[base] Bugs in migration process

2007-11-29 Thread Pawel Sztromwasser
. All the best, Pawel Sztromwasser - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http

Re: [base] Bugs in migration process

2007-11-29 Thread Pawel Sztromwasser
with MySQL here. See below for comments on each specific issue. Pawel Sztromwasser wrote: Hi, We are doing some preliminary migrations on testing databases to test if everything works fine with the migration script. We use Postgres 7.3.9 on both, Base1 and Base2 installations, so we will test

Re: [base] Bugs in migration process

2007-11-29 Thread Pawel Sztromwasser
Nicklas Nordborg wrote: Pawel Sztromwasser wrote: The second thing is transferring wizzzards. In our Base1 database those with /formatType=reportermap/, have column and row numbers in /mapping/ property proceeded by /_r_x /and/ _r_y/ respectively, not by /numCol/ and /numRow

Re: [base] BASE Lowess Normalization Plugin

2008-01-18 Thread Pawel Sztromwasser
Hey, Could you check if you are not using any filters in plugins view that could narrow results? Pawel Nick Loman wrote: Pawel Sztromwasser wrote: It seems like the plugin is there. Check if this plugin has been shared to your user (Administrate-Plugins-Definitions and find the plugin

Re: [base] BASE Lowess Normalization Plugin

2008-01-18 Thread Pawel Sztromwasser
/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Pawel Sztromwasser Computational Biology Unit Bergen Center for Computational Science

[base] How to connect to FTP server

2008-09-30 Thread Pawel Sztromwasser
Hi all, I have just upgraded to the latest BASE 2.8.2 and installed the base-FTP server. Everything went smoothly, but I have one, little silly question: how do I connect to the server? what is the address? I have tried various combinations of the host name where BASE is installed (with and

Re: [base] How to connect to FTP server

2008-09-30 Thread Pawel Sztromwasser
/browser/extensions/net.sf.basedb.ftp/trunk/ftp-config.xml#L29 Jari Pawel Sztromwasser wrote: Hi all, I have just upgraded to the latest BASE 2.8.2 and installed the base-FTP server. Everything went smoothly, but I have one, little silly question: how do I connect to the server? what

[base] Batch plugin import fails for administrator account

2008-10-31 Thread Pawel Sztromwasser
Hi, I had a session today explaining our lab users how to use batch import/annotate plugins and we came across a bug (maybe). It seems like the batch import plugin disregards some of these options (I would expect the 3rd one): In current project Owned by me Owned by others Shared to me To

Re: [base] Experiment overview loads very slowly

2009-01-16 Thread Pawel Sztromwasser
Done Nicklas Nordborg wrote: Thanks for this! It seems to a very thorough analysis of the problem. Can you create a ticket for this and at least link to this thread in the mailing list archive? /Nicklas Pawel Sztromwasser wrote: Nicklas Nordborg wrote: Hi Nicklas, I agree

Re: [base] File types assigned when extracting an archive

2009-03-05 Thread Pawel Sztromwasser
://base.thep.lu.se/ticket/978 explaining why it can't be fixed. A workaround is to match file extensions to MIME types that are linked with file types. /Nicklas Pawel Sztromwasser wrote: Hi, Is it possible to assign file type to files uploaded in archive and extracted on the fly? The file type

Re: [base] Tab2Mage export

2009-04-28 Thread Pawel Sztromwasser
Hi, I am also curious how development of ArrayExpress export is going? We would be very interested in having this plugin working with latest BASE2. We are exporting data to AE quite often and would have a great use of it. I even hacked existing plugin a little bit to get at least part of the

[base] Select button does not work in IE7.0 + XP Home SP3

2009-07-07 Thread Pawel Sztromwasser
Hi again, Another issue we got reported during session with users: in IE 7.0.5730.13 (XP Home SP3) Select buttons launching different window with appropriate lists of items in this context (I.e. select a Protocol when editing an Extract) do not work. New window does not pop up and an error is

[base] Files shared to a project give nasty exception when changing project

2009-07-07 Thread Pawel Sztromwasser
Hello, We came across this: http://base.thep.lu.se/ticket/1348 Best wishes, Paweł -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors

[base] Listing settings and new menu item

2009-07-07 Thread Pawel Sztromwasser
Hi, I have noticed a new menu item (I am not sure how *new* it is but I have just spotted it so it is new at least for me): File-Reset list settings. What is it for? Does it bring all the listings' columns to default? Or it does some more complicated stuff? We have been experiencing weird

[base] Illumina design not playing its role

2009-08-21 Thread Pawel Sztromwasser
Hello BASErs, After little hands-on session with BASE I have reported some bugs/comments on trac: http://base.thep.lu.se/ticket/1360#preview http://base.thep.lu.se/ticket/1361#preview These are rather minor things, but there is something that worries us more. I know that the array design

Re: [base] Illumina design not playing its role

2009-08-24 Thread Pawel Sztromwasser
Thank you! Nicklas Nordborg wrote: I have added two tickets. One is for the Bead summary importer in the Illumina package: http://baseplugins.thep.lu.se/ticket/240 The other is for the Overview functionality in the BASE web client: http://base.thep.lu.se/ticket/1362 We'll probably be

[base] Size limit of online file edit

2009-10-01 Thread Pawel Sztromwasser
because of its size. It took us a while to find out what is going on with some of the files being properly saved, while others were not. What do you think about it? All the best, Pawel Sztromwasser -- Come build with us

Re: [base] Size limit of online file edit

2009-10-01 Thread Pawel Sztromwasser
later today Nicklas Nordborg wrote: Pawel Sztromwasser wrote: I just tested it again (FF3.5.3). Here is how to reproduce: - upload a text file which is larger then 8kb - memorize file's size - edit file removing one character only - check the size again In my case removing one character

Re: [base] Size limit of online file edit

2009-10-02 Thread Pawel Sztromwasser
OK. Great thanks for solving this! Pawel Jari Häkkinen wrote: Nicklas Nordborg wrote: I downloaded and installed Tomcat 6.0.16 and got the same problem. It works with Tomcat 6.0.20. And our production server runs 6.0.16. So, it is time to upgrade. Jari

[base] BEAD summary importer in experiment details context

2010-02-24 Thread Pawel Sztromwasser
Hi, I don't get Illumina BEAD summary importer plugin as a choice of plugin when I click Import button in experiment's details. Is there any requirements that experiment has to fulfill so that plugin shows up in its context? It pops up after clicking import button in details of a rawbioassay

Re: [base] BEAD summary importer in experiment details context

2010-02-24 Thread Pawel Sztromwasser
data importer. Another weird thing I noticed is that all these plugins show version pre1.1 (instead of 1.3 which they are). Could it be that something got messed up during upgrade? We had this plugin installed and upgraded since version 1.1 or even before... Pawel Pawel Sztromwasser wrote

Re: [base] BEAD summary importer in experiment details context

2010-02-24 Thread Pawel Sztromwasser
for plugins from Illumina package. Is it because they are non-configurable? Are they included in this search? Pawel Nicklas Nordborg wrote: On 2010-02-24 13:05, Pawel Sztromwasser wrote: Hi, I don't get Illumina BEAD summary importer plugin as a choice of plugin when I click Import button

Re: [base] BEAD summary importer in experiment details context

2010-02-24 Thread Pawel Sztromwasser
It works now. Thanks! Nicklas Nordborg wrote: On 2010-02-24 14:56, Pawel Sztromwasser wrote: New clue: I don't get the BEAD Summary importer plugin on a plugins list when I choose Experiment in the Items column. This means that the plugin does not know that it is supposed to pop-up

Re: [base] Anyone using BASE with PostgreSQL?

2011-09-29 Thread Pawel Sztromwasser
Hi Nicklas, We are using PostgreSQL as BASE's back-end and are very happy with it. I am not familiar with the details of the installation and backup setup, since it is a department-wide installation administered by our techs. I could ask about the backup though, if you were interested. It is

Re: [base] Anyone using BASE with PostgreSQL?

2011-09-30 Thread Pawel Sztromwasser
: On 2011-09-29 12:29, Pawel Sztromwasser wrote: Hi Nicklas, We are using PostgreSQL as BASE's back-end and are very happy with it. I am not familiar with the details of the installation and backup setup, since it is a department-wide installation administered by our techs. I could ask about

[base] MO terms (annotations) for experiments

2011-10-25 Thread Pawel Sztromwasser
Hi Working with the MageTab export I have noticed that it would be great to have additional properties for experiments that could hold MGED Ontology annotations, e.g. Experiment Design, Replicate Type, Quality Control Type. Up to now we've been using the Experiment Design and Experiment Type

[base] Project defaults in batch-import and experiment validator

2011-10-25 Thread Pawel Sztromwasser
the defaults in advance. Best regards, Pawel Sztromwasser -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary

Re: [base] Project defaults in batch-import and experiment validator

2011-10-25 Thread Pawel Sztromwasser
next step forward. On Tue, Oct 25, 2011 at 1:01 PM, Nicklas Nordborgnick...@thep.lu.se wrote: On 2011-10-25 09:45, Pawel Sztromwasser wrote: Hello, I was wondering if the project defaults are used in batch importing, i.e. when a property is not specified in tab-delimited file but set

Re: [base] MO terms (annotations) for experiments

2011-10-25 Thread Pawel Sztromwasser
is better from the design point of view. Pawel On 25/10/11 13:34, Bob MacCallum wrote: On Tue, Oct 25, 2011 at 12:16 PM, Nicklas Nordborgnick...@thep.lu.se wrote: On 2011-10-25 09:22, Pawel Sztromwasser wrote: Hi Working with the MageTab export I have noticed that it would be great to have