Dicom Server not starting
Erik Manwaring
properly only to see this new error (thanks Kevin):
---------------------------------------------------------------------------------------------------------------------------------------------------------------------
root@xnat:/home/xnat/DicomServer/bin# ./arc-dcmstore start
libdir = /home/xnat.
DicomServer PID: 31922
root@xnat:/home/xnat/DicomServer/bin# java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (6b20-1.9.7-0ubuntu1~9.10.1)
OpenJDK Server VM (build 19.0-b09, mixed mode)
Exception in thread "main" java.lang.NoSuchMethodError:
org.apache.commons.cli.OptionBuilder.withArgName(Ljava/lang/String;)Lorg/apache/commons/cli/OptionBuilder;
at org.nrg.dcm.DicomServer.parse(DicomServer.java:258)
at org.nrg.dcm.DicomServer.main(DicomServer.java:362)
Original Errors fixed by putting in the correct path:
---------------------------------------------------------------------------------
./arc-dcmstore stop
./arc-dcmstore start
DicomServer PID: 20770
root@xnat:/home/xnat/DicomServer/bin# java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (6b20-1.9.7-0ubuntu1~9.10.1)
OpenJDK Server VM (build 19.0-b09, mixed mode)
Exception in thread "main" java.lang.NoClassDefFoundError:
org/nrg/dcm/DicomServer
Caused by: java.lang.ClassNotFoundException: org.nrg.dcm.DicomServer
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: org.nrg.dcm.DicomServer. Program will exit.
If anyone has some insight into the new errors I would definitely
appreciate your help.
Thank you,
Erik
Archie, Kevin
I suspect the problem now is in the Java classpath (which is set up in the arc-dcmstore script as the variable CLASSPATH).
Would you please try inserting the following line of code:
echo CLASSPATH = ${CLASSPATH}
into arc-dcmstore, maybe as the first line of the function launch_daemon (so, between the open bracket and the
first line "$JAVA" -server ...)
The output may give you some hints, or if it doesn't make any sense to you please send it to me and I'll see what I can make of it.
- Kevin
Thank you,
Erik
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Archie, Kevin
Try changing the LIBDIR in arc-dcmstore to /home/xnat/DicomServer/lib . (You can and probably should also delete the LIBDIR=${LIBDIR:-.} line.)
With LIBDIR set to /home/xnat, it's pulling in a bunch of libraries from XNAT, including an older and incompatible version of the Apache Commons CLI library that's masking the one DicomServer expects.
Erik Manwaring
I hope this looks like we are getting closer?
root@xnat:/home/xnat/DicomServer/bin# ./arc-dcmstore start
libdir = /home/xnat/DicomServer/lib.
The classpath is set to
/home/xnat/DicomServer/lib/xom-1.0.jar:/home/xnat/DicomServer/lib/DicomDB-2.0-SNAPSHOT.jar:/home/xnat/DicomServer/lib/xdat-beans-1.0-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/jmxtools-1.2.1.jar:/home/xnat/DicomServer/lib/activation-1.1.jar:/home/xnat/DicomServer/lib/dcm4che-net-2.0.21-SNAPSHOT.jar:/home/xnat/DicomServer/lib/jaxen-1.1.jar:/home/xnat/DicomServer/lib/servlet-api-2.5-6.1.11.jar:/home/xnat/DicomServer/lib/xmlParserAPIs-2.6.2.jar:/home/xnat/DicomServer/lib/ant-1.6.5.jar:/home/xnat/DicomServer/lib/xalan-2.6.0.jar:/home/xnat/DicomServer/lib/ExtAttr-1.5.jar:/home/xnat/DicomServer/lib/jetty-6.1.11.jar:/home/xnat/DicomServer/lib/jetty-naming-6.1.11.jar:/home/xnat/DicomServer/lib/jmxri-1.2.1.jar:/home/xnat/DicomServer/lib/DicomServer-xnat-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/dom4j-1.6.1.jar:/home/xnat/DicomServer/lib/slf4j-api-1.5.0.jar:/home/xnat/DicomServer/lib/log4j-1.2.15.jar:/home/xnat/DicomServer/lib/commons-cli-1.1.jar:/home/xnat/DicomServer/lib/json-20080701.jar:/home/xnat/DicomServer/lib/dcm4che-core-2.0.21-SNAPSHOT.jar:/home/xnat/DicomServer/lib/slf4j-log4j12-1.5.0.jar:/home/xnat/DicomServer/lib/commons-lang-2.4.jar:/home/xnat/DicomServer/lib/SessionBuilders-xnat-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/jdom-1.0.jar:/home/xnat/DicomServer/lib/hsqldb-1.8.0.10.jar:/home/xnat/DicomServer/lib/xercesImpl-2.4.0.jar:/home/xnat/DicomServer/lib/mail-1.4.jar:/home/xnat/DicomServer/lib/DicomUtils-1.0.jar:/home/xnat/DicomServer/lib/jms-1.1.jar:/home/xnat/DicomServer/lib/jetty-util-6.1.11.jar:/home/xnat/DicomServer/lib/dcm4xnat-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/icu4j-2.6.1.jar:/home/xnat/DicomServer/lib/xml-apis-1.3.02.jar:/home/xnat/DicomServer/lib.
DicomServer PID: 2796
root@xnat:/home/xnat/DicomServer/bin# java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (6b20-1.9.7-0ubuntu1~9.10.1)
OpenJDK Server VM (build 19.0-b09, mixed mode)
log4j:WARN No appenders could be found for logger (org.mortbay.log).
log4j:WARN Please initialize the log4j system properly.
java.io.FileNotFoundException: etc/DicomServer.xml (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:137)
at java.io.FileInputStream.<init>(FileInputStream.java:96)
at org.nrg.dcm.DicomServer.<init>(DicomServer.java:262)
at org.nrg.dcm.DicomServer.main(DicomServer.java:628)
root@xnat:/home/xnat/DicomServer/bin#
Thank you,
Erik
Archie, Kevin
The problem now is that the script can't find your DicomServer.xml configuration file. You'll need to either run the script from the directory /home/xnat/DicomServer:
cd /home/xnat/DicomServer; arc-dcmstore start
or set it in the script:
# Path of properties file containing configuration information
propsfile=${PROPERTIES:-/home/xnat/DicomServer/etc/DicomServer.xml}
or pass it in as the environment variable PROPERTIES:
PROPERTIES=/home/xnat/DicomServer/etc/DicomServer.xml arc-dcmstore start
Erik Manwaring
root@xnat:/home/xnat/DicomServer/bin# ./arc-dcmstore start
libdir = /home/xnat/DicomServer/lib.
The classpath is set to
/home/xnat/DicomServer/lib/xom-1.0.jar:/home/xnat/DicomServer/lib/DicomDB-2.0-SNAPSHOT.jar:/home/xnat/DicomServer/lib/xdat-beans-1.0-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/jmxtools-1.2.1.jar:/home/xnat/DicomServer/lib/activation-1.1.jar:/home/xnat/DicomServer/lib/dcm4che-net-2.0.21-SNAPSHOT.jar:/home/xnat/DicomServer/lib/jaxen-1.1.jar:/home/xnat/DicomServer/lib/servlet-api-2.5-6.1.11.jar:/home/xnat/DicomServer/lib/xmlParserAPIs-2.6.2.jar:/home/xnat/DicomServer/lib/ant-1.6.5.jar:/home/xnat/DicomServer/lib/xalan-2.6.0.jar:/home/xnat/DicomServer/lib/ExtAttr-1.5.jar:/home/xnat/DicomServer/lib/jetty-6.1.11.jar:/home/xnat/DicomServer/lib/jetty-naming-6.1.11.jar:/home/xnat/DicomServer/lib/jmxri-1.2.1.jar:/home/xnat/DicomServer/lib/DicomServer-xnat-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/dom4j-1.6.1.jar:/home/xnat/DicomServer/lib/slf4j-api-1.5.0.jar:/home/xnat/DicomServer/lib/log4j-1.2.15.jar:/home/xnat/DicomServer/lib/commons-cli-1.1.jar:/home/xnat/DicomServer/lib/json-20080701.jar:/home/xnat/DicomServer/lib/dcm4che-core-2.0.21-SNAPSHOT.jar:/home/xnat/DicomServer/lib/slf4j-log4j12-1.5.0.jar:/home/xnat/DicomServer/lib/commons-lang-2.4.jar:/home/xnat/DicomServer/lib/SessionBuilders-xnat-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/jdom-1.0.jar:/home/xnat/DicomServer/lib/hsqldb-1.8.0.10.jar:/home/xnat/DicomServer/lib/xercesImpl-2.4.0.jar:/home/xnat/DicomServer/lib/mail-1.4.jar:/home/xnat/DicomServer/lib/DicomUtils-1.0.jar:/home/xnat/DicomServer/lib/jms-1.1.jar:/home/xnat/DicomServer/lib/jetty-util-6.1.11.jar:/home/xnat/DicomServer/lib/dcm4xnat-1.4-SNAPSHOT.jar:/home/xnat/DicomServer/lib/icu4j-2.6.1.jar:/home/xnat/DicomServer/lib/xml-apis-1.3.02.jar:/home/xnat/DicomServer/lib.
DicomServer PID: 2923
root@xnat:/home/xnat/DicomServer/bin# java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (6b20-1.9.7-0ubuntu1~9.10.1)
OpenJDK Server VM (build 19.0-b09, mixed mode)
log4j:WARN No appenders could be found for logger (org.mortbay.log).
log4j:WARN Please initialize the log4j system properly.
root@xnat:/home/xnat/DicomServer/bin#
Archie, Kevin
Looks to me like it's running. Have you tried sending to it?
(The log4j message is a nuisance out of the depths of the embedded web server, Jetty. It can safely be ignored.)
Erik Manwaring
Is there a quick way to test it to make sure it is running properly?
I don't know the first thing about Dicom images - and am learning this
as we go.
Thank you for your help!
Erik
Archie, Kevin
2. Run DicomBrowser: http://nrg.wustl.edu/projects/DICOM/DicomBrowser-1.4/DicomBrowser.jnlp
3. Get some sample DICOM data: http://nrg.wustl.edu/projects/DICOM/sample1.zip
4. Unzip the sample data, then open the data directory in DicomBrowser
5. Set a field in the DICOM metadata to tell XNAT where to put the session:
Select the patient in the tree view on the left side of the DicomBrowser window
Use the Edit/Add new attribute... menu option to set Patient Comments (10,4000) to the value:
Project: your-project-name
6. Use the File/Send... menu option to send the files.
7. Check the prearchive page for your test project in XNAT.
Erik Manwaring
Nothing is showing up on the Prearchive page for my test project.
I went to the prearchive directory and I see the following:
root@xnat:/home/xnat/xnat_data/prearchive# ls -l
total 16
drwxr-xr-x 3 root root 4096 2011-04-20 15:33 20110420_153140
drwxr-xr-x 13 xnat xnat 4096 2010-03-30 12:08 demo
drwxr-xr-x 2 xnat xnat 4096 2011-04-20 15:32 DICOMTEST
drwxr-xr-x 2 xnat xnat 4096 2011-04-20 15:26 FREW
root@xnat:/home/xnat/xnat_data/prearchive#
The DICOMTEST folder is there, demo and FREW are projects too. What's
new is the "20110420_153140".
I dug deeper into that directory and found my files that I uploaded:
root@xnat:/home/xnat/xnat_data/prearchive/20110420_153140/Sample_ID/SCANS/4/DICOM#
ls -l
total 1132
-rw-r--r-- 1 root root 191906 2011-04-20 16:03
Sample_Patient.MR.head_DHead.4.100.20061214.091206.156000.7001418376.dcm
-rw-r--r-- 1 root root 191906 2011-04-20 16:03
Sample_Patient.MR.head_DHead.4.101.20061214.091206.156000.1933918380.dcm
-rw-r--r-- 1 root root 191908 2011-04-20 16:03
Sample_Patient.MR.head_DHead.4.10.20061214.091206.156000.2462218014.dcm
-rw-r--r-- 1 root root 191906 2011-04-20 16:03
Sample_Patient.MR.head_DHead.4.102.20061214.091206.156000.6488818382.dcm
-rw-r--r-- 1 root root 191906 2011-04-20 16:03
Sample_Patient.MR.head_DHead.4.103.20061214.091206.156000.4923818386.dcm
-rw-r--r-- 1 root root 191902 2011-04-20 16:03
Sample_Patient.MR.head_DHead.4.1.20061214.091206.156000.1632817982.dcm
-rw-r--r-- 1 root root 1886 2011-04-20 16:05 scan_4_catalog.xml
root@xnat:/home/xnat/xnat_data/prearchive/20110420_153140/Sample_ID/SCANS/4/DICOM#
It's good to see that the DICOM server is working - I just need a
better understanding of how to make sure files are in their
appropriate projects.
I don't see where in XNAT I would associate these to my project. I
followed the steps you outlined in your previous email and double
checked everything.
Let me know where I should be looking at this point.
Thank you!
Erik
deech
Are you an admin? It looks like the session that you added "20110420_153140" is unassigned and only a user with admin privileges on XNAT is able to see unassigned sessions in the prearchive.
-deech
Erik Manwaring
I can not find the session in XNAT - I found it on the server under:
/home/xnat/xnat_data/prearchive/
I don't see it in XNAT.
~Erik
Olsen, Tim
Is there an XML in this directory?
/home/xnat/xnat_data/prearchive/20110420_153140/
I'm guessing the files were received, but the XML wasn't built.
Is this the publicly available installation of XNAT 1.4, or is this a custom build of XNAT 1.5?
Tim
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Erik Manwaring [erik.ma...@gmail.com]
Sent: Wednesday, April 20, 2011 3:32 PM
Erik Manwaring
root@xnat:/home/xnat/xnat_data/prearchive/20110420_153140# ls -l
total 8
drwxr-xr-x 3 root root 4096 2011-04-20 15:33 Sample_ID
-rw-r--r-- 1 root root 2279 2011-04-20 16:05 Sample_ID.xml
root@xnat:/home/xnat/xnat_data/prearchive/20110420_153140#
The version is 1.4 taken from the Virtual Machine:
http://www.xnat.org/XNAT+Virtual+Machine
Thank you for your assistance with this!
Erik
Archie, Kevin
Step 5 in my instructions should have been where the project got set, but for some reason it didn't work. What was the exact text that you put into Patient Comments (0010,4000)?
You might want to read the full details of how to set up the DICOM metadata so that XNAT can determine the appropriate project: see the section "DicomServer and XNAT" in http://www.xnat.org/DicomServer .
Archie, Kevin
If you go to the prearchive from the Upload->Go to prearchive menu option (rather than the "View Prearchive" link on the project page), is one of the projects in the pull-down menu called "Unassigned"? That's where XNAT 1.4 displays sessions that couldn't be matched to a project, and I suspect it's where you'll find the session you uploaded.
- Kevin
-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Erik Manwaring
Sent: Wednesday, April 20, 2011 4:59 PM
To: xnat_di...@googlegroups.com
Subject: Re: [XNAT Discussion] Dicom Server not starting
/home/xnat/xnat_data/prearchive/
~Erik
Erik Manwaring
In step 5 I followed your example:
0010,4000
Value: DICOMTEST
and yes the Unassigned is where it's ending up.
Why isn't the data ending up in DICOMTEST though?
Thanks!
Erik
Archie, Kevin
That should be:
Project: DICOMTEST
Erik Manwaring
~Erik