[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

[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

[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

[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, property name=omim title=OMIM description= column=omim type=string length=255 link regexp=\d+

[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

[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

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

[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

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 upload

Re: [base] Offline files

a jsp and a new plug-in is needed. Jari dominic oyeniran wrote: -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

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 trigger a

Re: [base] Offline files

me... Micha Bayer writes: -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

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

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

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 trouble getting things to work with the Affymetrix class. Is there a unit test

[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] 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:

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

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 2.1.1).

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

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

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

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

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 On Tue, 3 Apr 2007 09:41:03 +0100, Micha Bayer wrote Hi Ana, Usually

[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

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

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. /Nicklas Micha Bayer wrote: Hi, I have come across a problem with how import configurations

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

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 ABNORMAL into raw bioassays. I have mapped this column to the 'Flags' field

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] 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

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

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

[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

[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] 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

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] 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 easier

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 Nicklas, There is no icon showing