Thanks for the stacktrace. It seems to be a bug in the
Base1PluginExecuter plug-in. It is trying to remap the raw data
associations after the bioassays have been merged. Obviously, this is
not possible if there is no raw data stored in the first place. The
Base1PluginExecuter need to be fixed with a check for this case.
I have created a ticket for this fix to be included with the BASE 2.17.2
release. Unfortunately there is no workaround.
http://base.thep.lu.se/ticket/1610
/Nicklas
On 2011-05-20 10:12, Irina 264 wrote:
from Stack trace tab:
View job -- Run plugin: Base1PluginExecuter
javascript:Main.openTabControlHelp('7a1ebdaa616cc46f',%20'main',%20'null')
Name Run plugin: Base1PluginExecuter
Description
Priority 5 (1 = highest, 10 = lowest)
StatusError: Raw data for raw data type: Affymetrix is not stored in
the database.
Percent complete
unknown
100%
Created 2011-05-20 18:10:30
Scheduled 2011-05-20 18:11:10
Started 2011-05-20 18:11:28
Ended 2011-05-20 18:11:42
Running time 14 seconds
Serververa097.its.monash.edu.au
Job agent /- none -/
User Irina Rusinova
ExperimentE-GEOD-6257
PluginBase1PluginExecuter (version 2.16.0)
Configuration MergeBioAssay
net.sf.basedb.core.BaseException: Raw data for raw data type: Affymetrix
is not stored in the database.
at
net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261)
at
net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510)
at
net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346)
at
net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471)
at
net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
at java.lang.Thread.run(Thread.java:636)
Date: Fri, 20 May 2011 09:21:12 +0200
From: nick...@thep.lu.se
To: basedb-users@lists.sourceforge.net
Subject: Re: [base] reporters on MergeBioAssay plug-in
On 2011-05-20 09:04, Irina 264 wrote:
Hi Nicklas,
Thanks for the quick reply.
I run RMAExpress with Affy data, then I done filtering with equal size
of arrays afterwards.
Then I run MergeBioAssay (with Base1pluginExecuter) to find average
between replicates (grouping assays by control and treatment with
method
‘arithmetic mean of intensity) and have this error message: “Error: Raw
data for raw data type: Affymetrix is not stored in the database.”
When I use Agilent data, i have no problems.
Did I explain better?
Yes... but I still have no idea why the error about raw data is coming
up... As far as I know the Merge BioAssay plug-in doesn't use raw data
for the calculations. It would be useful to get a complete stacktrace of
the error in order to locate the source of the problem.
Do you get the error while you are configuring the job? If so you should
be able to display more error information by clicking on the little [+]
icon in the configuration wizard.
Or, if you get the error while the plug-in is running, there is a Stack
trace tab in the job dialog.
/Nicklas
--
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
basedb-users-requ...@lists.sourceforge.net
--
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
basedb-users-requ...@lists.sourceforge.net
--
What Every C/C++ and Fortran developer Should Know!
Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost
