Re: [base] Data truncation: Out of range value

[Steve Taylor]

Hi Nicklas,

 I think you have mailed or filed a bug reporter about a similar problem
 before. See ticket #520: http://base.thep.lu.se/ticket/520

Ah, yes it's the same problem...thanks for fixing it.

 
 The problem was fixed in 2.2.3 so you need to upgrade your BASE
 installation to something newer.
 

Ok. Thanks for the advice. As stated in the bug report if you have an array 
design this also prevents the problem from occurring.

Steve




 /Nicklas
 
 
Hi,

I have extended BASE2.2.1 (MySQL Distrib 5.0.27) to accept ScanArray
files (very similar to GenePix) by changing extended-properties.xml
and updating the database.

The extended-properties.xml the intensity formula I am using is:

intensity-formula name=normalised_ratio_of_means title=Ch1
Normalised Mean / Ch2 Normalised Mean description=Ch1 Normalised
Mean / Ch2 Normalised Mean  formula channel=1 
expression=raw('ch1NMean') / formula channel=2 
expression=raw('ch2NMean') / /intensity-formula

I have uploaded some data in 'raw bioassay', but when I try and
create a 'New root bioassay set' I get what looks like a MySQL error.


Error: Run plugin: Formula intensity calculator Data truncation: Out
of range value adjusted for column 'ch1' at row 1

The stack trace is:

net.sf.basedb.core.BaseException: Data truncation: Out of range value
adjusted for column 'ch1' at row 1 at
net.sf.basedb.core.SpotBatcher.flush(SpotBatcher.java:161) at
net.sf.basedb.core.AbstractBatcher.close(AbstractBatcher.java:117) at
net.sf.basedb.util.IntensityCalculatorUtil.createRootBioAssaySet(IntensityCalculatorUtil.java:447)
 at
net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculatorPlugin.java:256)
 at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
 at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
 at java.lang.Thread.run(Thread.java:595) Caused by:
java.sql.BatchUpdateException: Data truncation: Out of range value
adjusted for column 'ch1' at row 1 at
com.mysql.jdbc.ServerPreparedStatement.executeBatch(ServerPreparedStatement.java:665)
 at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
 at net.sf.basedb.core.SpotBatcher.flush(SpotBatcher.java:155) ... 6
more

Can someone explain what this message means and what the Formula
Intensity Calculator is trying to do here?

Thanks for any help,

Steve

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Re: [base] Guest Role tweaks

[Nicklas Nordborg]

Bob MacCallum wrote:
 I just found that my guest user account was unable to get details
 of bioassayset transformations - for example it would say
 
 Plugin   - denied -
 Plugin configuration - denied -
 
 and the same under transformation and job.  This isn't ideal - a guest
 user would be very interested to know what transformations had been made.
 
 I double checked all the plugin definitions were readable by this user - and
 they were.
 
 I found that the problem could be fixed by giving the Guest Role read
 permission on Jobs.  At the same time I removed all create permissions for
 this role (files, directories, jobs).  Now I believe our guest user is truly
 read-only.
 
 The multi-user account option is invaluable here (it stops the user changing
 the password).
 
 hope that helps someone...

Nice to see that someone is really using the permission system.

I think there is a minor flaw in the design of jobs. They always get 
their permissions as if they are standalone items which means that only 
the user that created a job can view it (unless more permissions are 
granted to the roles as Bob has done). Jobs that are part of an 
experiment should really get their permissions from the experiment just 
as bioassay sets and transformations do. I don't know if it is possible 
to implement this with a reasonable amount of effort, but I'll check it out.

/Nicklas

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