[InterMine Dev] [Fwd: Exporting data to Galaxy]

Lewis, Brian Andrew brilewis at iupui.edu
Wed Sep 7 15:32:40 BST 2011


Okay, that must have been what was causing the error because after I added that and re-released the application, it's working fine now.  Thanks for all the help, Fengyuan.

~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Wednesday, September 07, 2011 8:56 AM
To: Lewis, Brian Andrew
Cc: dev at intermine.org
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Have you included the following line in you struts-config-model.xml?

<action path="/initGalaxyExportOptions"
        type="org.intermine.bio.web.struts.GalaxyExportOptionsController"/>

cheers
Fengyuan

On 07/09/11 13:29, Lewis, Brian Andrew wrote:
Okay...I found the file.  I checked it after going through the export procedure and this was the only relevant line I found (I didn't see any lines with the URL printed out):

07/09/11,08:15:40 ERROR org.apache.struts.action.RequestProcessor     - Invalid path /initGalaxyExportOptions was requested

~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Wednesday, September 07, 2011 6:36 AM
To: Lewis, Brian Andrew
Cc: dev at intermine.org<mailto:dev at intermine.org>
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Hi Brian,

Normally a log file called "intermine.log" will be generated in the dir where you launch your tomcat, in my case, it's under tomcat/bin/, in the file you should see all the logs you'd like to print out in your java class. Could you look for it?

Cheers
Fengyuan

On 06/09/11 18:28, Lewis, Brian Andrew wrote:
Fengyuan -

I added that line to the code but I'm not getting any output from the log.  The following property is present in my intermine.properties file in the home directory, so I would think it should be working:

webapp.logdir=/usr/local/apache-tomcat-6.0.33/logs/

I also checked the logging properties for Tomcat and all logs are set to "INFO" level.

This is the only output I'm seeing in catalina.out:

Sep 6, 2011 1:20:14 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/nntcmine] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Sep 6, 2011 1:20:14 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/nntcmine] appears to have started a thread named [WriteBatch Flusher] but has failed to stop it. This is very likely to create a memory leak.
Sep 6, 2011 1:20:14 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/nntcmine] appears to have started a thread named [Thread-47] but has failed to stop it. This is very likely to create a memory leak.
Sep 6, 2011 1:20:14 PM org.apache.catalina.startup.HostConfig checkResources
INFO: Undeploying context [/nntcmine]
Sep 6, 2011 1:20:15 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive nntcmine.war

And here's the output from localhost.2011-09-06.log file:

Sep 6, 2011 1:20:14 PM org.apache.catalina.core.ApplicationContext log
INFO:  [CompressingFilter/1.7] CompressingFilter is being destroyed...
Sep 6, 2011 1:20:15 PM org.apache.catalina.core.ApplicationContext log
INFO:  [CompressingFilter/1.7] CompressingFilter has initialized
Sep 6, 2011 1:20:15 PM org.apache.catalina.core.ApplicationContext log
INFO: action: []: Verifying ModuleConfig for this module
Sep 6, 2011 1:20:15 PM org.apache.catalina.core.ApplicationContext log
INFO: action: []: null
Sep 6, 2011 1:20:15 PM org.apache.catalina.core.ApplicationContext log
INFO: action: []: Verification of ModuleConfig has been completed

~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Tuesday, September 06, 2011 12:06 PM
To: Lewis, Brian Andrew
Cc: dev at intermine.org<mailto:dev at intermine.org>
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Hi Brian,

I've just tested it on 0.97, but it worked fine for me.

The URL is generate in GalaxyExportOptionsController.java line 195, could you please print "link" out in the log?

LOG.info("URL to Galaxy:\n" + link);

Cheers
Fengyuan

On 06/09/11 15:26, Lewis, Brian Andrew wrote:
It is 0.97, which is the latest version.

~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Tuesday, September 06, 2011 10:17 AM
To: Lewis, Brian Andrew
Cc: dev at intermine.org<mailto:dev at intermine.org>
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Hi Brian,

Based on the fact that you can actually send intermine data to Galaxy and the URL value is null, it should be an intermine issue. It looks to me you are working with a fairly old version of intermine, what version is it?

Cheers
Fengyuan

On 06/09/11 15:08, Lewis, Brian Andrew wrote:
Fengyuan -

I just checked and it looks like the 'URL' field is not being generated correctly (see attached image) since the value is blank.  Unfortunately the server isn't public, so I can't give you the URL.  I did attach my intermine.properties file as well, with some server details removed.

I did create a new data source tool for Galaxy and it is pointing to the correct URL of our InterMine instance.

Because of the nature of the issue, I really wasn't sure if this was a question for Galaxy's dev mailing list or InterMine's.

Thanks,
~ Brian

From: Fengyuan Hu [mailto:fh293 at cam.ac.uk]
Sent: Monday, September 05, 2011 8:23 AM
To: Lewis, Brian Andrew
Cc: dev at intermine.org<mailto:dev at intermine.org>
Subject: Re: [Fwd: [InterMine Dev] Exporting data to Galaxy]

Dear Brian,

Sorry for the slow reply.

First of all, it seems you've set up galaxy config in InterMine the right way. I've tried to reproduce your error, but it works fine for me to send data from a local InterMine to a local Galaxy.

The "URL" content should be programmatically generated by InterMine. Is your server public for me to test on? Or can you inspect it by firebug in firefox or chrome on the export page, there should be a hidden field called "URL" (see screenshot attached). Can you find it in your page? A further question is, did you create a new data_souce tool<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ctool.3E_tag_set>  for your mine or you are using an existing tool, such as modmine or flymine, etc. (this is set in web.properties as for "galaxy.url.value" key)?

I've also checked the source code for Galaxy data_source (galaxy-dist/tools/data_souce/data_source.py) , the error is indeed caused by the missing "URL" parameter in the http request. It looks quite odd to me so far.

Thanks
Fengyuan

On 05/09/11 10:39, julie at flymine.org<mailto:julie at flymine.org> wrote:

---------------------------- Original Message ----------------------------

Subject: [InterMine Dev] Exporting data to Galaxy

From:    "Lewis, Brian Andrew" <brilewis at iupui.edu><mailto:brilewis at iupui.edu>

Date:    Fri, September 2, 2011 6:53 pm

To:      "dev at intermine.org"<mailto:dev at intermine.org> <dev at intermine.org><mailto:dev at intermine.org>

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



I'm in the process of hooking up our instance of InterMine to an instance

of Galaxy (on the same server).  I figured out that I need to added the

section to tiles-defs-model.xml and modify the web.properties file as

well.  After re-deploying my mine, I'm able to get to the "Export to

Galaxy" page.  When I click "Export", the job does go to Galaxy but I get

the following error message back from Galaxy:



An error occurred running this job: The remote data source application has

not sent back a URL parameter in the request.



To anyone with experience hooking up these two apps, could you let me know

how to set this URL parameter?



Thanks,

Brian Lewis

_______________________________________________

dev mailing list

dev at intermine.org<mailto:dev at intermine.org>

http://mail.intermine.org/cgi-bin/mailman/listinfo/dev





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.intermine.org/pipermail/dev/attachments/20110907/275affa2/attachment-0001.html>


More information about the dev mailing list