[base] New Release of Tab2mageImport and Export Plugins

We are happy to announce the release of a new version of the Tab2Mage import and Tab2Mage export plugins available for download from the base2plugin website: Import: http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter Export:

Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter

vegard nygaard wrote: Dominic wrote: Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? No. I installed and tested the AnnotationTypeCvImporter with its own jar file and assumed it was the same. I now changed to use the

Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space

Jari Häkkinen wrote: Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section

Re: [base] Tab2Mage Importer has problems finding AnnotationTypeCvImporter

vegard nygaard wrote: Hi. This is for Dominic I guess. The last error I reported yesterday was from my own shortcutting and is fixed. (I had not yet made a design). Today I got an error when the plug-in tried to use the AnnotationTypeCvImporter. BASE error message: IMPORT FAILS: The

Re: [base] tab2mage exporter question

Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation that I wanted to ask you about. Our experiment

Re: [base] tab2mage exporter question

Nicklas Nordborg wrote: Dominic Oyeniran wrote: Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation

Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space

is : http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Just an information for other interested users too. Thanks, ¬Dominic Bob MacCallum wrote: Dominic Oyeniran writes: vegard nygaard wrote: I am trying out the Tab2Mage importer. When

Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space

And it is also linked from http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.Tab2MageImporter But the readme file is not very precise about this problem, it advices me not to use root. I disregarded that advice :(. If it will only run as a non-root user with a limited quota, that should

Re: [base] Null pointer exception on deleting affymetrix raw data

Nicklas Nordborg wrote: Dominic Oyeniran wrote: I am experiencing the problem with deletion of items. See the exception below. Description: When you start deleting from the trash can either with delete permanently or empty trash, the process dialog comes up but never finishes and throws

Re: [base] BatchDataImporter broken w/ 2.4?

Hi all, Sorry everyone for my late response or contribution, I have been away. I hope this short email will address some of the issues raised on the tab2mage importer Owing to the fact that the importer supports only affymetrix, genepix and agilent platforms, I reckon interested users can

Re: [base] Unable to view BioMaterials items after upgrade to 2.3.2

Hi James, Option 2 on that ticket (http://base.thep.lu.se/ticket/682) works quite well for me. Especially if your application/installation is not particularly gaining any substantial features of mysql 5.0.27. So migrating to a lower Mysql version should be ok. Do remember to backup your data

Re: [base] tab2mage/annotation questions

Hi Bob http://base.thep.lu.se/chrome/site/doc/html/userdoc/analysis/experiments_analysis.experiments.html#experiments_analysis.magexport Dumb question: An Annotation Type such as Age(hours) or body mass(kg) when applied to a biosource will be exported as a BioMaterialCharacteristic, right?

Re: [base] batch importer plugin is available for testing now

Hi Micha, Nice work. I tested the batch import today, on an affy experiment and I got the ff exception: = ===NEW BATCH IMPORT = = zn =HG-U133A.cdf experiment: Experiment[id=5; name=Batch Importer

Re: [base] Offline files

Hi, public class ZipFileImporter extends AbstractPlugin implements InteractivePlugin, AutoDetectingImporter { private static final SetGuiContext guiContexts = Collections.singleton(new GuiContext(Item.EXPERIMENT, GuiContext.Type.ITEM)); then I'll get an import tab

Re: [base] Offline files

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Micha Bayer Hi Micha, I have just finished writing one. The user uploads a zip file, a new directory is created in the user's raw data directory (with the same name as the zip file) and the files are

Re: [base] Changing CDF/CEL association

Hi, Since you are running the demo installation, your privileges may have been limited. I can unlink affy array design/ raw files association on my installation. Note: I have admin rights. Regards, Dominic -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf