Re: [base] batch data importer

Hi Abhishek, Sorry, I initially thought your message was about the new core batch importers. Yes, Nicklas is right, it looks like your zip file is missing the cdf file. Currently this needs to be included for Affy imports. Try again with this included. Cheers Micha ===

Re: [base] Tab2Mage export

Hi, Likewise! I too have hacked this plugin to make it work with version 2.9, and I have a version here that works for me and that we do use to export and submit stuff to ArrayExpress. I have also fixed a problem that prevented two-color experiments from being exported correctly. People are wel

Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- problem with name/ID mapping

Hi again, > Are you sure that everything is correctly linked? Use the "Experiment > overview" to find out. It should find > > 1) The raw bioassay(s) that doesn't have the annotation. > 2) The raw bioassays that has inherited the same annotation from > multiple parents. > > Maybe it is as simple

Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- problem with name/ID mapping

> -Original Message- > From: Nicklas Nordborg [mailto:[EMAIL PROTECTED] > Sent: 01 December 2008 10:10 > To: BASE ML > Subject: Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- > problem with name/ID mapping > > Micha Bayer wrote: > > Hi Nic

Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- problem with name/ID mapping

p://www.scri.ac.uk/staff/michabayer == > -Original Message- > From: Nicklas Nordborg [mailto:[EMAIL PROTECTED] > Sent: 27 November 2008 18:51 > To: BASE ML > Subject: Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- > problem with name/ID mapping > > M

Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- problem with name/ID mapping

> -Original Message- > From: Nicklas Nordborg [mailto:[EMAIL PROTECTED] > Sent: 21 November 2008 11:54 > To: BASE ML > Subject: Re: [base] mass annotation of raw bioassays in BASE 2.8.4 -- > problem with name/ID mapping > [...] > There is a new function in BASE 2.9 that can make this eas

[base] summary of how the new core batch importers can be used for importing whole experiments

Hi, I thought it might be useful for others to have a step-by-step account of how to import a whole experiment with the new core batch importers, so here it goes: My aim was to import the hybridization-related information for a whole experiment in a way that would provide MIAME-compliance for thi

Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4

Excellent -- that works. Thanks, guys. Is it reasonable to assume that people will want to attach their file if they specify the file name? If so, then it would make sense to make the "Data Directory" and "Data File Type" parameters mandatory in the import wizard if someone has specified a file

Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4

No, still no joy. > Are the raw data files "visible" to the plug-in? If you upload the > files > with ftp they are not automatically assigned to a project. I uploaded them with HTTP, and they have definitely been assigned to the project. > You need to > set the parameter defining how the plug-i

[base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4

Hello again, I can't get the raw bioassay batch importer to attach actual file objects to the raw bioassays I am importing. I have - provided a data column with file names in my data batch import file - mapped this column to the File property in the import config - provided a path to the data dir

[base] mass annotation of raw bioassays in BASE 2.8.4 -- problem with name/ID mapping

Hi, When configuring the mass annotation importer plugin, an error is thrown when one has mapped only the names of the raw bioassays, and not their ID: "A mapping for either 'Name' or 'Internal ID' must be given. " This happens even when the mapping for the name has already been provided. When

[base] error during batch import of raw bioassays -- BASE 2.8.4

Howdy again, I am trying out the new batch importers, and so far I have been impressed. But now I am stuck on the raw bioassays and I can't get the import to complete there. I have got it configured and the job starts running but then fails with this error: Invalid use of null. The 'rawDa

[base] batchimport example spreadsheet seems corrupted

Hi, I have been trying to look at the example file for the batch import but it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the file does load but then Calc instantly hangs. Has anyone else had the same problem? More to the point, has anyone got a version that works, or better

Re: [base] Array Express submissions

Hi Paulo, There is a plugin called the Tab2MageExporter and it exports an entire experiment in a spreadsheet format called Tab2Mage (http://tab2mage.sourceforge.net/) which is accepted by ArrayExpress as a one possible route of submission. However, the EBI are planning to substitute this format wi

Re: [base] Import of Agilent data

Hi Jan, Can I just clarify what exactly you mean here: 1. You have a single raw bioassay object and you want to load the data into this Or 2. you have multiple raw bioassays and want to load data into all of them in one go In the first case, there are core plugins shipped with BASE by default

Re: [base] Setting up an automatic import system

Hi Paulo, There are currently two plugins on the BASE plugins website that do this sort of thing. The batch importer plugin (http://baseplugins.thep.lu.se/wiki/uk.ac.scri.batchimporter) lets you load a batch of raw data files into BASE and these get associated with an experiment that you have pr

Re: [base] batchimporter plugin problem

Hi Bin, Try creating a new user with Administrator permissions and set an actual (fairly generous) quota value for that user. It looks to me like the import is failing because user root has not got an actual quota value allocated. I have to warn you though the batch importer is currently not gett

Re: [base] PermGen space error

Hi Bob, I seem to remember having the same problem with another webapp under Tomcat some time ago. Have a look at http://wiki.apache.org/tomcat/OutOfMemory. There it says: "A webapp that uses lots of libraries with many dependencies, or a server maintaining lots of webapps could exhauste the JVM

[base] problem upgrading to BASE 2.6 from 2.4.6

Hi, I just tried to upgrade BASE on my (XP) development machine from version 2.4.6 to 2.6 and I get an error when I execute the updatedb script. It looks like it builds the database ok but then it fails and complains that it cannot find the table base2.platforms. Is this the result of skipping re

Re: [base] Java memory error

Hi Matthew, 2gb seems an awful lot of memory to allocate, and I had a case some time ago when I was getting OutOfMemoryErrors that wouldn't go away when I allocated more and more. I then found some references on the web that suggested that in fact allocating too much memory itself can lead to OutO

Re: [base] Problem installing BASE 2.4.6

Hi, I am running BASE 2.4.6 on my development machine (which runs XP) under Tomcat 6.0.14 and Java 1.5.0_06, and it hasn't given me any grief so far. What version of Java are you running? Java 6 is not supported as far as I am aware -- perhaps that is the problem. Cheers Micha =

Re: [base] problems with my trashcan

Hi Bob, Looks like there is a Job item that used the batch importer and therefore you cannot delete the plugin definition while the Job item still exists. Try deleting that job and it should go. Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics

Re: [base] BASE2: problem parsing flag strings to floats

lto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Micha Bayer > Sent: 05 October 2007 10:21 > To: BASE ML > Subject: [base] BASE2: problem parsing flag strings to floats > > Hi, > > I am trying to import some raw data with flags such as "NORMAL" and > "ABNO

[base] BASE2: problem parsing flag strings to floats

Hi, I am trying to import some raw data with flags such as "NORMAL" and "ABNORMAL" into raw bioassays. I have mapped this column to the 'Flags' field in the raw data importer config for Genepix format (this is on BASE 2.3.0). For some reason the importer chokes on the values for the flags though a

Re: [base] BatchDataImporter broken w/ 2.4?

Hi, I haven't installed BASE 2.4 as yet -- will give it a go this afternoon and try out the batch importer with it. I have to admit to not having done any of the fixes/feature enhancements to the batch importer that were requested, quite simply because I was waiting for the Tab2MageImporter to m

Re: [base] [basedb-devel] problem with auto detection of raw data import configurations

s most likely is a problem with too unspecific regular > expression in the file format configurations. The isImportable() method > will only scan the file until it finds a line which matches the "Data > header" regular expression. The rest of the file is not checked. > > /Nic

[base] BASE2: API for storing normalized data

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 (using the BASE client API)

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

me > of > raw data file). And even more puzzling is the fact that for one of the > batchs it worked when I was logged as root and not when I was logged as > user > (in other cases the user login worked). So, I don´t really have a clue of > what could be wrong here. > Ana >

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

Hi Ana, Usually this indicates that you don't have a suitable raw data import configuration for the data you are trying to import. The best way to ensure that you do have one that works is to create a single new raw bioassay for testing purposes, import one of your data files into that, and i

Re: [base] Batch Data Importer plugin dev future?

Hi Jim We never actually got this far in the discussion on Monday, but I have since spoken to Dominic Oyeniran from the EBI who has developed a first version of the Tab2MAGE exporter module and he says that he will now work on the Tab2MAGE importer next (he is on this list too BTW). We have agre

Re: [base] Questions on Reporter IDs

Hi Emil, We are in the process of integrating GenePattern (http://www.broad.mit.edu/cancer/software/genepattern/) with BASE 2, and once we have a solution working we'll be happy to place it in the public domain. GenePattern supports all the things you are asking for below, and we like for the sa

Re: [base] Batch importer wish list: batch-associating an existingsingle scan item with every new raw biaossay during a job run

Hi James, glad to hear the plugin is getting put to good use. We are due to have a telecom with the BASE dev team on the 26th and we are then going to decide about the future of this plugin, among other things. It is well possible that we will turn it into something a lot more fancy and there h

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

Hi, > Ok, so I made a rookie mistake and forgot to clear the filter ... Happens to all of us :-) > However, I never fully got > through the installation without errors. I now have the following > problems: > > 1) I don't have an 'import' tab in the detail view of Experiments (base > 2.1.

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

Hi, Yes, I have had this happen too after giving it the wrong path. Sadly the only way to get rid of the duplicate entry seems to be to delete directly in the database. You need to find it in the data of the PluginDefinitions table and delete the entry, but be aware that it will keep refusing to d

Re: [base] batchimporter

Hi Steve, Not sure what's gone wrong there -- I have added the plugin to installations of both 2.1.1 and 2.2.1 and it worked fine. It also seems to have worked okay for the other people who have tried it out so far, so I am not sure what's happening. As far as I know the only thing you can do no

[base] BASE2: client default settings

Hi, I am just about to let some users loose on our BASE install here and I am trying to customize the local settings specific to our server, e.g. the administrators contact details as shown in get_account.jsp etc. >From a glance at the code it looks like there are client default settings somewhe

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

Hi again, That's these bugs all fixed (I hope): - change handling of dirs and files so that file is unzipped in its current dir - unclosed DbControl -- now fixed - User Quota for files needs to be greater than the file size to be imported -- code now checks - misreporting of raw data type fixed

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

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 =HG-U133A.cdf > experiment: Ex

[base] batch importer plugin is available for testing now

Hi, An early, alpha-quality version of the batch data import plugin is now available at http://lev.thep.lu.se/trac/baseplugins/wiki/BatchDataImporter This version has been through the first round of bug fixes but has then not been tested by anyone other than myself locally, so please feel free

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

ent: 13 February 2007 22:07 > To: BASE ML > Subject: Re: [base] BASE2: Affymetrix.java method calls throw exceptions > > 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 t

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

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? I may just not be doing t

Re: [base] Offline files

> -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Jari Häkkinen > Sent: 30 November 2006 15:42 > To: BASE ML > Subject: Re: [base] Offline files > > There is a possibility to get access to the subversion repository and > trac environment

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

Hi Emmanuel, The Catalina/work directory caches copies of your compiled JSP pages. It looks from the stacktrace like the JSP compiler can't write to the work directory because you don't have permissions to it -- check what they are set to. Cheers Micha == Dr Mi

Re: [base] Offline files

h scientist to > provide (with a little help MGEDifying the annotations). So far every > experiment I have loaded has come with some kind of spreadsheet (each one > in a > different format of course), so the leap to MAGE-TAB is not so great. > > Ok, enough from me... >

Re: [base] Offline files

> -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg > Sent: 29 November 2006 14:40 > To: BASE ML > Subject: Re: [base] Offline files > > Jari Häkkinen wrote: > > Hi all, > > > > Just a thought, I think the best choice to

Re: [base] Offline files

> -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg > Sent: 29 November 2006 14:40 > To: BASE ML > Subject: Re: [base] Offline files > > Jari Häkkinen wrote: > > Hi all, > > > > Just a thought, I think the best choice to t

Re: [base] Offline files

xperiment list jsp (a import tab is needed). > > In my naive view this will only affect a jsp and a new plug-in is needed. > > > Jari > > dominic oyeniran wrote: > > > > > > > > -Original Message- > > From: [EMAIL PROTECTED] > > [ma

Re: [base] Offline files

> -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Bob MacCallum > Sent: 29 November 2006 10:15 > To: BASE ML > Subject: Re: [base] Offline files [...] > At some point, someone will come up with a bulk loader which will > batch/bulk/mass

[base] long term future and support for BASE2

Hi, This is a non-technical question, for a change. We are about to make a fairly long-term commitment to BASE as our microarray platform and were wondering what the future looks like for BASE, in terms of support and funding (we're talking the next few years rather than months here). This is o

Re: [base] pb with jsvc/Tomcat

Sorry, I just sent an empty message to the list, apologies...(keyboard shortcuts can be a bad thing). Are you trying to run Tomcat as a service? You shouldn't really have any problems of this sort if you just go for the non-service binary version of Tomcat (http://mirror.public-internet.co.uk/apa

Re: [base] pb with jsvc/Tomcat

> -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Emmanuel Courcelle > Sent: 28 November 2006 10:15 > To: BASE ML > Subject: [base] pb with jsvc/Tomcat > > Hello everybody > > My question is not completely BASE-related, but may be so

Re: [base] logging in BASE2

sari.ac.uk/MichaBayer.htm = > -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg > Sent: 07 November 2006 10:53 > To: BASE ML > Subject: Re: [base] logging in BASE2 > > Micha Bayer wrote: > > Hi Nickla

[base] BASE 2 API: creating subdirectories in users' home directories

Hi again, Sorry for the barrage of messages from me recently but it's obviously early days for BASE 2 and whenever I have got stuck recently there hasn't been any existing messages to fall back on. I guess this will improve over time I am trying to write some code to do a combined zip file up

Re: [base] logging in BASE2

2426 http://www.scri.sari.ac.uk/MichaBayer.htm = > -Original Message- > From: [EMAIL PROTECTED] [mailto:basedb-users- > [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg > Sent: 07 November 2006 07:17 > To: BASE ML > Subject: Re: [base] logging in BASE2 >

[base] logging in BASE2

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? I have tried to change the log levels in the log4j.properties file in www\WEB-INF\classes\, and even deleted this file but it seems to have made no

Re: [base] BASE2: extended properties -- hyperlinks

cklas Nordborg > Sent: 31 October 2006 12:34 > To: BASE ML > Subject: Re: [base] BASE2: extended properties -- hyperlinks > > Micha Bayer wrote: > > Hi, > > > > I would like to add additional properties to the extended-properties.xml > > config file, and would l

[base] BASE2: extended properties -- hyperlinks

Hi, I would like to add additional properties to the extended-properties.xml config file, and would like to include URLs with them. In the following example entry, http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id={value}"; /> what does the regexp attribute in the link element refer

Re: [base] BASE2: Hibernate caching problem

Behalf Of Nicklas Nordborg > Sent: 25 October 2006 10:33 > To: BASE ML > Subject: Re: [base] BASE2: Hibernate caching problem > > Micha Bayer wrote: > > Hi, > > > > We have just installed the latest version of BASE2 (2.0.2 binaries) and > > are running some of

[base] BASE2: Hibernate caching problem

Hi, We have just installed the latest version of BASE2 (2.0.2 binaries) and are running some of our own client code against it. BASE is running under Tomcat 5.5.20 and with a MySQL 5.0.22 backend. When our code calls Application.start(), the following exception is thrown: SEVERE: Cannot cache an

[base] BASE2 API: interacting with multiple BASE2 installs

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 be only one service, for ma

[base] BASE2: cannot create new Experiment with existing raw data

Hi, I have just installed BASE2 and I have got as far as importing a raw data set with Agilent data. I would now like to try out some of the analysis plugins which apparently means I have to create a new experiment item first. When I try to do this I get an error after attaching my raw data to it: