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
>> '139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
>> 'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>
>>
>> and here's the stack trace excerpt.
>>
>> index=0,
>>
size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
>> index=0, size=0
>> at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
>> at
>>
org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
>>
>> at
>>
org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
>>
>> at
>>
org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
>>
>> at
>>
org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>>
>> at
>> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>>
>> At first glance it looks some elements Bridge requires are not contained
>> in the returned query result, which seems to have a couple of documents.
>>
>> Is it a bridge bug, or is the query result invalid?
>>
>> Thanks,
>> Takeo
>>
>>
Re: IHE Bridge deserialization error (XDS.a) [message #584498 is a reply to message #40493] Thu, 24 January 2008 21:10 Go to previous message
Matthew Davis
Messages: 269
Registered: July 2009
Senior Member
Hi Takeo,

The logger issue - I think the only way you'll be able to resolve that
is to decrease the sensitivity in the log4j.xml configuration file.
We'll take a look at the ebXML 2.1 issue and get back to you on that.

Thanks,
-Matt


Takeo Satomi wrote:
> Hello Matt,
>
> Thanks to your fix, I could successfully retrieve documents a couple of
> days ago, but today I got different errors. When I made non-stored SQL
> query for pid=139158 and aaid=1.3.6.1.4.1.21367.2005.3.7 the following
> error returned.
>
> ull/njava.util.NoSuchElementException
> at java.util.StringTokenizer.nextToken(Unknown Source)
> at
> org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extractExtrinsicObjectSlots(EbXML_2_1DocumentEn tryExtractor.java:486)
>
> at
> org.eclipse.ohf.ihe.xds.metadata.extract.EbXML_2_1DocumentEn tryExtractor.extract(EbXML_2_1DocumentEntryExtractor.java:20 8)
>
> at
> org.eclipse.ohf.ihe.xds.consumer.AbstractConsumer.processEbX ML_2_1QueryResults(AbstractConsumer.java:400)
>
> at org.eclipse.ohf.ihe.xds.consumer.Consumer.query(Consumer.jav a:142)
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:424)
>
> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
> at
> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>
> And with the stored query, I got the error below.
>
> Java heap space/njava.lang.OutOfMemoryError: Java heap space
> at java.lang.AbstractStringBuilder.expandCapacity(Unknown Source)
> at java.lang.AbstractStringBuilder.append(Unknown Source)
> at java.lang.StringBuffer.append(Unknown Source)
> at
> org.apache.log4j.helpers.PatternParser$LiteralPatternConvert er.format(PatternParser.java:412)
>
> at org.apache.log4j.PatternLayout.format(PatternLayout.java:495 )
> at org.apache.log4j.WriterAppender.subAppend(WriterAppender.jav a:293)
> at
> org.apache.log4j.RollingFileAppender.subAppend(RollingFileAp pender.java:249)
>
> at org.apache.log4j.WriterAppender.append(WriterAppender.java:1 50)
> at
> org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton. java:221)
> at
> org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOn Appenders(AppenderAttachableImpl.java:57)
>
> at org.apache.log4j.Category.callAppenders(Category.java:187)
> at org.apache.log4j.Category.forcedLog(Category.java:372)
> at org.apache.log4j.Category.debug(Category.java:241)
> at
> org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:184)
>
> at
> org.eclipse.ohf.ihe.xds.soap.AbstractXDSSoapClient.send(Abst ractXDSSoapClient.java:104)
>
> at
> org.eclipse.ohf.ihe.xds.consumer.Consumer.sendQuery(Consumer .java:533)
> at
> org.eclipse.ohf.ihe.xds.consumer.Consumer.invokeStoredQuery( Consumer.java:314)
>
> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:410)
>
> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
> at
> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>
> As for the latter it looks modifying log4j configuration would fix the
> problem as suggested in
> https://bugs.eclipse.org/bugs/show_bug.cgi?id=211941 - wouldn't it?
>
> I wish it can be fixed easily or is not a showstopper.
>
> Thanks,
> Takeo
>
> Matthew Davis wrote:
>
>> Hi Takeo,
>
>> This is a bug in the Bridge and will be fixed in the next build.
>
>> Thanks,
>> -Matt
>
>> Takeo Satomi wrote:
>>> Hello all,
>>>
>>> Today I've been looking for a public XDS registry which has
>>> pdf-embedded documents to see if my doc consumer works, and tried IBM
>>> registry
>>> ( http://lswin10.dfw.ibm.com:9081/IBMXDSRegistry/XDSa/Registry) but
>>> the latest IHE Bridge
>>> (org.eclipse.ohf.bridge.install_0.3.0.v20080108120654.zip) failed to
>>> deserialize the message returned from the server. The query was
>>>
>>> <query:AdhocQueryRequest
> xmlns:query="urn:oasis:names:tc:ebxml-regrep:query:xsd:2.1" ><query:ResponseOption
>
>>> returnComposedObjects="true" returnType="LeafClass"
>>> /><query:SQLQuery>SELECT doc.id FROM ExtrinsicObject doc,
>>> ExternalIdentifier patId WHERE doc.objectType =
>>> 'urn:uuid:7edca82f-054d-47f2-a032-9b2a5b5186c1' AND
>>> (patId.registryObject = doc.id AND patId.identificationScheme =
>>> 'urn:uuid:58a6f841-87b3-4a3e-92fd-a8ffeff98427' AND patId.value =
>>> '139158^^^&amp;10.1&amp;ISO') AND (doc.status IN ('Approved',
>>> 'Deprecated')) </query:SQLQuery></query:AdhocQueryRequest>
>>>
>>> and here's the stack trace excerpt.
>>>
>>> index=0,
> size=0/norg.eclipse.emf.common.util.BasicEList$BasicIndexOut OfBoundsException:
>
>>> index=0, size=0
>>> at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:5 35)
>>> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.sourcePatientInfoToP atientInfoType(IheXdsBridge.java:520)
>
>>>
>>> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.createXdsDocument(Ih eXdsBridge.java:547)
>
>>>
>>> at
> org.eclipse.ohf.bridge.ihe.IheXdsBridge.goQueryDocuments(Ihe XdsBridge.java:480)
>
>>>
>>> at
> org.eclipse.ohf.bridge.xds.AbstractXdsBridge.queryDocuments( AbstractXdsBridge.java:124)
>
>>>
>>> at
>>> org.eclipse.ohf.bridge.ws.OHFBridge.QueryDocumentsFind(OHFBr idge.java:154)
>>>
>>>
>>> At first glance it looks some elements Bridge requires are not
>>> contained in the returned query result, which seems to have a couple
>>> of documents.
>>>
>>> Is it a bridge bug, or is the query result invalid?
>>>
>>> Thanks,
>>> Takeo
>>>
>>>
>
>
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