Chad Matsalla wrote: > Greetings! > > I'm trying to export a basefile using "Run plugin: Bioassay set file > exporter". Neither 'normal' nor 'serial' versions succeed. > > I navigate to my bioassay set, click export, fill in the parameters[1] and > export fails[2] > > I'm doing this to troubleshoot a problem we're experiencing with a base1 > plugin. This plugin needs to operate on a serial basefile but in base2 the > plugin fails with this message[3]. I suspected (duh!) that the basefile is > not being generated. > > Thanks for your help!
I have now checked this and can inform everyone that I found several other bugs as well in the bioassay set exporter plugin. All bugs will be addressed in 2.3.1 release. See http://base.thep.lu.se/milestone/BASE%202.3.1 for more information [2] is caused by ticket #588. A workaround is to rename the formulas to only use alphabetical characters (a-z) or numbers in their names. No spaces or other characters are allowed. Anyway I am am afraid that it won't help since there is another bug (#589) in the serial format export that is not possible to workaround. I am not sure [3] is related to any of the already known bugs. To check this I need the BASE 1 configuration file for the plugin. /Nicklas > > Chad Matsalla > > > > [1] > Bioassay set Initial bioassayset > Fileformat BASEfile > Average on reporters false > Overwrite false > Save as /home/root/temp/basefile.base > Export as matrix or serial basefile. true > Reporter accession > Fields intensity1, intensity2, position, A, log10(ch1 * ch2) / 2, M, > log2(ch1 / ch2), Ratio, ch1 / ch2, block, bgPixels > > [2] > net.sf.basedb.core.InvalidDataException: Alias 'A, log10(ch1 * ch2) / 2' has > one or more invalid characters. Only a-z, A-Z and 0-9 is allowed. > at net.sf.basedb.core.query.Selects.expression(Selects.java:57) > at > net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileSerial(BioAssaySetEx > porter.java:298) > at > net.sf.basedb.plugins.BioAssaySetExporter.run(BioAssaySetExporter.java:937) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java > :88) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420) > at java.lang.Thread.run(Thread.java:595) > > [3] > java.lang.NullPointerException > at > net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileSerial(BioAssaySetEx > porter.java:298) > at > net.sf.basedb.plugins.Base1PluginExecuter.exportData(Base1PluginExecuter.jav > a:524) > at > net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:435) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java > :88) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420) > at java.lang.Thread.run(Thread.java:595) > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
