Re: [base] spot images error
Thanks, that was the problem. It is working now. One quirk/bug I came across is that after re-creating spot images for a bioassay, the images from the original creation still remain. Logging in and out of Base does not correct this. However, refreshing the webpage (which automatically logs you out) and then logging back in causes the new images to be displayed. Dion Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire Canada -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicklas Nordborg Sent: Thursday, March 27, 2008 2:59 AM To: BASE ML Subject: Re: [base] spot images error Lepp, Dion wrote: I am uing BASE 2.4.5 (build #3894; schema #40) Dion Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire Canada -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicklas Nordborg Sent: Wednesday, March 26, 2008 1:16 PM To: BASE ML Subject: Re: [base] spot images error Lepp, Dion wrote: I'm trying to create spot images from a tiff file (single layer from Scanarray software) and keep receiving an error with the following stack trace. The image is 5 um, and I'm using the parameters given in the .gpr file (xscale= 5, yscale=5, xoffset= 1155, yoffset = 1577) and a spot size = 32. I've tried a number of variations on these values with no luck. Any ideas? It happens because there is at least one spot which has a null value in it's X coordinate. It is not possible to extract the spot images unless the data contains X and Y coordinates and those spots should of course be ignored. We'll fix this in 2.6.2. /Nicklas - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketp lace ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] spot images error
Lepp, Dion wrote: Thanks, that was the problem. It is working now. One quirk/bug I came across is that after re-creating spot images for a bioassay, the images from the original creation still remain. Logging in and out of Base does not correct this. However, refreshing the webpage (which automatically logs you out) and then logging back in causes the new images to be displayed. I think that is your browser that caches the images. The reason that logging in and out helps is that the session ID is part of the URL to the images which means that they are reloaded by the browser. /Nicklas - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] spot images error
I'm trying to create spot images from a tiff file (single layer from Scanarray software) and keep receiving an error with the following stack trace. The image is 5 um, and I'm using the parameters given in the .gpr file (xscale= 5, yscale=5, xoffset= 1155, yoffset = 1577) and a spot size = 32. I've tried a number of variations on these values with no luck. Any ideas? java.lang.NullPointerException at net.sf.basedb.core.SpotImages.createSpotImages(SpotImages.java:487) at net.sf.basedb.plugins.SpotImageCreator.run(SpotImageCreator.java:148) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) at java.lang.Thread.run(Thread.java:595) Thanks, Dion Dion Lepp, M.Sc. Guelph Molecular Biology Research Unit Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada Telephone/Téléphone: 519-780-8090 Facsimile/Télécopieur: 519-824-2600 93 Stone Road West Guelph, Ontario N1G 5C9 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] image001.jpg- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
