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: http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageExporter
Hi Bob,
User with unlimited quota will be able to execute the plugin with the
new release which should appear soon on the download page.
Also, I have just investigated the plugin permission for the tab2mage
importer and think I have hit the reason why you may have had a failure
whilst running
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 T
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
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 r
> 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 s
e last email 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:
> > >
vegard nygaard wrote:
> I am trying out the Tab2Mage importer. When starting it from the "import"
> button in an experiment it quickly returns with an error. I am running it as
> root on base2.4.3 having added tab2mage importer and Annotation Type and CV
> Loader as plug-ins. Input file is the gen
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 every
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 exper
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Dominic Oye
Hello all,
This is to call the attention of all base2 users to the new plugins
available for download on the base2plugin website
(http://baseplugins.thep.lu.se/wiki/PluginDownload)
The plugins (itemised below) have been released in recent past and are
available to enhance BASing experience :
Hi Nicklas,
I can confirm that this is entirely an affymetrix issue.
¬Dominic
Nicklas Nordborg wrote:
> Dominic Oyeniran wrote:
>
>> The workaround works.
>> But thats after I removed each raw bioassay and its associated
>> experiment first and thereafter remove
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 come
IMER:
> >
> > This email is from the Scottish Crop Research Institute, but the views
> > expressed by the sender are not necessarily the views of SCRI and its
> > subsidiaries. This email and any files transmitted with it are
> confidential
> > to the intended re
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 stick
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 t
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, r
Hi Micha,
I did another test run with a non-root user, as you suggested and the
import failed (see the exception). I have stated what I noticed below.
Please check them out in addition to the suggestion by Nicklas
=
===NEW BATCH IMPORT =
==
Nicklas Nordborg wrote:
> Micha Bayer wrote:
>
>> Hi Dominic,
>>
>> Thanks for trying this out.
>>
>>
>>> I tested the batch import today, on an affy experiment and I got the
>>>
>> ff
>>
>>> exception:
>>>
>>> =
>>> ===NE
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
Hi,
>public class ZipFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
> private static final Set guiContexts =
> Collections.singleton(new GuiContext(Item.EXPERIMENT,
GuiContext.Type.ITEM));
>
>then I'll get an import tab created
-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
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 Of
installed the jdbc to mysql and try it with a
mini-program... I depured the privileges ... and voila !!!
THANKS!!!
dominic oyeniran escribió:
> Ok what is the netsensor password in this section of your code:
> [EMAIL PROTECTED] bin]# ./initdb.sh netsensor.
> Is it your mysql root passwo
another machine.
I have a doubt. JAVA has a jdbc to mysql installed or i have to download
and install one?
Thanks
dominic oyeniran escribió:
> Ok what is the netsensor password in this section of your code:
> [EMAIL PROTECTED] bin]# ./initdb.sh netsensor.
> Is it your mysql root password?
&g
achine and works.
I have a CMS that use MySQL in the same machine too
dominic oyeniran escribió:
> Pablo,
> Change the url to:
> db.url = jdbc:mysql://localhost:3306/base2
> and then do issue the initdb command.
>
> Dominic
>
> -Original Message-
&
@lists.sourceforge.net
Subject: Re: [base] A problem with intidb in BASE2.0RC1
Hi dominic
The database is on the same machine and is listening at 3306.
i copy the www directory of base package to /var/www/html/base2 so my
db.url is: localhost/base2. Is all right?
Thanks
dominic oyeniran escribió:
> Hi Pa
re to connect to MySQL server or privileges
of the user. My base2user have privileges to: create, update, delete,
drop, alter, insert
Thanks
dominic oyeniran escribió:
> Hi
>
> I reckon its something to do with the database setup parameters in your
base
> config file. Can u check
Hi
I reckon its something to do with the database setup parameters in your base
config file. Can u check it again or post it here and I can have a look at
it?
Regards,
Dominic
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Pablo Lemos
Ochandio
Sent: 20
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