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]
[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]
Re: [base] demo server updates and presets Q's
Thanks, I was just interested in what your policy is - I'm not suggesting any changes to it. I'll often look at the timeline and want to see the changes, but I'm not sure if they're in place yet. As for the presets, you were right, I had the owned by me selected. It now works as expected. Thanks, Dion Agriculture and Agri-Food Canada - Agriculture et Agroalimentaire Canada -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicklas Nordborg Sent: Monday, October 23, 2006 2:11 AM To: BASE ML Subject: Re: [base] demo server updates and presets Q's Lepp, Dion wrote: Hi all, I was wondering how often the base2 demo server is updated ie. are the changes shown in the Trac timeline reflected in the server immediately? No, the server has the latest released version. The reason is that there is a risk that updates won't work between arbitrary revisions. In the worst case it could lead to data corruption and that it is impossible to upgrade to the next release. That said, there is no guarnatee that this will not happen with released versions, but we have at least done some testing to make sure it doesn't happen. And if someone finds a problem we will try to fix it. Secondly, I am having trouble understanding the in current project preset, and the entire active project system for that matter. What I would expect is that when samples, hybs etc. are added, they will automatically be associated with the active project. If In current project is then selected in the presets, only those samples, hybs, etc. associated with the active will be displayed. In my hands, setting the active project or the in current project preset has no effect. Could someone please shed some light on this? Your description seems correct. What is probably happening is that you still have the Owned by me option selected. If you deselect that option and only leave the In current project option select you should only see items that are part of that project. /Nicklas - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] demo server updates and presets Q's
Hi all, I was wondering how often the base2 demo server is updated ie. are the changes shown in the Trac timeline reflected in the server immediately? Secondly, I am having trouble understanding the in current project preset, and the entire active project system for that matter. What I would expect is that when samples, hybs etc. are added, they will automatically be associated with the active project. If In current project is then selected in the presets, only those samples, hybs, etc. associated with the active will be displayed. In my hands, setting the active project or the in current project preset has no effect. Could someone please shed some light on this? 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 Guelph, Ontario N1H 2J8 [EMAIL PROTECTED] - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
