I found the problem and fixed it by moving the creation of the group parameter to the loadFromXml function in BatchQueue.
It does however seem like we have a problem with not all errors being shown when executing MZmine without the GUI. Cheers, Thomas -----Original Message----- From: Tomas Pluskal [mailto:plus...@oist.jp] Sent: 19. februar 2015 09:08 To: Developer discussion Subject: Re: [Mzmine-devel] Problem with RowsFilterModule in batch module Hi Thomas, That is very strange, indeed. I have no idea what is causing this. My suggestion is: dig deeper into the problem :) Cheers, Tomas > On Feb 19, 2015, at 16:58, TFRD (Thomas Franck Dyrlund) <t...@steno.dk> wrote: > > Thanks Tomas, the compiling works perfect! > > However, when I test the batch queue system from a command line, MZmine stops > without any errors when running the RowsFilterModule task: > [8:44:13|FINEST|TaskQueue]: Adding task "Filtering peak list rows" to > the task controller queue Press any key to continue . . . > > I’m running MZmine under Windows 7 32-bit using the following two commands in > a command prompt: > cd C:\MZmine\MZmine-2.13.1b\ > startMZmine_Windows.bat C:\Users\tfrd\Desktop\MZmine-batch-queue.xml > > The batch queue runs fine in the GUI version and if I remove the > RowsFilterModule task then everything runs fine from the command line also. > Any suggestions? > > /Thomas > > From: Tomas Pluskal [mailto:plus...@oist.jp] > Sent: 19. februar 2015 04:11 > To: Developer discussion > Subject: Re: [Mzmine-devel] Problem with RowsFilterModule in batch > module > > Hi Thomas, > > I noticed that there is a problem with the RowFilterModule when using the > batch module in both GUI and command mode. The problem is with the groups > parameter value which is not set when loading a batch queue from a file. I > have committed a change (3694) to solve the error – please let me know if you > see a problem with the commit. > > Looks fine to me, as a workaround until we improve the way to set the > parameters. > > > > I don’t know how to compile the current project in Eclipse locally so that I > can test the batch module in command mode with the change. I would therefore > appreciate if someone would test it for me or provide me with information > about how to compile the project in Eclipse locally on my machine. > > You can compile the whole project from the command line, by running "mvn > package" (assuming you have Apache Maven installed). > > From Eclipse, you can do the same by right mouse click on pom.xml -> > select Run As -> Maven build -> set "package" as build goal > <image001.png> > > > > > > Also, since all parameters seem to be verified before the batch queue begins > then the parameter settings check in l. 85-93 of BatchTask.java seems > redundant. Shouldn’t this be removed? > > I don't think it's redundant. Validity of some parameter values may depend on > the state of the project (e.g. how many raw data files the project has). The > state of the project can change during the batch, so it makes sense to > validate the parameters before running each step. > > Best, > > Tomas > > > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > WWW: https://groups.oist.jp/g0 > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > <MZmine-batch.xml><Console > output.txt>----------------------------------------------------------- > ------------------- Download BIRT iHub F-Type - The Free > Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your > Business Reports and Dashboards with Interactivity, Sharing, Native > Excel Exports, App Integration & more Get technology previously > reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg. > clktrk_______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890 ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! 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