Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Virendra]

Hi,

I have just downloaded XNAT and configured the build.properties file.
All pre-requisites are working fine.
The warning/error I get while running ./setup.sh is as follows:
========================================================

[root@ec1-19039 bin]# ./setup.sh

Using XDAT Installation: /home/xnat
Using JAVA_HOME: /usr/java/jdk1.5.0_11/

Verify Java Version (with java -version)
java version "1.5.0_11"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_11-b03)
Java HotSpot(TM) Client VM (build 1.5.0_11-b03, mixed mode, sharing)

Executing /home/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:setup
__ __
| \/ |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \ ~ intelligent projects ~
|_| |_\__,_|\_/\___|_||_| v. 1.0.2

Attempting to download commons-jelly-tags-xml-20030211.142705.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/commons-
jelly/jars/commons-jelly-tags-xml-20030211.142705.jar]:
java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/
maven/commons-jelly/jars/commons-jelly-tags-xml-20030211.142705.jar]:
jaError retrieving artifact from [http://government-grants.org/mirrors/
apache.org/commons-jelly/jars/commons-jelly-tags-
xml-20030211.142705.jar]: java.net.ConnectException: Connection timed
out
Error retrieving artifact from [http://maven-plugins.sourceforge.net/
maven/commons-jelly/jars/commons-jelly-tags-xml-20030211.142705.jar]:
java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/
maven/commons-jelly/jars/commons-jelly/jars/commons-jelly-tags-
xml-20030211.142705.jar]: java.net.ConnectException: Connection timed
out
WARNING: Failed to download commons-jelly-tags-
xml-20030211.142705.jar.
Attempting to download commons-jelly-tags-
interaction-20030211.143817.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/commons-
jelly/jars/commons-jelly-tags-interaction-20030211.143817.jar]:
java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/
maven/commons-jelly/jars/commons-jelly-tags-
interaction-20030211.143817.jar]: java.net.ConnectException:
Connection timed out
Error retrieving artifact from [http://www.ibiblio.org/maven/commons-
jelly/jars/commons-jelly-tags-interaction-20030211.143817.jar]:
java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://government-grants.org/mirrors/
apache.org/commons-jelly/jars/commons-jelly-tags-
interaction-20030211.143817.jar]: java.net.ConnectException:
Connection timed out
Error retrieving artifact from [http://maven-plugins.sourceforge.net/
maven/commons-jelly/jars/commons-jelly-tags-
interaction-20030211.143817.jar]: java.net.ConnectException:
Connection timed out
Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/
maven/commons-jelly/jars/commons-jelly/jars/commons-jelly-tags-
interaction-20030211.143817.jar]: java.net.ConnectException:
Connection timed out
WARNING: Failed to download commons-jelly-tags-
interaction-20030211.143817.jar.
The build cannot continue because of the following unsatisfied
dependencies:

commons-jelly-tags-xml-20030211.142705.jar (try downloading from
http://jakarta.apache.org/commons/jelly/libs/xml/)
commons-jelly-tags-interaction-20030211.143817.jar

Total time: 38 minutes 9 seconds
Finished at: Thu Jan 24 11:42:54 IST 2008
==================================================================

Please suggest what should I do now.
I have got links where I can download this common-jelly.jar file but
its not working.
the link is: http://mirrors.ibiblio.org/pub/mirrors/maven/commons-jelly/jars/
Should I execute the commons-jelly-tags-xml-1.0.jar file to run XNAT?
If yes, HOW?

And yes, You guys have done a tremendous job!

waiting for your reply.

[Timothy Olsen]

Sorry for you difficulty.

I just tested the setup script, and didn't encounter a problem here. It seems like this may be a problem which is on your local system.

Please confirm that there is not a firewall blocking access to the internet from the installation machine. These seems like a possible firewall issue.

The commons jar should have been available at the first link that Maven tried:
http://repo1.maven.org/maven/commons-jelly/jars/commons-jelly-tags-xml-20030211.142705.jar

Your output says the connection timed out. However, the URL works fine for me. Try visiting the link from an internet browser on the installation machine. If it works through that, but not from the install script then this is probably a firewall issue.

Tim

[Virendra]

Yeah! There is a firewall..I just forgot it. Our organization has some
restrictions. They don't provide authentication to some websites.
Anyways I have downloaded most of the required jar files. [Saw the
list in project.xml file :-) ].
Do I need to edit any file in XNAT pkg so that I can change the
location of download from local machine.

One more thing, I couldn't download these files as the link have been
removed from jakarta.apache.org and Google says there are no such
files .
Please provide me with a link so that I can download all these files
and run them from local machine.

List of jar files I didn't found :=
xdat.jar
,
commons-pool.jar
,
parser.jar
,

postgresql.jar
,

xml-apis.jar
,

xerces.jar
,

xalan.jar
,

velocity.jar,

jaxrpc.jar
,

axis.jar
,

commons-logging.jar
,

commons-discovery.jar
,

saaj.jar
,

jaf.jar
,

javamail.jar
,

PlexiViewer.jar
,

xdat.jar
,

xdat-store.jar
,

xdat-arcget.jar
,

xdat-arcread.jar
,

xdat-arcsim.jar
,

ant.jar
,

ij-1.39b.jar
,

jargon.jar
,

xnatsrb.jar.
Do I really need to make use of these files for running XNAT on my
machine?

[Virendra]

Hi again,

I created a local apache server and loaded the repository to the local
server made the installer point to the local server for acquiring the
required jars, but couldn't succeed as the work was quite tough.

Is there any Soln to run XNAT by modifying the files in the system or
the server?

[Timothy Olsen]

Virenda,

Glad to hear you've made some progress. The jars you are missing are actually already included in the release. So, you don't need to go find them.

I can directly give you the rest of the files you need. I'll send them directly to your virend...@gmail.com account.

Tim Olsen

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra

[Virendra]

Hi,
I unzipped all the content in the designated directories..But now too
its giving the same error.

Here's the output:

[root@localhost bin]# ./setup.sh

Using XDAT Installation: /home/xnat
Using JAVA_HOME: /usr/java/jdk1.5.0_11/

Verify Java Version (with java -version)
java version "1.5.0_11"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_11-b03)
Java HotSpot(TM) Client VM (build 1.5.0_11-b03, mixed mode, sharing)

Executing /home/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:setup
__ __
| \/ |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \ ~ intelligent projects ~
|_| |_\__,_|\_/\___|_||_| v. 1.0.2

Plugin cache will be regenerated
Directory /home/xnat/$ /home/xnat/plugin-resources/repository does not
exist. Attempting to create.
Attempting to download xdat-1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/
xdat-1.jar]: java.net.ConnectException: Connection timed out

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-1.jar]: java.net.ConnectException: Connection
timed out
Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/
xdat-1.jar]: java.net.ConnectException: Connection timed out
WARNING: Failed to download xdat-1.jar.
Attempting to download commons-collections-3.0.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

collections/jars/commons-collections-3.0.jar]:

java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-collections/jars/commons-collections-3.0.jar]:

java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

collections/jars/commons-collections-3.0.jar]:
java.net.ConnectException: Connection timed out
WARNING: Failed to download commons-collections-3.0.jar.
Attempting to download commons-configuration-1.0.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

configuration/jars/commons-configuration-1.0.jar]:

java.net.ConnectException: Connection timed out
Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-configuration/jars/commons-configuration-1.0.jar]:
java.net.ConnectException: Connection timed out


If you check the o/p, you will see that just after the maven logo, it
displays that plugin cache is generated..this means that it has
detected the cache folder..Only thing left is configuration.



I have pasted the contents of project.properties:=
maven.home.local=$ /home/xnat/plugin-resources

maven.repo.remote=http://repo1.maven.org/maven,http://
mirrors.ibiblio.org/pub/mirrors/maven,http://www.ibiblio.org/maven

Is the first line correct ?

Is there any change I have to do now?
Guide me..Bye

[Virendra]

PostgreSql is up and running...what can be the problem now?
Should I come at GMT-8 so that I don't have to wait for long for your
replies?

[Timothy Olsen]

This seems like a slightly different problem then the previous one. Previously, the problem was that Maven could not connect to remote resources to download files it needed. The problem here is that Maven is not finding the local repository directory which it requires (which is supplied with the XNAT download). Because it can't find the repository folder, it is looking elsewhere for jars, when it shouldn't need to.

The message:

Directory /home/xnat/$ /home/xnat/plugin-resources/repository does not exist. Attempting to create.

Doesn't make since. The jars XNAT is looking for are distributed with xnat. They are located in xnat/plugin-resources/repository. For example, the xdat-1.jar file is in xnat/plugin-resources/repository/xdat/xdat-1.jar.

Please confirm that the repository is there (i.e. /home/xnat/plugin-resources/repository).

After some consultation here, we think the problem may be related to the '/home/xnat$ ' which is prepended to the '/home/xnat/plugin-resources/repository' path in the message above. It seems like this path is getting confused somehow.

Unfortunately, we have never seen this behavior before, so we may not be able to give a quick answer.

Did you try adding the additional jars I sent to a fresh XNAT install? Or did you use the installation which had previously had problems? I would try deleting the old install and downloading a fresh copy... if you haven't already tried that. But, this is more of a guess.

What operating system are you running?

Anyone else have any ideas?

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra
Sent: Sunday, January 27, 2008 2:31 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Alexis]

Hi to all,

I didn't meet this kind of error. However, could it come from a
mistake in the build.properties ? Did you get errors while installing
tomcat ?
I agree the simplest test would be to try to reproduce it from a fresh
xnat download.

Alexis

[Virendra]

Hi,

The path you told me to check is present.(home/xnat/plugin-resources/
repository/jars/xdat/).
I had unzipped the files you sent me in the correct place..
My operating system is fedora core8.(kernel is 2.6).

There were no errors with tomcat while installing...It seems the
problem is with maven.
What should I do to install all the jar files from my system?
Thanks a lot for all your help till now.

[Timothy Olsen]

The xnat/plugin-resources/repository directory is the location where the jars are installed. The only jars which don't go there are the ones I sent you separately. So, it seems the jars are in the correct place, but they aren't being found by the Maven install script.

Did you try a fresh XNAT install? Perhaps, you could try installing it in a different location. That might expose what is going wrong.

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra
Sent: Tuesday, January 29, 2008 9:14 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Virendra]

Hi Tim,

I have installed xnat in root folder now.
I have edited project.properties as follows::

maven.home.local=/root/xnat/plugin-resources

maven.repo.remote=http://repo1.maven.org/maven,http://
mirrors.ibiblio.org/pub/mirrors/maven,http://www.ibiblio.org/maven

======================================================================================================================

The error is almost different now, It is::

[root@localhost bin]# ./setup.sh

Using XDAT Installation: /root/xnat

Using JAVA_HOME: /usr/java/jdk1.5.0_11/

Verify Java Version (with java -version)
java version "1.5.0_11"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_11-b03)
Java HotSpot(TM) Client VM (build 1.5.0_11-b03, mixed mode, sharing)

Executing /root/xnat/plugin-resources/maven-1.0.2/bin/maven xdat:setup

__ __
| \/ |__ _Apache__ ___
| |\/| / _` \ V / -_) ' \ ~ intelligent projects ~
|_| |_\__,_|\_/\___|_||_| v. 1.0.2

Attempting to download xdat-1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/

xdat-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/

xdat-1.jar]: java.net.UnknownHostException: www.ibiblio.org

WARNING: Failed to download xdat-1.jar.
Attempting to download commons-collections-3.0.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/commons-
collections/jars/commons-collections-3.0.jar]:

java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/
maven/commons-collections/jars/commons-collections-3.0.jar]:

java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-
collections/jars/commons-collections-3.0.jar]:

java.net.UnknownHostException: www.ibiblio.org

WARNING: Failed to download commons-collections-3.0.jar.
Attempting to download commons-configuration-1.0.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/commons-
configuration/jars/commons-configuration-1.0.jar]:

java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/
maven/commons-configuration/jars/commons-configuration-1.0.jar]:

java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

configuration/jars/commons-configuration-1.0.jar]:
java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download commons-configuration-1.0.jar.
Attempting to download commons-dbcp-1.2.1.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

dbcp/jars/commons-dbcp-1.2.1.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-dbcp/jars/commons-dbcp-1.2.1.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

dbcp/jars/commons-dbcp-1.2.1.jar]: java.net.UnknownHostException:
www.ibiblio.org
WARNING: Failed to download commons-dbcp-1.2.1.jar.
Attempting to download commons-lang-2.0.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

lang/jars/commons-lang-2.0.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-lang/jars/commons-lang-2.0.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

lang/jars/commons-lang-2.0.jar]: java.net.UnknownHostException:
www.ibiblio.org
WARNING: Failed to download commons-lang-2.0.jar.
Attempting to download commons-pool-1.2.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

pool/jars/commons-pool-1.2.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-pool/jars/commons-pool-1.2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

pool/jars/commons-pool-1.2.jar]: java.net.UnknownHostException:
www.ibiblio.org
WARNING: Failed to download commons-pool-1.2.jar.
Attempting to download jakarta-regexp-1.2.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/jakarta-
regexp/jars/jakarta-regexp-1.2.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/jakarta-regexp/jars/jakarta-regexp-1.2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/jakarta-
regexp/jars/jakarta-regexp-1.2.jar]: java.net.UnknownHostException:
www.ibiblio.org
WARNING: Failed to download jakarta-regexp-1.2.jar.
Attempting to download log4j-1.2.8.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/log4j/
jars/log4j-1.2.8.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/log4j/jars/log4j-1.2.8.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/log4j/
jars/log4j-1.2.8.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download log4j-1.2.8.jar.
Attempting to download parser-1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/parser/
jars/parser-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/parser/jars/parser-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/parser/
jars/parser-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download parser-1.jar.
Attempting to download postgresql-7.4.214.jdbc2.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/

postgresql/jars/postgresql-7.4.214.jdbc2.jar]:
java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/postgresql/jars/postgresql-7.4.214.jdbc2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/
postgresql/jars/postgresql-7.4.214.jdbc2.jar]:
java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download postgresql-7.4.214.jdbc2.jar.
Attempting to download stratum-1.0-b5.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/stratum/
jars/stratum-1.0-b5.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/stratum/jars/stratum-1.0-b5.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/stratum/
jars/stratum-1.0-b5.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download stratum-1.0-b5.jar.
Attempting to download xercesImpl-2.4.0.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/

xercesImpl/jars/xercesImpl-2.4.0.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xercesImpl/jars/xercesImpl-2.4.0.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/
xercesImpl/jars/xercesImpl-2.4.0.jar]: java.net.UnknownHostException:
www.ibiblio.org
WARNING: Failed to download xercesImpl-2.4.0.jar.
Attempting to download xml-apis-1.0.b2.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/xml-apis/
jars/xml-apis-1.0.b2.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xml-apis/jars/xml-apis-1.0.b2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/xml-apis/
jars/xml-apis-1.0.b2.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xml-apis-1.0.b2.jar.
Attempting to download xerces-J_1.4.0.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/xerces/
jars/xerces-J_1.4.0.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xerces/jars/xerces-J_1.4.0.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/xerces/
jars/xerces-J_1.4.0.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xerces-J_1.4.0.jar.
Attempting to download xalan-2.5.1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/xalan/
jars/xalan-2.5.1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xalan/jars/xalan-2.5.1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/xalan/
jars/xalan-2.5.1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xalan-2.5.1.jar.
Attempting to download velocity-1.3.1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/velocity/
jars/velocity-1.3.1.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/velocity/jars/velocity-1.3.1.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/velocity/
jars/velocity-1.3.1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download velocity-1.3.1.jar.
Attempting to download jaxrpc-1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/jaxrpc/
jars/jaxrpc-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/jaxrpc/jars/jaxrpc-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/jaxrpc/
jars/jaxrpc-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download jaxrpc-1.jar.
Attempting to download axis-1_3.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/axis/jars/
axis-1_3.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/axis/jars/axis-1_3.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/axis/jars/
axis-1_3.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download axis-1_3.jar.
Attempting to download commons-logging-1.0.4.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

logging/jars/commons-logging-1.0.4.jar]:
java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-logging/jars/commons-logging-1.0.4.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

logging/jars/commons-logging-1.0.4.jar]:
java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download commons-logging-1.0.4.jar.
Attempting to download commons-discovery-0.2.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/commons-

discovery/jars/commons-discovery-0.2.jar]:
java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/commons-discovery/jars/commons-discovery-0.2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/commons-

discovery/jars/commons-discovery-0.2.jar]:
java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download commons-discovery-0.2.jar.
Attempting to download saaj-1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/saaj/jars/
saaj-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/saaj/jars/saaj-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/saaj/jars/
saaj-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download saaj-1.jar.
Attempting to download activation-1.0.2.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/jaf/jars/
activation-1.0.2.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/jaf/jars/activation-1.0.2.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/jaf/jars/
activation-1.0.2.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download activation-1.0.2.jar.
Attempting to download javamail-1.3.2.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/javamail/
jars/javamail-1.3.2.jar]: java.net.UnknownHostException:
repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/javamail/jars/javamail-1.3.2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/javamail/
jars/javamail-1.3.2.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download javamail-1.3.2.jar.
Attempting to download PlexiViewer-1.1b2.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/

PlexiViewer/jars/PlexiViewer-1.1b2.jar]:
java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/PlexiViewer/jars/PlexiViewer-1.1b2.jar]:
java.net.UnknownHostException: mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/
PlexiViewer/jars/PlexiViewer-1.1b2.jar]:
java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download PlexiViewer-1.1b2.jar.
Attempting to download xdat-search-1.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/

xdat-search-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-search-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/

xdat-search-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xdat-search-1.jar.
Attempting to download xdat-store-1.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/

xdat-store-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-store-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/

xdat-store-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xdat-store-1.jar.
Attempting to download xdat-arcget-1.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/

xdat-arcget-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-arcget-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/

xdat-arcget-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xdat-arcget-1.jar.
Attempting to download xdat-arcread-1.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/

xdat-arcread-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-arcread-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/

xdat-arcread-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xdat-arcread-1.jar.
Attempting to download xdat-arcsim-1.jar.

Error retrieving artifact from [http://repo1.maven.org/maven/xdat/jars/

xdat-arcsim-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/xdat/jars/xdat-arcsim-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org

Error retrieving artifact from [http://www.ibiblio.org/maven/xdat/jars/

xdat-arcsim-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xdat-arcsim-1.jar.
Attempting to download ant-1.6.1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/ant/jars/
ant-1.6.1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/ant/jars/ant-1.6.1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/ant/jars/
ant-1.6.1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download ant-1.6.1.jar.
Attempting to download ij-1.39b.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/ij/jars/
ij-1.39b.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/ij/jars/ij-1.39b.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/ij/jars/
ij-1.39b.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download ij-1.39b.jar.
Attempting to download jargon-1.4.25.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/srb/jars/
jargon-1.4.25.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/srb/jars/jargon-1.4.25.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/srb/jars/
jargon-1.4.25.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download jargon-1.4.25.jar.
Attempting to download xnatsrb-1.jar.
Error retrieving artifact from [http://repo1.maven.org/maven/srb/jars/
xnatsrb-1.jar]: java.net.UnknownHostException: repo1.maven.org

Error retrieving artifact from [http://mirrors.ibiblio.org/pub/mirrors/

maven/srb/jars/xnatsrb-1.jar]: java.net.UnknownHostException:
mirrors.ibiblio.org
Error retrieving artifact from [http://www.ibiblio.org/maven/srb/jars/
xnatsrb-1.jar]: java.net.UnknownHostException: www.ibiblio.org
WARNING: Failed to download xnatsrb-1.jar.

The build cannot continue because of the following unsatisfied
dependencies:

xdat-1.jar
commons-collections-3.0.jar (try downloading from
http://jakarta.apache.org/commons/collections.html)
commons-configuration-1.0.jar (try downloading from
http://jakarta.apache.org/commons/configuration/index.html)
commons-dbcp-1.2.1.jar (try downloading from http://jakarta.apache.org/commons/)
commons-lang-2.0.jar (try downloading from http://jakarta.apache.org/commons/lang.html)
commons-pool-1.2.jar (try downloading from http://jakarta.apache.org/commons/pool/)
jakarta-regexp-1.2.jar
log4j-1.2.8.jar (try downloading from http://jakarta.apache.org/log4j/)
parser-1.jar
postgresql-7.4.214.jdbc2.jar
stratum-1.0-b5.jar (try downloading from http://jakarta.apache.org/turbine/stratum/)
xercesImpl-2.4.0.jar
xml-apis-1.0.b2.jar
xerces-J_1.4.0.jar
xalan-2.5.1.jar (try downloading from http://xml.apache.org/xalan-j/)
velocity-1.3.1.jar
jaxrpc-1.jar
axis-1_3.jar
commons-logging-1.0.4.jar (try downloading from
http://jakarta.apache.org/commons/logging.html)
commons-discovery-0.2.jar
saaj-1.jar
activation-1.0.2.jar (try downloading from http://java.sun.com/products/javabeans/glasgow/jaf.html)
javamail-1.3.2.jar (try downloading from http://java.sun.com/products/javamail/)
PlexiViewer-1.1b2.jar
xdat-search-1.jar
xdat-store-1.jar
xdat-arcget-1.jar
xdat-arcread-1.jar
xdat-arcsim-1.jar
ant-1.6.1.jar
ij-1.39b.jar
jargon-1.4.25.jar
xnatsrb-1.jar

Total time: 3 seconds
Finished at: Wed Jan 30 10:36:12 IST 2008

Please suggest what should I do? I am running into big trouble :(

[Virendra Maloo]

Hi again,
This is my build.properties file.
=========================

#WINDOWS USERS: The '\' character is not supported by Maven. Do not
use the '\' character in your file paths. Replace any '\' characters
with the '/'. The '/' works as a file path separator on UNIX and
WINDOWS.



maven.appserver.home = /root/apache-tomcat-5.5.25/



xdat.project.name=xnat

xdat.project.template=xnat

xdat.project.db.name=xnat

xdat.project.db.driver=org.postgresql.Driver

xdat.project.db.connection.string=jdbc:postgresql://localhost/xnat

xdat.project.db.user=wipro

xdat.project.db.password=wipro



#IMAGE FILE LOCATION (FOR USE WITH THE xnat TEMPLATE)

#Location where image data will be stored.

xdat.archive.location=/home/xnat/imdata



#Location where image data may be stored temporarily before it is
stored into the archive.

xdat.prearchive.location=/home/xnat/preimdata



#Location where cached image data should be stored

xdat.cache.location=/home/xnat/cacheimdata



#Location where thumbnails should be cached

xdat.project.image.thumbnail.location=/home/xnat/cacheimdata/
Thumbnails



#Location where Lo-Res images should be cached

xdat.project.image.lo_res.location=/home/xnat/cacheimdata/LoRes



xdat.smtp.server=blr-ec-mbx06.wipro.com/



xdat.admin_email=virendr...@wipro.com

xdat.url=http://localhost:9000



# 'xdat.require_login' must be set to 'true' or 'false'. It governs
whether or not users will be

# prompted to login when visiting the site. If true, users will be
required to login. If false,

# users will be automatically logged in using an XNAT guest account.

xdat.require_login=true





# 'xdat.enable_new_registrations' must be set to 'true' or 'false'.
Users are provided with a

# link on the Login.vm page to register for a new account. If this
variable is true, that newly

# registered account will be automatically enabled and the user will
be allowed to immediately login.

# If this is false, then an email will be sent to the admin
(xdat.admin_email) requesting that the

# account be enabled, and the user will be unable to login until the
account is enabled.

xdat.enable_new_registrations=false


Do I need to edit any file so that maven doesn't download jar files.
Please help.

[Timothy Olsen]

Virenda,

Your build.properties looks fine. You shouldn't need to have modified the project.properties file (we never touch it in our installs). However, the modifications you made seem fine.

Unfortunately, I'm running out of ideas.

Maven is unable to find the jars which are included in the xnat/plugin-resources/repository folder. This has never happened on any of our other installations.

Maven only tries to download jars from the internet, if it can't find the jars on its local file system. So the problem isn't that it is trying to access the internet. The problem is that it can't find the jars which are sitting a few directories away.

One last thing to try would be to copy the contents of xnat/plugin-resources/repository into ~/.maven/repository. Maybe Maven would be able to find them there. However, that would not identify the problem here (which may cause problems elsewhere).

Otherwise, perhaps you can try installing on a different machine. I just tested the current released version on one of our machines, and everything appeared fine.

Downloaded http://www.xnat.org/xnat_1_3_3.zip
Unzip xnat_1_3_3.zip
Cd xnat
Modify build.properties
./bin/setup.sh

Make sure that all of the steps are done by the same OS user.

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Wednesday, January 30, 2008 6:07 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Virendra Maloo]

Hi,

I tried ething, but problem's getting worse now..Is there any
possibility of modifying file in package through which we can remove
the downloading of packages.

I mean to say the software needs these jars in order to complete the
installation, but these jars will be installed before the setup is
launched and later setup file(or any required file) can be modified
such that it doesn't asks for installation of such jar files.

I urgently need to install the XNAT package in order to start my
project..I know this is a time consuming job but it might help other
users later in case if there's a firewall in the network.

Is XNAT compatible with fc8 ? Or, should I try installing XNAT on
fc7 ? (I don't feel there's problem with any version).

[Alexis]

Hi,

I still haven't any solution, but I had no problem to run xnat on
Fedora fc4, with both java 1.5 and 1.6. Correct me if I'm wrong, but
as maven seems to have a funny behaviour in a package wich usually
works fine, there are many chances that the problem is linked to an
envirronement setting : an env variable ? an alternative install of
maven ? ... In any case, Tim's idea to try on another machine should
stay the best test, and first method to investigate a basic working
install.

This make me think that it would be a good idea to list tested
configuration for severs.

Alexis

[Virendra Maloo]

Hi,

The big problem now is to search fc4!! why do u wnt me to run dis
pkg on an OS which is no longer in use or better say Obsolete!!

Can't this thing b done on fc8 or fc7 or the still running and in
demand fc6?

How can this be a problem related with envmnt vbl??

Did you/tim try to install the pkg on fc4 with jar files stored in
local system?
Looks like I have to try all option available...search begins for fc4
now!!
If there is still any kind of information available, please help me.

[Daniel Marcus]

We run on more recent version of fc without problem, so I don't recommend rolling back to an old version.  Perhaps try testing Maven on some non-XNAT projects, something simple from the Maven site, to see if you can make sure maven is configured properly.

 

Starting from scratch on a different machine sounds like a good idea.  Perhaps setup VMware so that you can work with a fresh system.  If the Harvard folks are listening to this thread, they may be able to help with that and perhaps even send you a virtual machine instance with XNAT already installed.

 

-Dan 

[Virendra Maloo]

Hi to All,

XNAT has been successfully installed on my system. Big thanks to
Mohana!!

[Timothy Olsen]

Excellent. That's great to hear. I'm sorry you had such a struggle.

Mohana, when you get a chance can you post the solution, to give the thread some resolution.

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Friday, February 01, 2008 4:19 PM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Mohana]

One dirty solution to bypass maven trying to look for jars at the
remote repository is to unzip the file http://nrg.wustl.edu/in_home_dir.zip
in the home directory of the user who is trying to install XNAT. You
may consider backing up existing the ~/.maven folder.

Postgres 8.2+ by default comes with pg_hba.conf set to use ident
sameuser and so if you get errors of the kind

A connection error has occurred: org.postgresql.util.PSQLException:
FATAL: Ident authentication failed for user

when you try to install XNAT, modify the pg_hba.conf file to look
like:


# TYPE DATABASE USER CIDR-ADDRESS METHOD

# "local" is for Unix domain socket connections only
local all postgres trust
local all
<XNAT_USER_NAME_HERE> md5
# IPv4 local connections:
host all all 127.0.0.1/32 md5
# IPv6 local connections:
host all all ::1/128 md5

and invoke pg_ctl reload.

Thats it! Volla !

Mohana

> commons-jelly-tags-xml-20030211.142705.jar (try downloading fromhttp://jakarta.apache.org/commons/jelly/libs/xml/)

[Virendra Maloo]

Oh! There was mistake on my part during the installation.
I need to know what changes have you made in pg_hba.conf file mohana .

[kjyogesh]

Hi virendra,

I am facing the same problem exactly what u
faced .. But i want to how you got XNAT installed successfully.. What
is ur mistake?So that i can easily find the same..

[kjyogesh]

Hi Timothy,

I am facing the same problem which virendra faced.
But still my problem was not getting solved. What will be his
mistake.?

[kjyogesh]

Please help me mohana,

I am with the same problem like virendra..
I am supposed to complete my installation and
start my project work from tomo..
So please help me to install xnat .
I changed the pg_hba.conf file and i want to know
how to reload...?

My email id:kjyo...@gmail.com

On Feb 2, 3:33 am, Mohana <mohanakann...@gmail.com> wrote:
> One dirty solution to bypass maven trying to look for jars at the

> remote repository is to unzip the filehttp://nrg.wustl.edu/in_home_dir.zip

[kjyogesh]

Hi Timothy,



Can u please send me the same jar files which u have
send to virendra maloo to my another gmail id.. . kjyo...@gmail.com..

On Jan 25, 8:18 pm, Timothy Olsen <t...@npg.wustl.edu> wrote:
> Virenda,
>
> Glad to hear you've made some progress. The jars you are missing are actually already included in the release. So, you don't need to go find them.
>

> I can directly give you the rest of the files you need. I'll send them directly to your virendrama...@gmail.com account.

[Mohana]

Hello,

XNAT uses a tool called Maven to manage its jars. Maven will go out
to the internet to find jars if it doesn't find them in its own cache.
So, if you populate the cache, them Maven won't need to go looking for
them.

The Maven cache is located in your home directory (a folder
called .maven).
Unzip the 'in_home_dir.zip' (download link: http://nrg.wustl.edu/in_home_dir.zip)
file into the home directory of the user who is installing XNAT
(creating/overwriting the USER_HOME/.maven/ directory).

Then, re-try the setup.sh. If you run into additional problems let me
know.

To refresh postgres run the command: pg_ctl reload

Mohana

On Feb 25, 10:29 pm, kjyogesh <yogesh....@gmail.com> wrote:
> Please help me mohana,
>
> I am with the same problem like virendra..
> I am supposed to complete my installation and
> start my project work from tomo..
> So please help me to install xnat .
> I changed the pg_hba.conf file and i want to know
> how to reload...?
>

> My email id:kjyog...@gmail.com

[Virendra Maloo]

Hi yogesh,

I hope you've installed xnat by this time.

[Virendra Maloo]

Is it like we can run the following command only once while installing
XNAT?

StoreXML -project PROJECT_NAME -l work/sample.xml -u admin -p admin -
allowDataDeletion true.

It gives an error when we try to re-run the command after deleting the
record which it uploads when run for the first time.

The error is:
bash: StoreXML: command not found

[Kevin Archie]

That error message means that your command shell can't find the StoreXML program because your path doesn't include the XNAT_HOME/bin directory. Please set the path -- I sent detailed instructions for this a week or two ago, so you should be able to find that message in the list archives.

- Kevin
________________________________________
From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo [virendr...@wipro.com]
Sent: Monday, March 10, 2008 7:17 AM

To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

Is it like we can run the following command only once while installing

[Timothy Olsen]

What directory are you executing the script from? You can reference the StoreXML with a path relative to your runtime directory. For example, we usually execute the Store from the XNAT_HOME directory. From there you would use 'bin/StoreXML ...'. Based on your path to the sample.xml, I'm guessing you are in the deployment directory, in which case you could use '../../bin/StoreXML ...'.

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Monday, March 10, 2008 7:18 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Virendra Maloo]

Hi,

I set the path and the storexml script ran successfully.
But why doesn't it run when we pass a new file to it. I tried
modifying the complete xml file and tried storing it but the script
gave this error
[root@ec4-t17-131509 xnat]# StoreXML -project xnat -l work/sample2.xml
-u admin -p admin -allowDataDeletion true
Unable to connect to web service.
SETTINGS LOCATION: /root/xnat/deployments/xnat/
WARNING: Data Type:xdat:userGroup has no columns which uniquely
identify it.
WARNING: Data Type:xnat:statisticsData has no columns which uniquely
identify it.
WARNING: Data Type:xnat:abstractStatistics has no columns which
uniquely identify it.
WARNING: Data Type:wrk:abstractExecutionEnvironment has no columns
which uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment has no columns which
uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment_notify has no columns
which uniquely identify it.
Found Document:work/sample2.xml
The prefix "xnat" for element "xnat:MRSession" is not bound.
ERROR: See log for details (logs/xdat.log).

The error in the xdat.log was :

StoreXML (admin)
2008-03-10 20:05:19,342 [main] INFO org.nrg.xdat.XDATTool - work/
sample2.xml,null,true
2008-03-10 20:05:19,342 [main] INFO org.nrg.xdat.XDATTool - Found
Document:work/sample2.xml
2008-03-10 20:05:19,781 [main] ERROR org.nrg.xft.XFT -
org.xml.sax.SAXParseException: The prefix "xnat" for element
"xnat:MRSession" is not bound.
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.nrg.xft.utils.XMLValidator.validateSchema(XMLValidator.java:
34)
at org.nrg.xdat.XDATTool.storeXML(XDATTool.java:170)
at org.nrg.xdat.XDATTool.storeXML(XDATTool.java:130)
at StoreXML.process(StoreXML.java:255)
at
org.nrg.xft.commandPrompt.CommandPromptTool._process(CommandPromptTool.java:
204)
at
org.nrg.xft.commandPrompt.CommandPromptTool.run(CommandPromptTool.java:
178)
at
org.nrg.xft.commandPrompt.CommandPromptTool.<init>(CommandPromptTool.java:
76)
at StoreXML.<init>(StoreXML.java:45)
at StoreXML.main(StoreXML.java:49)

-------------------------------------------------------------------------------------------------------------------------------

Also, while storing sample data, I got these errors, however I tried
all possible options with the command, but error was same.

[root@ec4-t17-131509 xnat]# StoreXML -project xnat -dir sample_data/
xml-base -r true -u admin -p admin -allowDataDeletion true

Missing Required Variable:
-allowDataDeletion OR -allowItemOverwrite: (either 'true' or 'false'):
Whether or not pre-existing data for this element which has no unique
indentifiers specified, should be overwritten. If 'true' the pre-
existing rows will be removed before the new rows are inserted. If
'false', then the new rows will be added (appended) without affect to
the pre-existing rows. (REQUIRED)



Use option -help for assistance.
[root@ec4-t17-131509 xnat]#
------------------------------------------------------------------------------------------------------------------------------
please help me with both of these.
Also, Is it the only way we can store data in the XNAT w/o GUI?

-Virendra

On Mar 10, 6:11 pm, Kevin Archie <karc...@npg.wustl.edu> wrote:
> That error message means that your command shell can't find the StoreXML program because your path doesn't include the XNAT_HOME/bin directory. Please set the path -- I sent detailed instructions for this a week or two ago, so you should be able to find that message in the list archives.
>
> - Kevin
> ________________________________________

> From: xnat_di...@googlegroups.com [xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo [virendra.ma...@wipro.com]

[Virendra Maloo]

After making a copy of sample.xml after slight modification , the
script ran successfully but it didn't made an entry in the mr session.

Why??

this is the output:=

[root@ec4-t17-131509 xnat]# StoreXML -project xnat -l work/sample1.xml

-u admin -p admin -allowDataDeletion true
Unable to connect to web service.
SETTINGS LOCATION: /root/xnat/deployments/xnat/
WARNING: Data Type:xdat:userGroup has no columns which uniquely
identify it.
WARNING: Data Type:xnat:statisticsData has no columns which uniquely
identify it.
WARNING: Data Type:xnat:abstractStatistics has no columns which
uniquely identify it.
WARNING: Data Type:wrk:abstractExecutionEnvironment has no columns
which uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment has no columns which
uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment_notify has no columns
which uniquely identify it.

Found Document:work/sample1.xml
XERCES - XML Document is valid
Loaded XML Item:Subject
Validation: PASSED
Item modifications stored.
Item Successfully Stored.
[root@ec4-t17-131509 xnat]#

[Virendra Maloo]

I have actually found one unusual situation here.
Whenever I modified the sample.xml in the work folder, and ran the
storexml script, everytime it changed original record in the xnat;
i.e ; it modified the XNAT_002MR1 with different values (different id,
dob,etc) instead of creating new record.
why is this happening?

[Timothy Olsen]

Virenda,

This is the expected behavior. The ID field in the subject xml is the unique identifier for the subject. When you restore a document with the same ID value, this is assumed to be a modification of the previously stored subject. So, any changes would be stored to the same subject record. This is also the case with experimentData/ID.

Each of your subjects should have a different (unique) subject id. If you are storing data through the web interface (which is the most common way), this will be handled for you. If you are building xml docs yourself, then you will need to make sure the ID value is different for each one (otherwise you will overwrite the previous one, as you discovered).

I hope this helps.

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Tuesday, March 11, 2008 6:28 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Timothy Olsen]

Virendra,

This is actually a problem with the format of the xml you modified. If you add the xml namespace declarations in your root element, then this problem should go away.

xmlns:xnat="http://nrg.wustl.edu/xnat" xmlns:prov="http://www.nbirn.net/prov" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

It would look something like this...

<xnat:MRSession xmlns:xnat="http://nrg.wustl.edu/xnat" xmlns:prov="http://www.nbirn.net/prov" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ID="XNAT002_MR1">
....
</xnat:MRSession>

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo

[Virendra Maloo]

I tried storing data from 'storexml', (calling it from script).
But I remember it took less time when ran during installation, and now
it takes almost 6-7 seconds to store(insert) a record.
Why is this happening?
The output is:
[root@ec4-t17-131509 xnat]# export PATH=/root/xnat/bin:$PATH
[root@ec4-t17-131509 xnat]# ./algen_code_sample.sh
++ ./algen.sh

Unable to connect to web service.
SETTINGS LOCATION: /root/xnat/deployments/xnat/
WARNING: Data Type:xdat:userGroup has no columns which uniquely
identify it.
WARNING: Data Type:xnat:statisticsData has no columns which uniquely
identify it.
WARNING: Data Type:xnat:abstractStatistics has no columns which
uniquely identify it.
WARNING: Data Type:wrk:abstractExecutionEnvironment has no columns
which uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment has no columns which
uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment_notify has no columns
which uniquely identify it.

Found Document:work/sample1.xml
XERCES - XML Document is valid
Loaded XML Item:Subject
Validation: PASSED
Item modifications stored.
Item Successfully Stored.

Unable to connect to web service.
SETTINGS LOCATION: /root/xnat/deployments/xnat/
WARNING: Data Type:xdat:userGroup has no columns which uniquely
identify it.
WARNING: Data Type:xnat:statisticsData has no columns which uniquely
identify it.
WARNING: Data Type:xnat:abstractStatistics has no columns which
uniquely identify it.
WARNING: Data Type:wrk:abstractExecutionEnvironment has no columns
which uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment has no columns which
uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment_notify has no columns
which uniquely identify it.

Found Document:work/latest.xml

XERCES - XML Document is valid
Loaded XML Item:Subject
Validation: PASSED
Item modifications stored.
Item Successfully Stored.

++ set +x
[root@ec4-t17-131509 xnat]#
--------------------------------------
In the above output you may check that it is not the same output when
we store data for the first time through 'StoreXML' cmd.
Also, it took almost 20 seconds to insert just two records!!
Imagine a situation, where we have to insert 100's of records, In that
case, the system will fail..

It ain't possible that StoreXML is the only way for inserting sample
data in to the db.
I am calling storeXML through a script and it actually, is not a good
solution for a load generation problem. What should I do to save cpu
time?
-----------------------------------------------------------
Also, Is this the solution for the problem I am talking about?
If yes , why doesn't this command run?

[root@ec4-t17-131509 xnat]# StoreXML -project xnat -dir sample_data/
xml-base -r true -u admin -p admin -allowDataDeletion true

Missing Required Variable:
-allowDataDeletion OR -allowItemOverwrite: (either 'true' or 'false'):
Whether or not pre-existing data for this element which has no unique
indentifiers specified, should be overwritten. If 'true' the pre-
existing rows will be removed before the new rows are inserted. If
'false', then the new rows will be added (appended) without affect to
the pre-existing rows. (REQUIRED)

Use option -help for assistance.
[root@ec4-t17-131509 xnat]#
--------------------------------------------

Any help would be highly appreciated..
-Virendra

[Timothy Olsen]

>But I remember it took less time when ran during installation, and now

>it takes almost 6-7 seconds to store(insert) a record.

>Why is this happening?

 

Are you re-storing the same document (possible with a few changes)?  If so, the second store will be slower than the first.  This is because it will need to query each table to see what has changed.

 

Also, a large amount of the execution time here is the initialization of XNAT.  This can be prevented by using web services.  Normally, if you use the StoreXML with the -project attribute (and the xdat.url in build.properties is set properly), the tool will automatically use the web services.  Otherwise, a set of scripts for using the web services is available at http://www.xnat.org/tools.html#client.

 

>Imagine a situation, where we have to insert 100's of records, In that

>case, the system will fail..

 

We do this, and the system doesn't fail.  Generally, the slower stores are caused by large documents.  Small documents store relatively quickly.  Large documents are usually the result of image analysis.  Speed generally isn't an issue during image analysis because most steps in the analysis take much longer then 6-7 seconds.

 

If you are able to use the web services, this should save on your cpu time.

 

> StoreXML -project xnat -dir sample_data/ xml-base -r true -u admin -p admin -allowDataDeletion true

 

This command looks proper, except there is a space between sample_data/ and xml-base.  If that is there in your command, then it could cause the error you are seeing.

 

Hope this helps,

Tim Olsen

 

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Wednesday, March 12, 2008 9:51 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

 

 

I tried storing data from 'storexml', (calling it from script).

[Virendra Maloo]

Tim,

I ran this command again and it gave the same error;Again.
(I placed a space between folder name and xml-base)

[root@ec4-t17-131509 xnat]# StoreXML -project xnat -dir sample_data/
xml-base -r true -u admin -p admin -allowDataDeletion true

Missing Required Variable:
-allowDataDeletion OR -allowItemOverwrite: (either 'true' or 'false'):
Whether or not pre-existing data for this element which has no unique
indentifiers specified, should be overwritten. If 'true' the pre-
existing rows will be removed before the new rows are inserted. If
'false', then the new rows will be added (appended) without affect to
the pre-existing rows. (REQUIRED)

---------------

Should I insist on sample data provided by you for inserting large
amount of sample data?
----------------

I feel the command line tools are moreover same and doesn't make more
difference.
------------------

I would like to know if there is any way through which I can store all
the xml files with less time.(help me if it is the same command listed
above)

-Virendra

[Timothy Olsen]

I am confused. Are you intentionally placing a space between the folder name and xml-base? If so, this will prevent your command from working.

Try reorganizing your options, so that the -allowDataDeletion tag comes before the -dir tag. In practice the tag order shouldn't matter. But, this will test to see if something else in your command syntax is causing the issue.

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Thursday, March 13, 2008 1:30 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

[Virendra Maloo]

This might be one useful change in the XNAT website.
Many of the executables given in the quick tutorial have a long dash,
which needs to be replaced by hyphen .
--------------
I tried running the command:

StoreXML -project xnat -dir sample_data/xml-base -r true -u admin -p
admin -allowDataDeletion true

and it ran successfully.
-----------------------------
and then at the xnat_home, I ran this command which too ran
successfully.

bin/update.sh -Ddeploy=true
------------------------------
But now, when the data should have been uploaded in the db, it still
doesn't displays it in the
mr session.!! (I have restarted tomcat several times).

What should I do to get this sample data.

[Timothy Olsen]

Virendra,

 

The StoreXML script stores XML documents into the database.  After storing the documents, the MR records should show up in the MR browse and have subsequent MR Reports.

 

The 'bin/update.sh' script is used for updating the XNAT installation.  It has nothing to do with uploading data.

 

Is your problem that the MR records aren't showing up in the MR listings/reports?  Or is your problem that the data files associated with those sessions aren't showing up in the MR report?

If you want to be able to view the image data through the website, you'll need to follow the directions within the documentation:

 

Viewing Sample Data Images

 

Tim Olsen

 

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Virendra Maloo
Sent: Friday, March 14, 2008 1:39 AM
To: xnat_discussion
Subject: Re: Installation trouble due to commons-jelly-tags-interaction-20030211.143817.jar

 

 

This might be one useful change in the XNAT website.

[Virendra Maloo]

Tim,

In order to view the MR records on the MR listings, we need to run bin/
update.sh as it is given in the view sample data section.

Still , There is no new MR records in the reports!
I don't know why.(everything worked fine as far as executing commands
are concerned)

Why is there no xnat.war file in the target folder now?
Is it so as I directly included -Ddeploy=true tag to the bin/update.sh
command.

-Virendra

[Imran Shah]