Re: [base] Base2 install errors

2006-04-08 Thread Nicklas Nordborg
something is going wrong with the java mysql drivers as you suggest. thanks, Sam On Fri, 2006-04-07 at 07:57 +0200, Nicklas Nordborg wrote: Sam Hunter wrote: Hi, I'm new to Base, and am trying to set it up for testing. I am install on Ubuntu with base-2.0RC1. I downloaded and install

Re: [base] how to link labeled extracts to intensity columns or channels

2006-08-15 Thread Nicklas Nordborg
Petr Divina wrote: Hello, how can I link (= associate) a particular labeled extract that was used in a multi-color hybridization to a particular intensity column in the raw bioassays (or particular channel in the experiment) ? It is not possible. /Nicklas I have an 8-channel raw data

Re: [base] Migrate script fails, no error messages

2006-08-25 Thread Nicklas Nordborg
Chris Wiita wrote: Alright, that makes sense. The first time I ran the script the error was different, and in repeating the script, I never noticed it was way off in the first place! I turned logging, dropped both BASE2 DBs and recreated them, and ran initdb.sh. It was successful.

Re: [base] Nimblegen

2006-08-29 Thread Nicklas Nordborg
Keith Ching wrote: Hi, I am looking into using BASE2 to store ChIP-chip data from the NimbleGen platform. Each whole genome scan has 14 million probes, divided up into 38 arrays of 370k probes each. What is the feasibility of storing this information in BASE2? Say we had 100+ whole

[base] BASE 2.0 has been released

2006-08-31 Thread Nicklas Nordborg
Hello all, I am happy to announce that BASE 2.0 is now available for download: http://base.thep.lu.se/wiki/DownloadPage Installation instructions and other documentation are available at the BASE 2 home page: http://base.thep.lu.se/ /Nicklas

Re: [base] Migrate script fails, no error messages

2006-09-01 Thread Nicklas Nordborg
? Send a reply to me off the list. Thank you very much. /Nicklas --Chris W Nicklas Nordborg wrote: Chris Wiita wrote: Alright, that makes sense. The first time I ran the script the error was different, and in repeating the script, I never noticed it was way off in the first place

Re: [base] BASE2 + Solaris crashes recommended JVM

2006-09-15 Thread Nicklas Nordborg
Emil Lundberg wrote: Hi all, We are trying to go from BASE 2 RC1 to 2.0, and neither updating nor initializing a new database seems to be working properly. Question is; is it just us, or a BASE/Java/MySQL versions mismatch? If the latter, are there any officially recommended/supported

Re: [base] BASE2 + Solaris crashes recommended JVM

2006-09-18 Thread Nicklas Nordborg
I am not able to reproduce the error. Unfortunately there is a glitch in the error handling which causes a second error to hide the original one. If you turn on debugging there might be some more information displayed. You turn on debugging by editing the

[base] Base 2.0.1 released

2006-10-02 Thread Nicklas Nordborg
Hello all, BASE 2.0.1 is now available for download at: http://base.thep.lu.se/wiki/DownloadPage Most fixes are related to the migration program and the Base 1 plugin executor. /Nicklas - Take Surveys. Earn Cash.

Re: [base] BASE2 API: interacting with multiple BASE2 installs

2006-10-06 Thread Nicklas Nordborg
Micha Bayer wrote: Hi, I am working on a web service that talks to a BASE2 install to get data out (for an analysis pipeline) and then store data back into it. We are supporting three separate institutions which eventually will all have separate BASE2 installs, but I would like there to

Re: [base] change owner

2006-10-13 Thread Nicklas Nordborg
Robin LIECHTI wrote: Dear Base2 Users, I am a curator (and administrator) of a Base2 installation and I have to load experiment data from several users. So I log in as the administrator, I create the samples, extracts... and load the data. Is there a way of changing the owner of the

[base] Any interest in running BASE on Oracle?

2006-10-17 Thread Nicklas Nordborg
Hello all, I am just wondering if anybody is interested in running BASE 2 on an Oracle database? The reason that I ask is that I think it is possible to fix the things that is causing the current implementation not to work on Oracle. But we are not spending time on this if there is no

Re: [base] demo server updates and presets Q's

2006-10-23 Thread Nicklas Nordborg
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

Re: [base] updating to Base 2.1 with postgresql

2006-11-02 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Hello I have setup for a few days a new Base2 installation, running with postgresQL. I know that the update process wan not safe with psql, due a bug in hibernate. However, the updating process ran without problem from 2.0.2 to 2.0.3 This updgrade didn't

Re: [base] Workaround for upgrading a Postgres database

2006-11-06 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Nicklas Nordborg a écrit : Hello Postgres users, We have now published some information about a workaround to make it possible to upgrade a BASE installation running on a Postgres database. Hi Nicklas Thanks for the workaround. I did the updatedb.sh as you

Re: [base] 2 questions about Plugin configuration

2006-11-06 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Hi Nicklas Here are the first 44 lines of the file I tried to dos2unix-ify, it did not change anything for Base. Thanks for your help ! I have now tested with your file and it works perfectly. Perhaps it is a browser-related problem. I have tested with Internet

Re: [base] logging in BASE2

2006-11-06 Thread Nicklas Nordborg
Micha Bayer wrote: Hi, I am running BASE2.1 under Tomcat 5.5 and I am getting my catalina.out log swamped by BASE log statements. Is there any way I can turn this off? It doesn't sound normal. What kind of log messages do you get? I have tried to change the log levels in the

[base] create slide wizard numbering

2006-11-06 Thread Nicklas Nordborg
Under Array Slides / Create multiple the Start at field is limited to 3 digits. is it possible to increase this to 4 digits as we continuously number our slides and it's in the thousands already. ( ie. i'd like to make slides 1100-1150 ) Oops, it shouldn't be. Only the number of

Re: [base] Plugin configuration (nearly fixed !)

2006-11-07 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: The only significant change you have made is Rgn R? to Rgn R. Does it still work if you change this to Rgn R\E.\Q? Great: I took the autogenerated regex, replaced Rgn ? by Rgn R\E.\Q without changing anything else and it worked. However, I changed also the

Re: [base] Plugin configuration (still some pb)

2006-11-08 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: file we have been testing on the Rgn R² column should be column number 32 and the mapping to use \32\. hum... rather 33, I think (it was 33 in Base 1.2). Does the column numbers start at 0 or at 1 ? As I wrote in the previous mail: The columns are

Re: [base] file storage system question

2006-11-08 Thread Nicklas Nordborg
Keith Ching wrote: it seems you can make a String annotation type and attach it to raw bioassay and fill it with a href=javascript:Main.downloadFile('34537569891fa9bf', 142) img border=0 class=icon title=Download the contents of this file src=/base2/images/download.gif/a which will

Re: [base] file storage system question

2006-11-09 Thread Nicklas Nordborg
Keith Ching wrote: True, the session id is good only once.. but in subsequent logins, BASE2 will ask to reauthenticate and after success you can still download the file. still, of course.. i would rather have the download link be auto generated upon import of the datafile. is it

Re: [base] logging in BASE2

2006-11-10 Thread Nicklas Nordborg
Micha Bayer wrote: Mystery solved. This is nothing to do with BASE -- it's Tomcat's fault. It looks like the Tomcat people have changed tack and they are now including a log4j.xml config file by default with Tomcat (it used to be a log4j.properties file, which is what I was initially looking

Re: [base] question on biosources and messages in base2

2006-11-15 Thread Nicklas Nordborg
Audrey Bihouee wrote: Hi everybody, I just upgrade from base1.2 to base2, and I have a few questions : - What are exactly Biosources ? Does it match with the sample origin in base 1 ? But, I can't see any ontology (tree structure) as in base 1. Have anybody details on it ? It

Re: [base] error deleting jobs inside trashcan

2006-11-22 Thread Nicklas Nordborg
Reha Yildirimman wrote: Hello, I have a few import jobs that froze and never finished the imports. After I started a jobs that finished the task I am left with those unfinished jobs still listed inside the execute section of Jobs which I can't delete after moved to the trashcan. The

Re: [base] JEP extra value calculator

2006-11-27 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Hello I am testing the analysis capabilities of Base 2.1, and I do not understand the plugin called JEP extra value calculator: what is its aim, and how does it work ? It can calculate new values for each spot using the intensities and other already existing

Re: [base] Offline files

2006-11-28 Thread Nicklas Nordborg
Giovanni Coppola wrote: Hi everybody, I have two questions: 1) is there a way to download images or raw data files in batches? No. 2) while I was trying that (to download more than one file at once), in the 'Files and Directories' tree, I accidentally moved Offline some files, and now

Re: [base] Imagene data import

2006-11-28 Thread Nicklas Nordborg
Anup Parikh wrote: We have been using base 1.2 for a year now. The batch importer we had created for base 1 is useless for base2. Therefore we are moving to using the UI to import each chip. We are using the ImaGene quantitation software and which seems to be supported in base2. But I

Re: [base] Offline files

2006-11-29 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: What does mean to move offline ? Is it the same as: Delete THEN Empty trash ? No it is not. A file exists in two places. As an entry in the database and as a file on the disk. The Move offline feature is used when you want to delete the file on disk but keep the

Re: [base] Offline files

2006-11-29 Thread Nicklas Nordborg
Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file is not already

Re: [base] Offline files

2006-11-29 Thread Nicklas Nordborg
Micha Bayer wrote: I am just talking to my boss about code ownership issues but I can probably offer up my stuff one way or another, and people can then either cannibalise it and turn it into a plugin, or adopt it (or a modified version) into the core etc etc -- happy with any solution

Re: [base] Offline files

2006-11-29 Thread Nicklas Nordborg
Micha Bayer wrote: Hi Jari, That sounds perfectly reasonable when you put it like this, but I was put off going down that route by a post to the list from Nicklas http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html) where he says that it is best to not use a

Re: [base] JEP extra value calculator again...

2006-11-30 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Hi all. Sorry to bother you again with this point, but I still does not understand everything... I tried to define a new type, called float colored: it is a float, colored with min value as 0, max as 0, mid as 5 I want to add 2 values to my data: -2 * (ch(1) /

Re: [base] Offline files

2006-11-30 Thread Nicklas Nordborg
Micha Bayer wrote: So am I right in thinking that if I change this to the following... public class ZipFileImporter extends AbstractPlugin implements InteractivePlugin, AutoDetectingImporter { private static final SetGuiContext guiContexts =

Re: [base] Réplicates in base 2

2006-12-08 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Hello We are trying to create an experiment composed with: -4 slides -3 times each reporter on each slide So, we have up to 12 replicates for each reporter (sometimes less because some flagged spots were filtered out). How to make a final bioassay set with

Re: [base] Location of original source files

2006-12-08 Thread Nicklas Nordborg
. There is however no information that links a rawbioassay to the file that was used for importing the data. It has nothing to do with the file names. /Nicklas Am I off track? Cheers Charles On Dec 8, 2006, at 9:00 AM, Nicklas Nordborg wrote: Keith Ching wrote: Hi, I am trying to write

Re: [base] Conversion from string to int after plate import - bug while exporting

2006-12-11 Thread Nicklas Nordborg
david vilanova wrote: Thanks Nicklas for you quick answer regarding the conversion from string to int. I have decided to import the data using the string to int conversion. However I'm trying to export the plate wells back again to a file using the default exporter and get a bug. I'm

Re: [base] Réplicates in base 2

2006-12-14 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Nicklas Nordborg a écrit : Emmanuel Courcelle wrote: Hello We are trying to create an experiment composed with: -4 slides -3 times each reporter on each slide So, we have up to 12 replicates for each reporter (sometimes less because some flagged spots were

Re: [base] downloading files

2006-12-19 Thread Nicklas Nordborg
Keith Ching wrote: I have a List of File objects. what is the best way to zip them all together and download it? I assume that you want to this with a plugin. I think the best way is to create a new File (net.sf.basedb.core.File) object and then use java.util.zip.ZipOutputStream for writing

Re: [base] walk thru

2006-12-22 Thread Nicklas Nordborg
Gabe Dagani wrote: Greetings, Has anyone created a simple walkthru for setting up a simple experiment, uploading GPR, GPS, TIFF files into a project and doing some analysis? I am just a beginner and the manual is outdated for base 2.0. The test procedure that we use before a new

Re: [base] GPR import plugin error

2007-01-10 Thread Nicklas Nordborg
david vilanova wrote: Hello, I'm trying to import a GPR file and had some problems. I have submitted the bug to the base ticketing system. The problem comes from assigning incorrect wavelengths to the dyes CY5 and CY3 (view opened ticket #467). In the bug descriptions I also submit the

Re: [base] Spot images

2007-01-22 Thread Nicklas Nordborg
david vilanova wrote: Hello, Following the advise given to emanuel for the generation of the spots, I went through the example but could'nt manage to create the spots. Do i have to submit three time the tiff file to create the spots in the editor (it's asking for jpeg files°. Anyway the

Re: [base] Windows

2007-01-22 Thread Nicklas Nordborg
[EMAIL PROTECTED] wrote: Hello, I have use the package Easyphp1.7 (PHP4, PHPMyAdmin) on windows to developp a database, and I would like to know if it is possible to install BASE with it or How to install BASE on Windows? BASE 1 is using PHP and in some parts C/C++. It is not possible to

Re: [base] Spot images follow-up

2007-01-22 Thread Nicklas Nordborg
david vilanova wrote: Hello, I have tried with: PixelSize=10 ImageOrigin=4440,1000 I have double checked the image within genepix and the coordinates (expressed in µm) are correct (gpr file matches with the tiff file). 1µm correspond to 10pixels in genepix. I think it is the other way

Re: [base] Fwd: Permissions question

2007-01-23 Thread Nicklas Nordborg
david vilanova wrote: Hello, I'm having problem to setup permissions. How can i give permissions to all users to create a new raw bioassay from a scan. Actually I can only do it with account root. I did try to allow the group of users to write access,use,read to raw bioassays in the

Re: [base] SPOT IMAGES Problem found

2007-01-23 Thread Nicklas Nordborg
david vilanova wrote: Hi folks, I finally managed to identify the problem. As i said in my previous email i tried a tif image with only a signe channel: [EMAIL PROTECTED] SPOTS]$ ls * -rw-r--r-- 1 david bioinfo 9,1M Jan 23 12:19 532.tif -rw-r--r-- 1 david bioinfo 9,3M Jan 23 12:20 635.tif

Re: [base] can you run a plugin outside of the web interface?

2007-01-24 Thread Nicklas Nordborg
Keith Ching wrote: Hi, i have written a plugin that takes a spreadsheet and creates samples - rawbioassay and links the data file to the rawbioassay. is there a way i can also run the plugin without going through the web interface.. ie. initiate running it from another program? No,

Re: [base] Stopping Base after MySQL crash

2007-01-31 Thread Nicklas Nordborg
Marie Mooney wrote: Hi. I don't know much about BASE 1.2 but I think that you must have the MySQL running for stopBase.php to work. And you must also have MySQL running to be able to upgrade from 1.2.14 to 1.2.17. So you have to find a way to start the MySQL server again. /Nicklas I am

Re: [base] Problem importing into ReporterLists

2007-01-31 Thread Nicklas Nordborg
Reha Yildirimman wrote: Hello, I am trying to import Reporter into a new reporter list inside a fresh,new base2 installation, getting the following error: Caused by: java.sql.SQLException: Unknown column 'reporterda0_.' in 'field list' Can you please submit the entire stacktrace

Re: [base] Imagene data format

2007-02-06 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Nicklas Nordborg a écrit : Emmanuel Courcelle wrote: Hello I am trying to configuration the Raw data importer plugin for use with Imagene files. I do not know how to map theproperties Block, MetaGridX, MetaGridY 1/ There is no Block column in the file, but I

Re: [base] Bug fix release 2.2.1 is available now

2007-02-12 Thread Nicklas Nordborg
Keith Ching wrote: hmm.. i had restored back to 2.1.2, then upgraded to 2.2.1 and it was working ok until i took ownership of some jobs as root.. then went to the trash can. it gave me this error: Object with id: 2 was not of the specified subclass: net.sf.basedb.core.data.BioMaterialData

Re: [base] BASE2: Affymetrix.java method calls throw exceptions

2007-02-13 Thread Nicklas Nordborg
Micha Bayer wrote: Hi, I am trying to add Affymetrix support for the batch import plugin I have been working on, and I am having trouble getting things to work with the Affymetrix class. Is there a unit test for this class that I could look at for finding out about proper use of this class?

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

2007-02-20 Thread Nicklas Nordborg
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: = ===NEW BATCH IMPORT = = zn

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

2007-03-15 Thread Nicklas Nordborg
Jeremy Davis-Turak wrote: On 3/14/07, Nicklas Nordborg [EMAIL PROTECTED] wrote: Can someone please give us a hint about how to reproduce this behavior? When I add a new plugin, BASE will complain if I enter an incorrect path. Nicklas, To reproduce this error, I would try creating

Re: [base] export function: permission denied

2007-03-22 Thread Nicklas Nordborg
Reha Yildirimman wrote: Hello, everytime I try to export a tab-delimited file or xml file (from e.g. extracts, biosources or any other place) I get the following error: *** # Permission denied: Immediate execution is not allowed for this plugin. *** I gave the user I use read,write

Re: [base] export function: permission denied

2007-03-26 Thread Nicklas Nordborg
Ana Conesa wrote: At 19:17 22/03/2007, you wrote: Reha Yildirimman wrote: Hello, everytime I try to export a tab-delimited file or xml file (from e.g. extracts, biosources or any other place) I get the following error: *** # Permission denied: Immediate execution is not allowed for this

Re: [base] multi-experiment processed data summaries

2007-03-29 Thread Nicklas Nordborg
Bob MacCallum wrote: Developers: are there any plans for BASE2 web gui plugins? Well, yes and no. It is something that we would like to have and we have a ticket for it (http://base.thep.lu.se/ticket/436). At the moment it is not top-priority though so it is difficult to say when (and if)

Re: [base] merged data

2007-04-11 Thread Nicklas Nordborg
Julie Naito wrote: Is this the case with BASE version 1.2.16? Sorry, I assumed you were asking about BASE 2. I guess the statement about that the same sample must end up in the same channel is true also for BASE 1. I don't know if that requires different file formats or not in the Imagene

Re: [base] NullPointerException when running raw data importer for new ScanArray CSV raw data table

2007-04-12 Thread Nicklas Nordborg
Collett, James R wrote: Dear BASErs, I'm having problems configuring the raw data importer to import data from a ScanArray CSV file into a new raw data table that I created by modifying raw-data-types.xml. Every plugin configuration I try returns a NullPointerException error. Can you

Re: [base] updating extended-properties.xml

2007-04-12 Thread Nicklas Nordborg
Simon McGowan wrote: Hi, We have run into problems after editing the raw-data-types.xml and extended-properties.xml files. After each edit the server was stopped, I ran updatedb.sh and updateindexes.sh and restarted the server. However we can now no longer see any reporters via the

Re: [base] how can i interact with the spot creator plugin from outside the system

2007-04-12 Thread Nicklas Nordborg
Chad Matsalla wrote: Nicklas Nordborg wrote: Can you tell me how to create the appropriate file objects when the files are here and not connected to the base datbaase? This is not possible. The plugin expects net.sf.basedb.core.File objects not java.io.File object. And you can't work

Re: [base] java.lang.NullPointerException while importing raw data

2007-04-16 Thread Nicklas Nordborg
Jean-Pierre Gauthier wrote: Hi BASErs, I am a new Base2 user and I have a java.lang.NullPointerException when trying to import Genepix raw data in: View-Raw Bioassays..-Import My raw data importer seems to work well. I have looked for extra spaces but all looks OK.. Could somebody help

Re: [base] unknowns

2007-04-17 Thread Nicklas Nordborg
Peter Juvan wrote: Q: How to denote unknown values in a tab-delimited result file (for example M-values of reporters with zero intensity) so that BASE does not interpret them as zeros? Empty places are not OK, they are interpreted as zeros (at least in Base 1.2.17). In BASE 2, empty string

Re: [base] genepix 6.0/6.1, multi-image tif-s, spot finding,

2007-04-20 Thread Nicklas Nordborg
Nice work! It seems like you have spent some time on this. Do you have some code and/or images that can be useful for us? The image and data we have access to are from Genepix 4.1. I think that adding parameters for which image to use in a multi-image TIFF should be easy to implement. This can

Re: [base] GROUP clause error

2007-04-23 Thread Nicklas Nordborg
Jean-Pierre Gauthier wrote: We are using BASE 2.2.1 and Mysql Ver 14.7 distrib 4.1.12 We have only tested BASE with MySQL 5.0. Can you upgrade and check if it works? I think it may be a problem with the older MySQL version. Unfortunately, we can't support anything before 5.0 and I don't think

Re: [base] genepix 6.0/6.1, multi-image tif-s, spot finding,

2007-04-23 Thread Nicklas Nordborg
Chad Matsalla wrote: Nicklas wrote: Nice work! It seems like you have spent some time on this. I certainly have. JAI isn't exactly intuitive. No, it isn't. Do you have some code and/or images that can be useful for us? I certainly do. I basically check to see if the user provided

Re: [base] some base 2 bugs/features (raw data and array design import)

2007-04-23 Thread Nicklas Nordborg
Bob MacCallum wrote: Hi, I just spent the afternoon getting to know the array design and raw data import into BASE2 - starting with genepix format - and have come across a few things. I'm using BASE 2.2.2 (build #3172; schema #30). I have looked through the fixes for 2.2.3 and decided

Re: [base] some base 2 bugs/features (raw data and array design import)

2007-04-24 Thread Nicklas Nordborg
In the meantime you can try using a splitter regexp that also removes white-space. Try something like \s*\t\s* instead of just \t. I have not tested this but it might be enough to make it work. I guessed there would be a neat trick like this, but couldn't think of it last night.

Re: [base] Analsis error

2007-04-26 Thread Nicklas Nordborg
See my previous reply to this error. http://sourceforge.net/mailarchive/message.php?msg_name=462CAC84.7020801%40thep.lu.se /Nicklas Jean-Pierre Gauthier wrote: Hi BASEr's I have some trouble to perform my analysis thus I send you what I have done. Could somebody say me what is wrong? We

Re: [base] GROUP clause error

2007-05-02 Thread Nicklas Nordborg
Chad Matsalla wrote: Gretings! I see this as well. It's because this query: SELECT COUNT(*) AS `mapCount` FROM `base2_dynamic`.`D320RawParents` `rawmap` WHERE `rawmap`.`cube` = 3 GROUP BY `rawmap`.`column`, `rawmap`.`position` ORDER BY COUNT(*) DESC should say: SELECT COUNT(*) AS

Re: [base] migrator script causes lots of exceptions

2007-05-02 Thread Nicklas Nordborg
If you are using MySQL 5.0.27 this is caused by a bug in that version. Either use an older version of MySQL or remove 'useCursorFetch=true' the db.url setting in your base.config file. The second option may give you out-of-memory problems if you have a large database. In that case, you must

Re: [base] file format matching problems

2007-05-02 Thread Nicklas Nordborg
Steve Taylor wrote: Hi, I got a confusing message when I was using the Experiments Import. Basically, BASE was expecting a zip file and I was (perhaps stupidly) trying to upload a single file. The BASE WWW interface returned: 'We couldn't find any file format mathing the file

Re: [base] Why aren't you allowed to change the Array Design for a Raw Bioassay?

2007-05-11 Thread Nicklas Nordborg
Chad Matsalla wrote: Greetings, I think the subject is quite clear. I have a Raw Bioassay in which the user forgot to specify the array design at creation time. The user went on to do a bunch of analyses but the experiment validator said the Raw Bioassay had no array design. When you edit

Re: [base] creatItem err while migrate from 1.2 to 2.2.2

2007-05-15 Thread Nicklas Nordborg
Bernd Schwendele wrote: Hi, I have a problem with the mirgrate-script. I do not have any glue what this message means. It seems like the migration of BASE 1 plug-in definitions is broken. If you don't need those you can disable that part of the migration. Change the 'includePlugins'

Re: [base] Problems creating samples and the supervisor role

2007-05-24 Thread Nicklas Nordborg
Serge Eifes wrote: Dear Nicklas Nordborg, I have a similar problem as pointed out in the mail from 2007-03-05 by = Ana Conesa. In one of your replies from 2007-03-06 you give a link to a mail on how to solve this problem but this link only points to some kind of spam mail not related

Re: [base] BASE2: API for storing normalized data

2007-05-29 Thread Nicklas Nordborg
Micha Bayer wrote: Hi, Is there a way of programmatically storing externally normalized microarray data in BASE? I have been looking through the API but can't seem to find an obvious way of doing this. We run a workflow outside BASE (currently in GenePattern) which pulls data out of BASE

Re: [base] affymetrix

2007-05-31 Thread Nicklas Nordborg
Emmanuel Courcelle wrote: Hello Trying to use BASE with affymetrix data. I think we missed something... but don't know what We have created: -An array design called ATH1-121501, from the file ATH1-121501.CDF -Several raw bioassays fro several .cel files, when I click on the bioassays

Re: [base] creatItem err while migrate from 1.2 to 2.2.2

2007-06-05 Thread Nicklas Nordborg
Bernd Schwendele wrote: Hi, The next problem is: After a successful migration, I miss the pictures. :s I now wonder, what went wrong this time. I don't know. Can you explain what pictures you are missing? /Nicklas - This

Re: [base] Migrating to Base2 and to postgresql ?

2007-06-07 Thread Nicklas Nordborg
Patrice Durosay wrote: Hello We are migrating Base 1.2.27 to Base 2.2.3. As the db transfert is made through a jdbc, it would be possible to migrate it to a postgresql db. Is it possible, did somebody tried it ? It should be possible but we have not tested it. If BASE 1 is on MySQL

Re: [base] affymetrix

2007-07-16 Thread Nicklas Nordborg
Bob MacCallum wrote: Emmanuel Courcelle wrote: Hello Trying to use BASE with affymetrix data. me too! 2/ I can't see any new Reporter in the View/Reporters You need to import the reporter from a reporter annotation file (.csv). See

Re: [base] inherited annotations GUI suggestion

2007-07-18 Thread Nicklas Nordborg
Bob MacCallum wrote: A useful GUI addition would be another column on the Raw bioassays list view called 'Has inherited annotations'. The content of that column would be a simple yes/no. Alternatively, it could be called 'Inherited annotations' and could provide more information. Without

Re: [base] small gui feature suggestion

2007-07-18 Thread Nicklas Nordborg
Bob MacCallum wrote: I don't know if this would be dangerous, but how about: shift-click on the (+) symbol (new sample, new extract, new scan etc) will create the new object with the default settings in other words it would be equivalent to clicking on the (+) and then immediately

Re: [base] inherited annotations GUI suggestion

2007-07-19 Thread Nicklas Nordborg
Bob MacCallum wrote: Thanks for that Nicklas, I had only checked out the overview feature briefly once before. It's very powerful (being able to disable certain warnings is nice). And the Properties tab of the experiment page does indeed list the inherited annotations for each experimental

Re: [base] Guest Role tweaks

2007-07-20 Thread Nicklas Nordborg
Bob MacCallum wrote: I just found that my guest user account was unable to get details of bioassayset transformations - for example it would say Plugin - denied - Plugin configuration - denied - and the same under transformation and job. This isn't ideal - a guest user

Re: [base] BASE 2 Illumina arrays

2007-07-31 Thread Nicklas Nordborg
Nicklas Nordborg wrote: Jeremy Davis-Turak wrote: I have implemented the incorporation of Illumina data into our BASE system, along with a raw data importer. Our version requires that the gene_profile.csv be split up into separate files, which we have done with an R script. This can also

Re: [base] svn check out of BASE2 WS enabled

2007-07-31 Thread Nicklas Nordborg
Virginie Garcia wrote: Hi all, I try to download to webservices enabled version of BASE with svn as mentioned on the plugins page (http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients). When I check out the web services branch (svn co

Re: [base] BASE 2 Illumina arrays

2007-08-01 Thread Nicklas Nordborg
Jeremy Davis-Turak wrote: Hi Nicklas, I uploaded some data files to the Ticket. Thanks a lot! That was exactly what we needed. Here is a brief summary of what the data looks like: 1) Annotation data: CSV file. It's too bad that it's a CSV, because some of the fields contain commas!

Re: [base] Error: Table 'base2dynamic.D2Spot' doesn't exist

2007-08-08 Thread Nicklas Nordborg
Sergio Contrino wrote: dear base, i was attempting to 'create a new bioassay root' for an experiment with the array affymetrix 250sty, using Plier. i get the error Error: Table 'base2dynamic.D2Spot' doesn't exist This error is a bit strange since the table should automatically be

Re: [base] import of affymetrix data - which approach

2007-08-10 Thread Nicklas Nordborg
Reha Yildirimman wrote: I have another approach and if that seems ineffective to you please drop me a line! We also had that approach to begin with. However we were a bit worried about database performance since the Affymtrix chips contains a lot probes. Since most tools needed the CEL

Re: [base] get reporter ID from 2 columns

2007-08-10 Thread Nicklas Nordborg
Reha Yildirimman wrote: Hello, when configuring a raw-data-importer plug-in one has to state the column where the reportet ID is given. Is it possible to instead state 2 columns which when merged give the reporter ID ? And if yes how can I add another character like - in between those 2

Re: [base] Error uploading CDF file

2007-09-05 Thread Nicklas Nordborg
jesse paquette wrote: Hi, I'm trying to get BASE up and running, and I've hit a snag attempting to load a CDF file. The HTTP Status 500 page popped up with the following information: org.apache.jasper.JasperException: Unable to compile class for JSP: We know about this problem

Re: [base] BASE 2.4 on Windows

2007-09-07 Thread Nicklas Nordborg
jesse paquette wrote: Thanks Jari, Was the above the only things you needed to do to get BASE to run on MS Windows? Not completely. I submitted a bug ticket via user base. On the Create plugin page, I get a java.lang.ClassFormatError (page admin/plugindefinitions/index.jsp) with

Re: [base] Error uploading CDF file

2007-09-07 Thread Nicklas Nordborg
jesse paquette wrote: Ok, I deleted the extra line at the end of the show_exception file. The new error message is: File creation in base.config[userfiles] failed There can be two reasons: 1) The path specified in base.config for the userfiles property doesn't exists 2) The user that

Re: [base] Error uploading CDF file

2007-09-10 Thread Nicklas Nordborg
jesse paquette wrote: Ok, I deleted the extra line at the end of the show_exception file. The new error message is: File creation in base.config[userfiles] failed There can be two reasons: 1) The path specified in base.config for the userfiles property doesn't exists 2) The user that

Re: [base] following 2.1 getting started

2007-09-10 Thread Nicklas Nordborg
jesse paquette wrote: Hello all, In section 1c the getting started manual asks me to configure a Reporter map importer plugin for Genepix. I've set up the Reporter importer and Raw data importer plugins, but there is no entry in the plugins list for Reporter map importer. Has this been

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

2007-09-17 Thread Nicklas Nordborg
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 the exception below The

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

2007-09-18 Thread Nicklas Nordborg
Dominic Oyeniran wrote: The workaround works. But thats after I removed each raw bioassay and its associated experiment first and thereafter remove all the other items by emptying the trash. Note I have multiple experiments loaded :affy, genepix and agilent from Biosource to

Re: [base] 2.4.2 = 2.4.3 - any database schema change?

2007-10-02 Thread Nicklas Nordborg
Dave Hau wrote: 2.4.3 release followed closely after 2.4.2 release. I would like to upgrade from 2.4.2 to 2.4.3, but was just wondering if I could keep my database and just copy the entire 2.4.3 www directory to my tomcat server. Preferably I would like to not have to nuke the entire

Re: [base] Base2 and MeV - fold change

2007-10-04 Thread Nicklas Nordborg
[EMAIL PROTECTED] wrote: : Hi! I'm Pietro, a young bioinformatic from Italy who is trying to make Base2 usable for the researchers here where I work. The problem cames out when I try to make fold change filter on Base2-MeV. As you know MeV allow fold change filter only if you

Re: [base] How to use wildcard characters when filtering in BASE2

2007-10-04 Thread Nicklas Nordborg
vegard nygaard wrote: I am trying to make a sub selection of my data filtering for spots with id starting with SP. I used the Expression builder and tried: rep('externalId') == SP* and rep('externalId') == SP% Does the Expression builder support wildcards? No it doesn't. In the ticket

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