trying to upload EEG data
skenny
for users to upload a .RAW file to our xnat repository and i was
surprised to learn that the applet does not accept eeg data. from what
i can tell xnat desktop seems to be the method of choice for users who
are not so command-line savvy (?) but i'm not able to get it to upload
a file for me:
i specify the location of my 'XNAT archive' (using the same url i
navigate to to access it on the web): insularis.neuro.uci.edu:8080/
xnat and i get 'Cannot connect to XNAT Server'
specifying that same url as my 'Remote archive' produces 'unable to
connect to remote repository' and the xnd logfile is empty.
i'm guessing there is a basic setting that i need to tweak here but
wasn't able to find it in the doc.
thanks for any help
~sk
skenny
following error:
[skenny@martini ~]$ XNATRestClient -host http://insularis.neuro.uci.edu:8080/xnat
-u skenny -p ***** -m PUT -remote "/data/projects/test/subjects/dude/
experiments/dude_eeg_1/scans/1/files/testeeg.RAW" - local test.RAW
ERROR CODE 13: Web Service Exception: http://insularis.neuro.uci.edu:8080/xnat/
org/apache/commons/codec/DecoderException.
Error logged in /home/skenny/error.log
[skenny@martini ~]$ cat error.log
Tue Jan 31 01:00:53 PST 2012 skenny@http://insularis.neuro.uci.edu:
8080/xnat/:java.lang.NoClassDefFoundError: org/apache/commons/codec/
DecoderException
at
org.apache.commons.httpclient.HttpMethodBase.<init>(HttpMethodBase.java:
220)
at
org.apache.commons.httpclient.methods.ExpectContinueMethod.<init>(ExpectContinueMethod.java:
93)
at
org.apache.commons.httpclient.methods.EntityEnclosingMethod.<init>(EntityEnclosingMethod.java:
119)
at
org.apache.commons.httpclient.methods.PutMethod.<init>(PutMethod.java:
76)
at XNATRestClient.execute(XNATRestClient.java:195)
at XNATRestClient.process(XNATRestClient.java:100)
at WSTool.perform(WSTool.java:130)
at XNATRestClient.main(XNATRestClient.java:296)
Caused by: java.lang.ClassNotFoundException:
org.apache.commons.codec.DecoderException
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:
301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 8 more
thanks!
~sk
Herrick, Rick
The error message is a bit odd. The decoder exception usually indicates that something's gone wrong during the decoding process on the server side, which could mean a number of things, dropped data during transmission, invalid characters in the posted data, invalid checksum, etc. But a missing DecoderException class is a metaproblem. It means that something's missing in the web app, since the DecoderException should be there and calmly convey information to you about what went wrong with the decoding process.
So a few things:
* What version of XNAT are you using?
* Can you look in the WEB-INF/lib folder of the deployed web app and see if there's a commons-codec-*.jar in there?
* If you'd like to upload some of your anonymized EEG data somewhere, I can have a look at it and see what we might be able to do with it.
HTH...
thanks!
~sk
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-Dan
skenny
> XNAT does have built-in support for EEG session and scan data, but for the EEG data to be uploaded, it really depends on what format it's in. The uploader applet SHOULD, in theory, handle the data so long as it uses DICOM, but I don't believe that RAW EEG data is DICOM compliant (I'm not really familiar with that type of data, so I'm only going off what I can find through the Googletubez regarding the format).
it is collected on an EGI system and i've been told that we could
potentially upload it in the following formats: simple binary, tab-
delimited text, EGIS (an EGI format), MAT-file, persyst.
if any of those are helpful (?)
>
> The error message is a bit odd. The decoder exception usually indicates that something's gone wrong during the decoding process on the server side, which could mean a number of things, dropped data during transmission, invalid characters in the posted data, invalid checksum, etc. But a missing DecoderException class is a metaproblem. It means that something's missing in the web app, since the DecoderException should be there and calmly convey information to you about what went wrong with the decoding process.
>
> So a few things:
>
> * What version of XNAT are you using?
> * Can you look in the WEB-INF/lib folder of the deployed web app and see if there's a commons-codec-*.jar in there?
lib/commons-codec-1.5.jar
-rw-r--r-- 1 tomcat tomcat 73098 Jan 25 22:32 /usr/share/tomcat5/
webapps/xnat/WEB-INF/lib/commons-codec-1.5.jar
formats is preferable.
i've been *assuming* people tend to upload arbitrary file formats to
xnat that they want to associate with projects/experiments (is that a
false assumption?) and they generally do so using XNATRestClient?
>
> HTH...
>
>
>
>
>
>
>
> -----Original Message-----
> From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of skenny
> Sent: Tuesday, January 31, 2012 3:27 AM
> To: xnat_discussion
> Subject: [XNAT Discussion] Re: trying to upload EEG data
>
> i am also trying to do the upload via XNATRestClient and getting the following error:
>
Herrick, Rick
The long answer is... I don't have the time to give you the long answer this afternoon :) I'll work on writing up how to do this when I get back into the office tomorrow.
