What version of DicomServer should be used with XNAT 1.4

[Glenn]

I am not able to archive MR sessions in an XNAT 1.4 installation. When
I complete the data entry on the archive page and click the Archive
button, nothing happens.

xdat.log contains the following:

File Edit Options Buffers Tools
Help
2008-05-16 08:25:08,034 [http-80-Processor24] ERROR
org.nrg.xnat.ajax.Prearchive - Unable to load image session data for /
space/nexus/35/\
users/prearchive/20080516_082255/INVESTIGATORS_Buckner_1
2008-05-16 08:25:52,288 [http-80-Processor24] WARN
org.nrg.xnat.ajax.Prearchive - moved session /space/nexus/35/users/
prearchive/2008051\
6_082255/INVESTIGATORS_Buckner_1 to /space/nexus/35/users/prearchive/
CBS, but unable to delete original directory.

DicomServer.log contains:

ERROR [pool-1-thread-1] org.nrg.dcm.xnat.MRSessionBuilder
(SessionBuilder.java:194) - Session /space/nexus/35/users/prearchive/
20080516_0\
82255/INVESTIGATORS_Buckner_1.xml summary failed
java.io.FileNotFoundException: /home/xnat/XNAT/XNAT-Appliance/
nexus-1-4-Ubuntu/Local/Storage/prearchive/20080516_082255/
INVESTIGATORS_Buc\
kner_1/RAW/1.MR.INVESTIGATORS_Buckner.
9.134.20070802.173019.840000.8060909281.dcm (No such file or
directory)
at java.io.FileInputStream.open(Native Method)

[Kevin Archie]

Glenn,

I'd usually recommend building from the source code, but that's even more complicated than usual right now. I'll put together a build today and post it sometime this afternoon.

- k
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Glenn [glenn....@gmail.com]
Sent: Friday, May 16, 2008 8:36 AM
To: xnat_discussion
Cc: gabriele...@harvard.edu; tok...@nmr.mgh.harvard.edu
Subject: What version of DicomServer should be used with XNAT 1.4

[Glenn]

Kevin,

Where can I get the source code? I looked for it on the web page and
didn't find it.

Glenn

On May 16, 10:06 am, Kevin Archie <karc...@npg.wustl.edu> wrote:
> Glenn,
>
> I'd usually recommend building from the source code, but that's even more complicated than usual right now. I'll put together a build today and post it sometime this afternoon.
>
> - k
> ________________________________________

> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Glenn [glenn.hoff...@gmail.com]

> Sent: Friday, May 16, 2008 8:36 AM
> To: xnat_discussion

> Cc: gabriele_farie...@harvard.edu; toke...@nmr.mgh.harvard.edu

[Kevin Archie]

That's why it's more complicated than usual. We had some trouble with the CVS repository a week or two ago that we're recovering from in our spare time -- projects will generally only get restored to the server as they're requested. It'll take me a couple of hours to get DicomServer and all its dependencies together. Sorry about the delay.

- k
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Glenn [glenn....@gmail.com]
Sent: Friday, May 16, 2008 9:29 AM
To: xnat_discussion
Subject: Re: What version of DicomServer should be used with XNAT 1.4

[Kevin Archie]

Here's a 1.4-compatible DicomServer. Consider it as beta as the rest as 1.4.

http://nrg.wustl.edu/projects/DICOM/DicomServer-1.5.tar.gz

Sometime in the next week or so I'll post the URL for a Subversion repository containing the source.

- k

[Glenn]

Kevin,

I created a new XNAT installation this morning from the
xnat_1_4b_032508 release and then tried to use it with the
DicomServer-1.5 release. Once again, when I hit the Archive button,
nothing happened. The entry in xdat.log was:

2008-05-19 08:24:49,216 [http-80-Processor25] ERROR

org.nrg.xnat.ajax.Prearchive - Unable to load image session data for /
space/nexus/35/\

users/prearchive/20080519_073422/INVESTIGATORS_Buckner_1
2008-05-19 08:24:57,092 [http-80-Processor24] ERROR
org.nrg.xdat.servlet.XDATAjaxServlet -
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)


Glenn

On May 16, 3:43 pm, Kevin Archie <karc...@npg.wustl.edu> wrote:
> Here's a 1.4-compatible DicomServer. Consider it as beta as the rest as 1.4.
>
> http://nrg.wustl.edu/projects/DICOM/DicomServer-1.5.tar.gz
>
> Sometime in the next week or so I'll post the URL for a Subversion repository containing the source.
>
> - k
>
> -----Original Message-----
> From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Kevin Archie
> Sent: Friday, May 16, 2008 9:43 AM
> To: xnat_di...@googlegroups.com
> Subject: RE: What version of DicomServer should be used with XNAT 1.4
>
> That's why it's more complicated than usual. We had some trouble with the CVS repository a week or two ago that we're recovering from in our spare time -- projects will generally only get restored to the server as they're requested. It'll take me a couple of hours to get DicomServer and all its dependencies together. Sorry about the delay.
>
> - k
> ________________________________________

[Anda Pacurar]

Hi Kevin

I'm trying to edit the configuration file DicomServer.xml as suggested into
the README document that comes with the DicomServer-1.5 .
The readme document makes reference to
"prearc" is the full pathname of the prearchive directory, but I cannot see
any key named prearc in the DicomServer.xml - should I edit instead arcspec
key with the full path of the prearchive dir?
The same for the "schema" key - I can't identify this key in the file

In the arc-dcmstore - should the VERSION be kept as 14a1 or should I assign
another value to this var
VERSION=${VERSION:--xnat-14a1}

Thank you,
Anda

[Kevin Archie]

Yes, sorry, the README and the arc-dcmstore script haven't been keeping up with the code. Neither "prearc" nor "schema" elements are used anymore. Also, VERSION should now be 1.5.

Thanks,

- k
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Anda Pacurar [apac...@rotman-baycrest.on.ca]
Sent: Tuesday, May 20, 2008 8:01 AM
To: xnat_di...@googlegroups.com

[Anda Pacurar]

Hi Kevin

What exactly is the format of the hidden server-pid file? What means the
process ID of the dicom Server - from where can I get that info? Should
contain the number 14058?

[anda@enterprise config]# ./arc-dcmstore start
Dicom Server PID: 14058
./arc-dcmstore: line 44: /opt/xnat/Prearchive/.server-pid: No such file or
directory

Tx.

[Kevin Archie]

That file should contain the UNIX process ID of the DicomServer. We store it to make "arc-dcmstore stop" work -- we just kill the server process.

The error message you're seeing suggests to me that the script is having trouble writing to the server-pid file, maybe because the directory that's supposed to contain it (/opt/xnat/Prearchive) doesn't exist. The error is actually mostly harmless -- it just means that "arc-dcmstore stop" won't work because we haven't retained the server PID.

- k
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Anda Pacurar [apac...@rotman-baycrest.on.ca]

Sent: Wednesday, May 21, 2008 9:16 AM

[anda]

Hi Kevin

I have trying to run Dicomserver few days ago and tested today this
morning. It seems that the network connection was not close last time:

[anda@enterprise config]# ./arc-dcmstore start

Dicom Server PID: 29314

./arc-dcmstore: line 44: /opt/xnat/Prearchive/.server-pid: No such
file or directory

[anda@enterprise config]# java version "1.6.0_03"
Java(TM) SE Runtime Environment (build 1.6.0_03-b05)
Java HotSpot(TM) Server VM (build 1.6.0_03-b05, mixed mode)

java.net.BindException: Address already in use
at java.net.PlainSocketImpl.socketBind(Native Method)
at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:359)
at java.net.ServerSocket.bind(ServerSocket.java:319)
at
org.dcm4che2.net.NetworkConnection.bind(NetworkConnection.java:621)
at org.dcm4che2.net.Device.startListening(Device.java:712)
at org.nrg.dcm.DicomServer.start(DicomServer.java:426)
at org.nrg.dcm.DicomServer.main(DicomServer.java:409)


Should I force the connection to close by restarting the server? - any
other suggestion?

Thank you.
Anda

On May 21, 10:42 am, Kevin Archie <karc...@npg.wustl.edu> wrote:
> That file should contain the UNIX process ID of the DicomServer.  We store it to make "arc-dcmstore stop" work -- we just kill theserverprocess.
>

> The error message you're seeing suggests to me that the script is having trouble writing to theserver-pid file, maybe because the directory that's supposed to contain it (/opt/xnat/Prearchive) doesn't exist.  The error is actually mostly harmless -- it just means that "arc-dcmstore stop" won't work because we haven't retained theserverPID.
>
>   - k
> ________________________________________
> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Anda Pacurar [apacu...@rotman-baycrest.on.ca]

> Sent: Wednesday, May 21, 2008 9:16 AM
> To: xnat_di...@googlegroups.com
> Subject: Re: What version of DicomServer should be used with XNAT 1.4
>
> Hi Kevin
>

> What exactly is the format of the hiddenserver-pid file? What means the
> process ID of thedicomServer- from where can I get that info? Should
> contain the number 14058?
>
> [anda@enterprise config]# ./arc-dcmstore startDicomServerPID: 14058

> ./arc-dcmstore: line 44: /opt/xnat/Prearchive/.server-pid: No such file or
> directory
>
> Tx.
> Anda
>
>
>
> ----- Original Message -----
> From: "Kevin Archie" <karc...@npg.wustl.edu>
> To: <xnat_di...@googlegroups.com>
> Sent: Tuesday, May 20, 2008 9:39 AM
> Subject: RE: What version of DicomServer should be used with XNAT 1.4
>
> Yes, sorry, the README and the arc-dcmstore script haven't been keeping up
> with the code.  Neither "prearc" nor "schema" elements are used anymore.
> Also, VERSION should now be 1.5.
>
> Thanks,
>
>   - k
> ________________________________________
> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On

> Behalf Of Anda Pacurar [apacu...@rotman-baycrest.on.ca]

> time -- projects will generally only get restored to theserveras they're

> requested.  It'll take me a couple of hours to get DicomServer and all its
> dependencies together.  Sorry about the delay.
>
>   - k
> ________________________________________
> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On

> >   at java.io.FileInputStream.open(Native Method)- Hide quoted text -
>
> - Show quoted text -

[anda]

Hi Kevin

I'm not sure how this DIcomServer tool should work:

Should I start the service only once and then when I use the
DicomServer command lines to retrieve data from a pacs archive....
automatically will the data be stored on the prearchive and some
metadata stored on the db?


Tx.
Anda

> > From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf OfAndaPacurar [apacu...@rotman-baycrest.on.ca]

> > Sent: Wednesday, May 21, 2008 9:16 AM
> > To: xnat_di...@googlegroups.com
> > Subject: Re: What version of DicomServer should be used with XNAT 1.4
>
> > Hi Kevin
>
> > What exactly is the format of the hiddenserver-pid file? What means the
> > process ID of thedicomServer- from where can I get that info? Should
> > contain the number 14058?
>
> > [anda@enterprise config]# ./arc-dcmstore startDicomServerPID: 14058
> > ./arc-dcmstore: line 44: /opt/xnat/Prearchive/.server-pid: No such file or
> > directory
>
> > Tx.
> >Anda
>
> > ----- Original Message -----
> > From: "Kevin Archie" <karc...@npg.wustl.edu>
> > To: <xnat_di...@googlegroups.com>
> > Sent: Tuesday, May 20, 2008 9:39 AM
> > Subject: RE: What version of DicomServer should be used with XNAT 1.4
>
> > Yes, sorry, the README and the arc-dcmstore script haven't been keeping up
> > with the code.  Neither "prearc" nor "schema" elements are used anymore.
> > Also, VERSION should now be 1.5.
>
> > Thanks,
>
> >   - k
> > ________________________________________
> > From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On

> > Behalf OfAndaPacurar [apacu...@rotman-baycrest.on.ca]

> > - Show quoted text -- Hide quoted text -

[Kevin Archie]

The "Address already in use" error probably means that you already have a DicomServer running. If the process ID isn't in the .server-pid file, you'll need to kill the other DicomServer by hand before starting a new one. (So, 'ps' with appropriate arguments for your system to figure out the process id, followed by 'kill -9 {process-id}').

- Kevin
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of anda [apac...@rotman-baycrest.on.ca]
Sent: Monday, May 26, 2008 9:30 AM

[Kevin Archie]

DicomServer is a server process that acts only as a passive listener -- as a DICOM C-STORE SCP. You'll start it once, generally at system startup, and leave it running. Client processes (e.g., a scanner or DicomBrowser) that can act as C-STORE SCUs can connect to the server to deliver files. The server will write XML session documents for the received files.

- k
________________________________________

From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of anda [apac...@rotman-baycrest.on.ca]

Sent: Monday, May 26, 2008 9:41 AM