Download Images doesn't work for XNAT 1.5

[Shuhua Wu]

Download Images failed in our testing.

Some foundings:

Java console:
java.io.FileNotFoundException: http://hostname/xnat/archive/catalogs/stored/1306439377934.xml


1306439377934.xml exists in cache/4/catalogs/

URL pattern /archive/* is missing in web.xml


Is this a bug or we haven't installed/upgraded properly?

Thanks,
Shuhua

[Olsen, Tim]

That is a bug. I've fixed it and just pushed the fix to the public dev repository. You can pull it from there.

https://bitbucket.org/nrg/xdat_release/src/d8a2ee79c5ef/plugin-resources/originals/application-web.xml

Place that file in your XNAT_HOME/plugin-resources/originals/application-web.xml and run your update.sh -Ddeploy=true command. That should resolve the issue.

Tim

Some foundings:

1306439377934.xml exists in cache/4/catalogs/

Thanks,
Shuhua

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[Adam Harding]

Thanks Tim. The installation was built from a fork containing
customizations so we'll test & pull.

Adam

On May 26, 4:40 pm, "Olsen, Tim" <ols...@mir.wustl.edu> wrote:
> That is a bug.  I've fixed it and just pushed the fix to the public dev repository.  You can pull it from there.
>

> https://bitbucket.org/nrg/xdat_release/src/d8a2ee79c5ef/plugin-resour...

>
> Place that file in your XNAT_HOME/plugin-resources/originals/application-web.xml and run your update.sh -Ddeploy=true command.  That should resolve the issue.
>
> Tim
>
> -----Original Message-----
> From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Shuhua Wu
> Sent: Thursday, May 26, 2011 3:03 PM
> To: xnat_discussion
> Subject: [XNAT Discussion] Download Images doesn't work for XNAT 1.5
>
> Download Images failed in our testing.
>
> Some foundings:
>
> Java console:
> java.io.FileNotFoundException:http://hostname/xnat/archive/catalogs/stored/1306439377934.xml
>
> 1306439377934.xml exists in cache/4/catalogs/
>
> URL pattern /archive/* is missing in web.xml
>
> Is this a bug or we haven't installed/upgraded properly?
>
> Thanks,
> Shuhua
>
> --
> You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
> To post to this group, send email to xnat_di...@googlegroups.com.
> To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com.

> For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.

[Olsen, Tim]

That fork contains some bug fixes that will be released as part of 1.5.1 (at this rate it will be released Tuesday). We haven't finished our testing of all of the changesets, but the last one (the application-web.xml) should be good to go.

[Adam Harding]

We're aiming to implement the "big" upgrade from 1.4 to 1.5 before
next week in knowledge of the fact we'll just miss 1.5.1, but it looks
like we do need this fix. We'll apply 1.5.1 a little later.

The patched file applied successfully & we'll test shortly.

Adam

[Shuhua Wu]

Thank you Tim.

The FileNotFoundException is fixed. However, another exception broke
the images download.

org.xml.sax.SAXParseException: Premature end of file.
at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:
195)
at
com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:
174)
at
com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:
388)
at
com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:
1414)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl
$PrologDriver.next(XMLDocumentScannerImpl.java:1059)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:
648)
at
com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:
140)
at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:
511)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
808)
at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:
737)
at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:
119)
at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:
1205)
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl
$JAXPSAXParser.parse(SAXParserImpl.java:522)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
at org.nrg.xdat.bean.reader.XDATXMLReader.parse(XDATXMLReader.java:
997)
at org.nrg.xnat.fileManager.DownloaderApplet
$InitSessionThread.InitSession(DownloaderApplet.java:699)
at org.nrg.xnat.fileManager.DownloaderApplet
$InitSessionThread.run(DownloaderApplet.java:554)


The xml file can be pulled by http://hostname/xnat/archive/catalogs/stored/1306503931787.xml
its content:
<?xml version="1.0" encoding="UTF-8"?>
<cat:Catalog xmlns:arc="http://nrg.wustl.edu/arc" xmlns:cat="http://
nrg.wustl.edu/catalog" xmlns:fs="http://nrg.wustl.edu/fs"
xmlns:phd="http://nrg.wustl.edu/phd" xmlns:pipe="http://nrg.wustl.edu/
pipe" xmlns:prov="http://www.nbirn.net/prov" xmlns:val="http://
nrg.wustl.edu/val" xmlns:wrk="http://nrg.wustl.edu/workflow"
xmlns:xdat="http://nrg.wustl.edu/security" xmlns:xnat="http://
nrg.wustl.edu/xnat" xmlns:xnat_a="http://nrg.wustl.edu/
xnat_assessments" xmlns:xsi="http://www.w3.org/2001/XMLSchema-
instance">
<cat:sets>
<cat:entrySet ID="PREDICTHD_E11173">
<cat:sets>
<cat:entrySet ID="RAW">
<cat:entries>
<cat:entry
URI="https://hostname/xnat/data/experiments/PREDICTHD_E11173/scans/
T1-30/resources/SNAPSHOTS/files?
format=zip&amp;projectIncludedInPath=true&amp;subjectIncludedInPath=true"
format="ZIP"/>
<cat:entry
URI="https://hostname/xnat/data/experiments/PREDICTHD_E11173/scans/
T1-30/resources/DICOM/files?
format=zip&amp;projectIncludedInPath=true&amp;subjectIncludedInPath=true"
format="ZIP"/>
<cat:entry
URI="https://hostname/xnat/data/experiments/PREDICTHD_E11173/scans/
T2-30/resources/SNAPSHOTS/files?
format=zip&amp;projectIncludedInPath=true&amp;subjectIncludedInPath=true"
format="ZIP"/>
<cat:entry
URI="https://hostname/xnat/data/experiments/PREDICTHD_E11173/scans/
T2-30/resources/DICOM/files?
format=zip&amp;projectIncludedInPath=true&amp;subjectIncludedInPath=true"
format="ZIP"/>
</cat:entries>
</cat:entrySet>
</cat:sets>
</cat:entrySet>
</cat:sets>
</cat:Catalog>




Thanks,
Shuhua

On May 26, 4:40 pm, "Olsen, Tim" <ols...@mir.wustl.edu> wrote:

> That is a bug.  I've fixed it and just pushed the fix to the public dev repository.  You can pull it from there.
>

> https://bitbucket.org/nrg/xdat_release/src/d8a2ee79c5ef/plugin-resour...

>
> Place that file in your XNAT_HOME/plugin-resources/originals/application-web.xml and run your update.sh -Ddeploy=true command.  That should resolve the issue.
>
> Tim
>
> -----Original Message-----
> From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Shuhua Wu
> Sent: Thursday, May 26, 2011 3:03 PM
> To: xnat_discussion
> Subject: [XNAT Discussion] Download Images doesn't work for XNAT 1.5
>
> Download Images failed in our testing.
>
> Some foundings:
>
> Java console:
> java.io.FileNotFoundException:http://hostname/xnat/archive/catalogs/stored/1306439377934.xml
>
> 1306439377934.xml exists in cache/4/catalogs/
>
> URL pattern /archive/* is missing in web.xml
>
> Is this a bug or we haven't installed/upgraded properly?
>
> Thanks,
> Shuhua
>
> --
> You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
> To post to this group, send email to xnat_di...@googlegroups.com.
> To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com.

> For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.

[Olsen, Tim]

I wasn't able to reproduce this. Does it happen consistently with different data sets/ scan combinations?

Tim

________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Shuhua Wu [shuh...@gmail.com]
Sent: Friday, May 27, 2011 9:21 AM
To: xnat_discussion
Subject: [XNAT Discussion] Re: Download Images doesn't work for XNAT 1.5

[Shuhua Wu]

I uploaded two samples from www.xnat.org to different new projects.
Failed to download both.

Shuhua

On May 27, 10:43 am, "Olsen, Tim" <ols...@mir.wustl.edu> wrote:
> I wasn't able to reproduce this.  Does it happen consistently with different data sets/ scan combinations?
>
> Tim
>
> ________________________________________

> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Shuhua Wu [shuhu...@gmail.com]

> The xml file can be pulled byhttp://hostname/xnat/archive/catalogs/stored/1306503931787.xml

[Shuhua Wu]

The "org.xml.sax.SAXParseException: Premature end of file" disappears
when we switch tomcat from 7.0 to 6.0 or 5.5.

Shuhua

On May 27, 12:46 pm, Shuhua Wu <shuhu...@gmail.com> wrote:
> I uploaded two samples fromwww.xnat.orgto different new projects.

[Olsen, Tim]

So, are you saying that you only see this exception in Tomcat 7?

Tim

________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Shuhua Wu [shuh...@gmail.com]
Sent: Friday, May 27, 2011 2:45 PM
To: xnat_discussion

[Shuhua Wu]

Yes.

On May 27, 3:16 pm, "Olsen, Tim" <ols...@mir.wustl.edu> wrote:
> So, are you saying that you only see this exception in Tomcat 7?
>
> Tim
>
> ________________________________________

> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Shuhua Wu [shuhu...@gmail.com]

> Sent: Friday, May 27, 2011 2:45 PM
> To: xnat_discussion
> Subject: [XNAT Discussion] Re: Download Images doesn't work for XNAT 1.5
>
> The "org.xml.sax.SAXParseException: Premature end of file" disappears
> when we switch tomcat from 7.0 to 6.0 or 5.5.
>
> Shuhua
>
> On May 27, 12:46 pm, Shuhua Wu <shuhu...@gmail.com> wrote:
>
>
>

> > I uploaded two samples fromwww.xnat.orgtodifferent new projects.

[Herrick, Rick]

Shuhua,

Are you by any chance using different VMs with the different Tomcat installations? The error is occurring here:

com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next()

Everything after that is just preparing the error for delivery. The com.sun... version of the XMLDocumentScannerImpl class is in the rt.jar of the 1.6 VM.

If you do have Tomcat 7 configured to run with another version of the JVM, try switching to using the same version of the JVM that works with Tomcat 5.5 or 6.

[Adam Harding]

Rick,

The only change between the two deployments was the freshly un-tgz-ed
Tomcat version into which they were deployed; i.e. same JDK,
environment variables, etc. That may be insufficiently many
differences to use Tomcat 7 (for all I know), but such a drop-in
change has been working with our in-house apps.

I don't have experience with this, but it appears Tomcat 7 introduced
configuration changes to XML validation. The XML seems straightforward
and validates against recent xmllint.

Adam

> > > I uploaded two samples fromwww.xnat.orgtodifferentnew projects.

> ...
>
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