[base] BASE 3.19.1 has been released

2021-12-14 Thread Nicklas Nordborg via basedb-users

Hello all,

We have released BASE 3.19.1 today. This is a bugfix release that
contains fixes for some minor problems and a few enhancements.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.19.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.19 has been released

2021-08-13 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.19 today. This is a new major release with
some new features and improvements as well as some bugfixes. File 
uploading now support drag-and-drop from the local computer to upload 
multiple files in one go.


For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.19=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.18.2 has been released

2021-06-14 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.18.2 today. This is a bugfix release that
contains enhancements and fixes for some minor problems.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.18.2=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.18.1 has been released

2021-05-04 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.18.1 today. This is a bugfix release that
contains enhancements and fixes for some minor problems.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.18.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.18 has been released

2021-02-24 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.18 today. This is a new major release which
several new features and improvements. Most of them are related to
improvements in Item list functionality and filtering.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.18=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.17.1 has been released

2021-01-19 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.17.1 today. This is a bugfix release that
contains enhancements and fixes for some minor problems.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.17.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.17 has been released

2020-10-22 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.17 today. This is a new major release which
several new features and improvements. Some examples:

 * Support for listing and filtering on child items in table lists
 * Annotations on files

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.17=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.16.1 has been released

2020-05-19 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.16.1 today. This is a bugfix release that
contains enhancements and fixes for some minor problems.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.16.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas



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[base] BASE 3.16 has been released

2020-03-03 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.16 today. This is a new major release with a 
main focus on support for newer versions of Java, Tomcat and PosgreSQL.


 * Java 11 or higher and Tomcat 9 or higher is now required
 * PostgreSQL 11 or higher is recommended
 * Support for displaying, filtering and exporting data from
   parent items in some table listings

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.16=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.15.2 has been released

2019-09-16 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.15.2 today. This is a bugfix release that
fixes for some minor problems.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.15.2=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.15.1 has been released

2019-08-14 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.15.1 today. This is a bugfix release that
contains enhancements and fixes for some minor problems.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.15.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.15 has been released

2019-04-11 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.15 today. This is a new major release which
several new features and improvements. Some examples:

 * Excel file support in batch importers and exporters
 * Support for Java 11, Tomcat 9 and PostgreSQL 11
 * Better handling of text files with unknown encoding

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.15=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.14.1 has been released

2019-02-06 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.14.1 today. This is a bugfix release that
fixes an issue that prevents a user from changing the password and
a few other things.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.14.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.14 and BASE 3.13.1 has been released

2019-01-08 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.14 and BASE 3.13.1 today. This 3.14 release 
which mostly consists of preparations for supporting Java 11 (and newer) 
and improvements to the login system. The 3.13.1 release is a bugfix 
release with some minor fixes.


For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.14=type=1
http://base.thep.lu.se/query?milestone=BASE+3.13.1=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.13 has been released

2018-08-23 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.13 today. This is a new major release which
mostly consists of improvements targeted for plug-in and extension
developers.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.13=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.12.3 has been released

2018-06-04 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.12.3 today. This is a bugfix release that
fixes some minor issues.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.12.3=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.12.2 has been released

2018-04-16 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.12.2 today. This is a bugfix release that
fixes a critical bug in the annotation importer plug-in.

For more information, see:
http://base.thep.lu.se/query?milestone=BASE+3.12.2=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.12 has been released

2018-03-14 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.12 today. This is a new major release which
consists of several unrelated improvements and bug fixes.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.12=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] xdoclet in ant build

2017-12-10 Thread Nicklas Nordborg
No, we have not really considered moving away from using xdoclet for 
creating the mapping files to Hibernate. I am aware that this is not the 
most modern approach, but it has served us well so far. It might be 
possible to move to JPA, but I am pretty sure that this will not be an 
easy task. The *.hbm.xml files generated by are pre-processed in our 
startup code where we add and change things before we hand them over to 
the Hibernate configuration. It might be possible to solve this in 
another way if the configuration is JPA-based but I have not looked into 
that.


I think it would be easier to just get rid of xdoclet and have the 
*.hbm.xml files in the source repository. It's an extra manual step to 
keep things synchronized, but considering that we rarely make any major 
database changes it should not be too difficult.


/Nicklas

On 2017-12-09 01:27, Muench, Joanna E wrote:
I’m working with a well-established BASE-based installation. One of our 
goals has been to move the build into CI. I have switched from ant to 
gradle without too much difficulty, although needed to call xdoclet from 
a spawned ant task. Given that JPA annotations are now the recommended 
mapping mechanism for Hibernate, I wondered if you had ever looked into 
migrating from xdoclet to JPA annotation? It is something we’re 
considering, and would appreciate knowing if there are major issues with 
that migration.


Also, I’m happy to share how to build in gradle, if anyone is interested.

Thanks!

*/Joanna Muench/*

Software Engineering

Hutch Data Commonwealth

O 206.667.2320

jmue...@fredhutch.org



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[base] BASE 3.11.2 has been relased

2017-11-23 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.11.2 today. This is a bugfix release that
fixes some minor bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.11.2=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.11.1 has been released

2017-06-07 Thread Nicklas Nordborg

Hello all,

We have released BASE 3.11.1 today. This is a bugfix release that
fixes some old and new bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.11.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] Question about BASE

2017-05-16 Thread Nicklas Nordborg
On 2017-05-15 23:32, Tyree Lush wrote:
> Good evening,
>
> I was wondering if someone could confirm whether the BASE software can
> be installed on a virtual server with full functionality. If it does and
> there are specs that are mandatory, could that be provided?

BASE should work just fine on a virtual server. Specs depends a lot on 
number of users and amount of data you are putting in. The amount of 
memory assigned to Tomcat is typically the most critical. For testing 
purposes 1GB should be enough and for a production installation maybe 
4GB. Note that you'll need memory for the OS and database as well.

Hope this helps.

/Nicklas


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[base] BASE 3.11 has been released

2017-05-10 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.11 today. This is a new major release which
mostly consists of improvements related to project-specific annotations 
that was introduced in the previous BASE relase.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.11=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.10.1 has been released

2017-04-28 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.10.1 today. This is a bugfix release that
fixes a few minor issues.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.10.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.10 has been released

2017-01-31 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.10 today. This is a new major release which 
among other things include some interesting new features for projects 
and annotations.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.10=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.9.2 has been released

2016-11-23 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.9.2 today. It is mainly a fix for an upgrade
problem that may cause an upgrade from BASE 3.7 to BASE 3.8 to fail.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.9.2=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.9.1 has been released

2016-08-23 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.9.1 today. This is a bugfix release that
fixes a few minor issues.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.9.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.9 has been released

2016-06-09 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.9 today. This is a new major release which among 
other things include performance enhancements when using PostgreSQL and 
better support for files larger than 2GB.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.9=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.8 has been released

2016-04-27 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.8 today. This is a new major release which among 
other things include a major performance improvement in the Annotation 
batch importer plug-in and several other enhancements related to 
annotations.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.8=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.7.2 has been released

2016-04-22 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.7.2 today. This is a critical bugfix release 
that fixes an issue that may cause unauthorized users to access files on 
the BASE web server.

BASE versions between 2.11 and 3.7.1 are affected and we recommend all 
users to upgrade to this BASE release. If upgrading is not possible the 
static cache should be disabled by setting 'cache.static.disabled=true' 
in the base.config file. Don't forget to restart the BASE web server.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.7.2=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.7.1 has been released

2016-03-07 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.7.1 today. This is a bugfix release that
fixes a few minor issues.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.7.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.7 has been released

2016-01-11 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.7 today. This is a new major release which among 
other things introduces a 'Kit' item for keeping track of chemicals and 
other things used in the lab.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.7=type=1

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.6.3 has been released

2015-11-25 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.6.3 today. This is a bugfix release that
includes a fix for a critical permission issue related to projects and 
some other minor fixes and improvements.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.6.3=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.6.1 has been released

2015-10-19 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.6.1 today. This is a bugfix release that
fixes a critical issue with some JSP files that could not be compiled.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.6.1=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.6 has been released

2015-10-08 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.6 today. This is a new major release that
has been focused on giving more control over experimental factor values 
to the owner of the experiment.

  * Experimental factors are now stored as part of the experiment
instead of as part of the raw bioassays. This is useful when
sharing raw data between users and projects.

  * It is possible to clone annotations from parent items instead
of just inheriting them. This is useful for protecting downstream
analysis from updates to the original annotations.

Also note that BASE 3.6 now requires Java 8 and Tomcat 8. Java and 
Tomcat should be updated before updating BASE.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.5=type

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.5.3 has been released

2015-09-18 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.5.3 today. This is a bugfix release that fixes a 
few minor issues.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.5.3=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.5.2 has been released

2015-05-05 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.5.2 today. This is a bugfix release that fixes a 
critical issue related to item lists that was introduced in the BASE 
3.5.1 release.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.5.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.5.1 has been released

2015-04-29 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.5.1 today. This is a bugfix release that
fixes a critical issue related to item lists and some other minor
issues.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.5.1group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.5-beta-1 has been released

2015-03-31 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.5-beta-1 today. This is a new major release that 
is focusing on new features for filtering and annotations. Among other 
things:

  * It is possible to filter with OR logic in tables
  * Batch inhering annotations
  * Filtering on inherited annotation in tables
  * New 'item list' feature that makes it possible for complex
filtering on parent/child relationships

A side-effect is that BASE 3.5 is not fully binary compatible with 
earlier releases. Custom extensions or plug-ins that use the 
'Biomaterial list API' are affected. See 
http://base.thep.lu.se/chrome/site/3.5-beta/html/appendix/incompatible.html 
for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.5group=type

Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/3.5-beta/html/admin/installation.upgrade.html
We recommend to use this version for testing only. Do not use on 
production servers!

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.4.2 has been released

2015-03-18 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.4.2 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.4.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.4.1 has been released

2015-02-10 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.4.1 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.4.1group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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look and join the conversation now. http://goparallel.sourceforge.net/
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[base] BASE 3.4 has been released

2015-01-14 Thread Nicklas Nordborg
Hello all,

After fixing a few issues with the beta version, BASE 3.4.0 has now
been released. One new feature is the possibility to install skins. 
Check out the example skins at
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.skincollection

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.4group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.3.3 has been released

2014-11-16 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.3.2 today. This is a bugfix release that
includes fixes for several issues as well as some enhancements.

Most importantly it fixes a bug that caused the remaining quantity for 
biomaterial items to become incorrect in some cases (ticket #1873). The 
bug was introduced in BASE 3.3. To fix any incorrect values a manual 
step is needed after the upgrade. See 
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html 
for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3.3group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.3.2 has been released

2014-10-22 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.3.2 today. This is a bugfix release that
includes fixes for several issues as well as some enhancements.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.3.1 hase been released

2014-09-26 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.3.1 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3.1group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] BASE Schema

2014-09-04 Thread Nicklas Nordborg
On 2014-09-03 19:45, Rachad El-Badrawi wrote:
 Hi All,

 We are considering BASE as the molecular diagnostics backend system for
 a project, and I was trying to figure out some of the backend workings
 of the schema. I would appreciate some feedback on the following:

 1) Is there a document that explains the PG schema that BASE uses, as
 far as the role of each table, and how it fits in the global model for BASE?

The best documentation related to this can be found at 
http://base.thep.lu.se/chrome/site/latest/html/developer/api/data_api.html

It's not really a database schema, but a mix of java classes and how 
they map to the database. It should be fairly up to date but may lack 
some information about the latest new features. There are lots of 
details and you probably also want to read 
http://base.thep.lu.se/chrome/site/latest/html/developer/documentation/magicdraw.html


 2) Is there an instance of BASE which includes a comprehensive project
 that shows the meaningful use for the database?

There is a BASE demo server at http://base2.thep.lu.se/demo/ but it has 
not been maintained for some time so I think what you can see there may 
not be very helpful.

There is also a document describing a manual test procedure that is 
performed before any new major release at: 
http://base.thep.lu.se/chrome/site/latest/test/roles/index.html

This test go through most major features in BASE, but in a real scenario 
one would probably want to automate some of the steps since it requires 
a lot of clicking...

Also, the test data set we use is not publicly available so it may 
require several changes to work with other kind of data.


 At a more detailed level:

 3) Patients/Subjects are entered as Biosources (from the web front end),
 and are saved in the BioMaterials table. Samples from these subjects are
 added as Samples (from the web front end) and are saved in the same
 BioMaterials table, too. Same for extracts. To relate these entries
 together, one can make use of the parent_id column and the discriminator
 level (i.e. 1, 2, 3). Is this explanation accurate?

Kind of, but it is not the full picture...

The parent_id column is a shortcut that is used only for items that has 
a single parent. If you, for example, pool several extracts into a 
single one, the parent_id column can't be used. The actual parent/child 
relationship is always stored in the BioMaterialEvents and 
BioMaterialEventSources2 tables, and is only duplicated in the parent_id 
column if possible.


 4) Is there a way of entering/saving that a specific sample has been
 analyzed/complete?

You could use annotations for that. That is more or less what we do 
currently, combined with other annotations for flagging if something 
needs to re-done.


 5) The number in the column event_type in the BioMaterialEvents table,
 what does it reference?

It is the type of the event. Every biomaterial has a single CREATION (1) 
event, then they can have any number of OTHER (3) events and BIOASSAY 
(2) creation events.


 6) Where is the sample type saved in the database?

In the ItemSubtypes table.

Hope this helpful, you are always welcome with more questions.

/Nicklas


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[base] BASE 3.3 has been released

2014-08-18 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.3! It is a new major release that includes 
several new features and enhancements. It may require some changes to 
the BASE server and/or and upgrade of the browser used to access BASE:

 * We now require Java 7 and Tomcat 7 on the server. If you
   are still using older versions, they should be upgraded
   before upgrading BASE.

 * The web interface has been reworked behind the scenes. Some
   (very old) browser may no longer work. It should be safe with
   IE 10 or a recent Firefox version.

 * The security in the web interface has been tightened in order
   to prevent cross-site scripting attacks. This can affect
   extensions. See the documentation for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas


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[base] BASE 3.3-beta-2 has been released

2014-06-26 Thread Nicklas Nordborg
A new beta-version of BASE 3.3 is now available for download. This fixes 
some minor issues since the last release. I don't expect any major 
issues to popup, but due to summer vacations a final BASE 3.3 release 
should not be expected until August or September.

/Nicklas


 Original Message 
Subject: [basedb-devel] BASE 3.3-beta-1 has been released
Date: Wed, 4 Jun 2014 09:52:30 +0200
From: Nicklas Nordborg nicklas.nordb...@med.lu.se
Reply-To: BASE dev basedb-de...@lists.sourceforge.net
To: BASE ML basedb-users@lists.sourceforge.net, BASE dev 
basedb-de...@lists.sourceforge.net, 
basedb-annou...@lists.sourceforge.net

Hello all,

We have released BASE 3.3-beta-1 today! It is a new major
release that includes several new features and enhancements.

 * We now require Java 7 and Tomcat 7 on the server. If you
   are still using older versions, they should be upgraded
   before upgrading BASE.

 * The web interface has been reworked behind the scenes. Some
   (very old) browser may no longer work. It should be safe with
   IE 10 or a recent Firefox version.

 * The security in the web interface has been tightened in order
   to prevent cross-site scripting attacks. This can affect
   extensions. See the documentation for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.3-beta/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] Files with FTP locations only

2014-06-26 Thread Nicklas Nordborg
 So, I am currently working on an extension that add support for
 accessing external files via FTP, FTPS and SFTP (see
 http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be
 able to release a first version later this week if you want to try it.

I have now Xfiles 1.0. You'll need the BASE 3.3 beta 2 release to make 
it work. Download and documentation is available on:

http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles

/Nicklas



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Re: [base] Files with FTP locations only

2014-06-24 Thread Nicklas Nordborg
On 2014-06-24 11:55, Bob MacCallum wrote:
 Hi Nicklas et al,

 Getting up to speed with BASE3 and NGS - so far all seems good - even
 upgrading our own API code has gone smoother than I expected.  Thanks!

Great to hear that it is going well.


 A possible feature request for general discussion:

 Would it be possible to have placeholder files in the BASE file system
 which weren't on disk but had an FTP location stored in the DB?   It
 would be a bit like the current offline option but for our use case
 (fastq and BAM files stored elsewhere and never processed by BASE3 or
 plugins) we would never even upload the files in the first place (I
 can't find a way to create a file that is offline from the start).

 The debate for other users/devs would be: should BASE automatically
 retrieve the files when needed?  I say no need for that - treat them
 like offline files are currently (if I understand correctly how offline
 files work).

There is already the *external files* feature. It can accessed with New 
URL in the BASE file manager. It's not the same as an *offline* file 
since by default BASE will try to check if it exists and download some 
metadata (such as size and modification date). And BASE will also 
retrieve the file if is requested by a plug-in or a user tries to 
download or view it.

The external files feature is pluggable and the BASE core only provide 
support for files that can be accessed with http or https. In theory it 
is possible to register unsupported URLs (eg. ftp://...) but I guess 
error messages will popup here and there.

As it happens, we discussed a similar problem last week. Up until now, 
our approach has been to simply store the file path as an annotation on 
bioassay items. In the future we'll need to provide access for external 
researchers to our data, but we really don't want to have them on our 
internal file servers so the idea is to let BASE act as a proxy.

So, I am currently working on an extension that add support for 
accessing external files via FTP, FTPS and SFTP (see 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be 
able to release a first version later this week if you want to try it.

If you prefer the *offline* files feature there is unfortunately no 
support in the GUI for creating offline files without first uploading 
them. A possible solution would be to modify the New URL dialog to 
make the URL field optional, and use this to decide between 
offline/external file.

If you have any other ideas please let me know...

/Nicklas


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[base] BASE 3.3-beta-1 has been released

2014-06-04 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.3-beta-1 today! It is a new major
release that includes several new features and enhancements.

* We now require Java 7 and Tomcat 7 on the server. If you
  are still using older versions, they should be upgraded
  before upgrading BASE.

* The web interface has been reworked behind the scenes. Some
  (very old) browser may no longer work. It should be safe with
  IE 10 or a recent Firefox version.

* The security in the web interface has been tightened in order
  to prevent cross-site scripting attacks. This can affect
  extensions. See the documentation for more information.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.3group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.3-beta/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] array design GTF import - not 9 columns

2014-05-26 Thread Nicklas Nordborg
Thanks for testing this. It feels like it was a long time ago this was 
implemented and we have not really started to use it yet. Anyway, you 
are correct that the problem is something deeper than the usual importer.

To make GTF files parsable by the regular importers, there is a 
pre-parsing step that add headers and rewrites the attributes column 
(column 9) so that each attribute value is tab-separated instead of 
semicolon-separated.

It is the pre-parser that complains if a line doesn't have at least 9 
columns. I checked the code and found a TODO comment about 
implementing support for comments, but for some reason it has been 
overlooked. It should be easy enough to implement this, and I can 
probably fix this for the next (BASE 3.3) release.

But for now, the importer will choke on anything that is not a Field 
line as described by http://www.ensembl.org/info/website/upload/gff.html

/Nicklas


On 2014-05-23 18:17, Bob MacCallum wrote:
 Hi all,

 [mods please delete the mail I sent from my gmail account, or add me
 with that account but with no delivery, thank]

 Just upgraded from 2-3 and now trying out the NGS feaures.  Quick
 question about GTF import for array designs...

 When doing array design-import the importer is complaining:

 Error: A line must have at least 9 columns, at line: 1
 stack trace below
 (using GTF reporter map importer (version 3.2.5-dev))

 The same error came up when we first created the array design (because I
 checked the validate files box.

 I know the first line has fewer columns because it has some # commented
 lines

 so in the importer configuration I configured the Ignore field like
 this:  ^#.*

 But still the same error...

 Even if I set Default error handling = skip it's the same.  Seems to be
 something deeper than the usual tab delimited importer parser settings.

 I guess we should make a new GTF file with no comments but I just wanted
 to check if this was the intended behaviour?

 cheers,
 Bob


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Re: [base] reseting root password

2014-02-16 Thread Nicklas Nordborg
On 2014-02-17 02:39, Ross Chapman wrote:
 Hi all

 I have inherited the management of a BASE 2 solution for managing
 microarray data.

 I do not have access to the Root password, but I do have administrator
 rights.

 Am I able to reset the root password, will this have any impact on how
 BASE operates?

As an administrator you should be able to change the password of the 
root account. This should not cause any problems.

/Nicklas


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Re: [base] Base 3.2 installation on Mac OS 10.6 server

2013-09-11 Thread Nicklas Nordborg
Seems to me like there is some problem with the Tomcat installation. 
Unfortunately I am not very familiar with Mac so I am afraid I won't be 
of much help here.

Have you checked if you can access the Tomcat welcome page?

http://localhost:8080/

/Nicklas

On 2013-09-11 10:57, Laurent Troxler wrote:

 Le 10 sept. 2013 à 20:26, Nicklas Nordborg nicklas.nordb...@med.lu.se
 mailto:nicklas.nordb...@med.lu.se a écrit :

 On 2013-09-10 16:35, Laurent Troxler wrote:
 Thank you Nicolas for your answer.
 It helped me to find out that I had missed the base.config file password
 setting.
 I thus could go through the all process.

 Great.

 I am now facing an other problem linked to Tomcat.
 After setting the symbolic link between Tomcat and Base, when I go on
 the webpage http://hostname:8080/base2
 I get alternatively  :

 The /Library/Tomcat/work directory and subdirectories are directories
 where Tomcat store temporary working files. Usually this is not
 something one has to worry about. I can think of two reasons why the
 directory referenced in the error message is empty:

  1. The Tomcat process doesn't have write permission on the directory
 I have given the full rights to every one on
 /Library/Tomcat/work/Catalina/localhost/base2
 drwxrwxrwx  8 root  _appserveradm  272 22 aoû 11:47
 /Library/Tomcat/work/Catalina/localhost/base2
 Should it also need to change the owner ? But I do not know which user
 is Tomcat using

  2. The disk is full
 there is over a hundred Go, It should be enough

 It might be possible that there is more information in one of Tomcat's
 log files (though I can't tell which one, the logging setup of Tomcat is
 still a bit of a mystery to me...). At least, it seems like Tomcat is up
 and running so it shouldn't be a Java issue.

 going through the log files here is what I can get:
 system.log: repeating those two lines
 Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @
 CGErrorBreakpoint() to catch errors as they are logged.
 Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat):
 Throttling respawn: Will start in 8 seconds

 /Library/Tomcat/logs/catalina.2013-09-11.log :
 Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap
 initClassLoaders
 SEVERE: Class loader creation threw exception
 java.lang.InternalError: Can't connect to window server - not enough
 permissions.
 at java.lang.ClassLoader$NativeLibrary.load(Native Method)
 at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
 at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
 at java.lang.Runtime.loadLibrary0(Runtime.java:823)
 at java.lang.System.loadLibrary(System.java:1045)
 at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
 at java.awt.Toolkit.clinit(Toolkit.java:1627)
 at sun.awt.AppContext$2.run(AppContext.java:240)
 at sun.awt.AppContext$2.run(AppContext.java:226)
 at java.security.AccessController.doPrivileged(Native Method)
 at sun.awt.AppContext.initMainAppContext(AppContext.java:226)
 at sun.awt.AppContext.access$200(AppContext.java:112)
 at sun.awt.AppContext$3.run(AppContext.java:306)
 at java.security.AccessController.doPrivileged(Native Method)
 at sun.awt.AppContext.getAppContext(AppContext.java:287)
 at com.sun.jmx.trace.Trace.out(Trace.java:180)
 at com.sun.jmx.trace.Trace.isSelected(Trace.java:88)
 at
 com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.isTraceOn(DefaultMBeanServerInterceptor.java:1830)
 at
 com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerDynamicMBean(DefaultMBeanServerInterceptor.java:929)
 at
 com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerObject(DefaultMBeanServerInterceptor.java:916)
 at
 com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerMBean(DefaultMBeanServerInterceptor.java:312)
 at com.sun.jmx.mbeanserver.JmxMBeanServer$2.run(JmxMBeanServer.java:1195)
 at java.security.AccessController.doPrivileged(Native Method)
 at
 com.sun.jmx.mbeanserver.JmxMBeanServer.initialize(JmxMBeanServer.java:1193)
 at com.sun.jmx.mbeanserver.JmxMBeanServer.init(JmxMBeanServer.java:225)
 at com.sun.jmx.mbeanserver.JmxMBeanServer.init(JmxMBeanServer.java:170)
 at
 com.sun.jmx.mbeanserver.JmxMBeanServer.newMBeanServer(JmxMBeanServer.java:1401)
 at
 javax.management.MBeanServerBuilder.newMBeanServer(MBeanServerBuilder.java:93)
 at
 javax.management.MBeanServerFactory.newMBeanServer(MBeanServerFactory.java:311)
 at
 javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:214)
 at
 javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:175)
 at
 sun.management.ManagementFactory.createPlatformMBeanServer(ManagementFactory.java:302)
 at
 java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:504)
 at
 org.apache.catalina.startup.Bootstrap.createClassLoader(Bootstrap.java:183

Re: [base] Base 3.2 installation on Mac OS 10.6 server

2013-09-10 Thread Nicklas Nordborg
On 2013-09-09 16:04, Laurent Troxler wrote:
 Hello  all, Ì am new at Base and trying to install it on a Mac OS
 10.6 server. Looking in the mailing list archives did not bring me
 any helping information, Mac OS does not appear often. Therefore I
 submit you my problem. After downloading and unpacking Base, setting
 Apache, MySQL, TomCat, and configuring Base I reached the step of the
 database initialization with the instruction : ./initdb.sh
 [base_root_login] base_root_password Below is what I get in return on
 my terminal. I am using the Base root login and password defined in
 MySQL but it looks like it is not recognized. Is there anyone having
 faced such problem in similar configuration or having suggestion

It seems like the root problem is that MySQL is not letting the BASE
installation to connect to the database.

The first step is to verify/make sure that you can connect manually to 
MySQL using the same username and password as you have specified in the 
base.config file. Depending on how networking is set up it may help to 
replace 'localhost' with '127.0.0.1' when granting access to MySQL and 
in the 'base.config' file (db.url setting).

/Nicklas


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[base] BASE 3.2.3 has been released

2013-09-09 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.2.3 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.3group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.2.2 has been released

2013-04-10 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.2.2 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.2.1 has been released

2012-12-13 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.2.1 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2.1group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] Error on Biomaterials LIMS

2012-11-22 Thread Nicklas Nordborg
On 2012-11-22 19:40, Paulo Nuin wrote:
 Hi

 We have a couple of instances of BASE installed in our systems. We are
 getting a problem whenever we are accessing entities created in the
 Biomaterial LIMS, either samples or biosources:

This is a Tomcat configuration problem and is described in the 
installation documentation:

http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html

Check the section about STRICT_QUOTE_ESCAPING and make sure that this is 
set to 'false'.

Hope this helps.

/Nicklas

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Re: [base] Schema

2012-11-12 Thread Nicklas Nordborg
On 2012-11-13 03:32, Paulo Nuin wrote:
 Hi

 Is there any available image/diagram of the current schema?

Not really. The closest thing is the diagrams that can be found in each 
of the subsections at 
http://base.thep.lu.se/chrome/site/latest/html/developer/api/data_api.html

The diagrams give an object-centric view with some (but not complete) 
information to how everything is mapped to the underlying database. To 
find out about the details you would need to check the code or a real 
database after installation.

/Nicklas


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Re: [base] DataQuery.order(...) 2.x API question

2012-10-09 Thread Nicklas Nordborg
On 2012-10-09 13:11, Bob MacCallum wrote:
 Hi all,

 I'm trying to get a Reporter query from the BASE2.x API which is
 basically ORDER BY RAND(123) - to get reproducible random order (I
 can explain *why* in another email if anyone cares to know).

 I tried this

 DataQuerynet.sf.basedb.core.data.ReporterData repQuery =
 net.sf.basedb.core.Reporter.getQuery();

 repQuery.order(Orders.asc(new HqlExpression(RAND(123), xxx)));

 But it seems that HqlExpression isn't for public use.  I can't find
 something like Expressions.hql.

This can be found in net.sf.basedb.core.query.Hql.expression(...)

 Could somebody please save me a ton of time and tell me how to put
 some arbitrary SQL into the ORDER BY clause of a DataQuery?

Note that it is not SQL that is needed but HQL (Hibernate Query 
Language). Don't know if RAND() is available in HQL. If not, it should 
be possible to create a custom Hibernate dialect and use that in the 
'db.dialect' setting in base.config. I have never done that so I don't 
know any details or how hard/easy it is.

Another possibility is to use Reporter.getDynamicQuery() instead which 
lets you work with SQL, but code-wise it's a bit harder to work with 
since you have to process the result row-by-row and column-by-column 
instead of as ReporterData objects.

/Nicklas


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Re: [base] DataQuery.order(...) 2.x API question

2012-10-09 Thread Nicklas Nordborg
On 2012-10-09 17:24, Bob MacCallum wrote:
 Just for closure, I am now in business.

 [mysqld]
 tmp_table_size = 5G


 Background for whoever cares:

 I'm running something reporter-wise in parallel (4 threads) and wanted
 roughly equal workload per chunk of reporters (some reporters have
 more experiments+data than others) so having them in random order
 before chunking does the trick.

 The tmp tables that the SELECT * FROM Reporters ORDER BY RAND(123)
 creates are 3.2G each (times 4) and while doing this there's some
 serious I/O clogging the machine but it pulls through.  If only gnu
 parallel had a -stagger [secs] option!


ORDER BY RAND() is known for performance issues once the number of rows 
grows large. I guess it is because MySQL need to create a temporary 
table with *all* the original data plus the random number for each row 
before the data can be sorted.

It might be more efficient to first do 'select id from Reporters' 
(you'll need to use the Reporter.getDynamicQuery() for this), put all 
id's in an array, randomize that in memory and then bring in the actual 
reporter data one by one (or 100 by 100 or something). That should at 
least avoid the temporary table issue since the id's can be pulled in 
directly from the primary key index. In theory it should be quicker, but 
I guess it has to be verified in practice as well.

/Nicklas


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Re: [base] Setting up a new root bioassay set

2012-10-02 Thread Nicklas Nordborg
On 2012-10-02 00:27, McClelland, Erin wrote:

 Hi
 Tried to post this earlier but it didn't seem to work - apologies if
 this is a duplicate message.

 We have run into a problem setting up a new root bioassay set - we
 continually get an error message similar to the following: Duplicate
 entry '22-1' for key 'PRIMARY' -  (see stack trace below).  Initially we
 did not have a reporter map imported for the new array we are using and
 had some problems with that importation - not sure if that would affect
 the root bioassay set as the reporters now seem to be in BASE. We are
 using data output from ImaGene. We are unsure how to address this
 problem and wondered if you have any suggestions.


It's difficult to say exactly what has happened here, but the error 
indicates some kind of duplicate position/reporter information in the 
raw data. This can be checked by going to the Raw data tab of one of 
the raw bioassays. Each entry in this table should have a unique 
position, but possibly there are at least two with position=1.

If that is the case, new raw bioassays has to be created and the raw 
data has to be re-imported. Make sure that the array design has imported 
reporters since that is required to make the positions unique.

Hope this helps.

/Nicklas


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Re: [base] Can BASE (v2.12.1) import files directly from the server it's running on?

2012-09-20 Thread Nicklas Nordborg
On 2012-09-20 01:26, Hugh Brown wrote:
 Hi everyone -- my department is running BASE version 2.12.1.  We have
 some users outside our department, and their network connection is
 rather slow.  At the moment, they're importing files rather
 circuitously: uploading them to our server for pre-processing,
 downloading the results, then uploading them to BASE via their
 browser.  The end result is many round trips for large data files.
 
 I'm wondering if BASE, perhaps through a plugin, supports importing
 files from the server it's running on.  I found a message from 2007
 about this idea

   
 http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00218.html

 but as far as I can see, this is not in BASE2.  Have I missed anything?

No, you have not missed anything. There is no functionality for 
importing files directly from the server. Although it would be possible 
to implement this as a plug-in or as an External file extension (but 
this require at least BASE 3.0). In any case, I can imagine all sorts of 
security/permission-related issues with this.

 About the only other alternative I can think of is installing the FTP
 server plugin, then have the users connect via FTP from the server
 itself (ie, over the loopback interface).  Is there any reason that
 would not work?

I think this would work very well. And if you only need the FTP support 
locally then there is no need to open up firewalls, etc. which is always 
a hassle with FTP.

/Nicklas


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[base] BASE 3.2 has been released

2012-09-13 Thread Nicklas Nordborg
Hello all,

We are happy to announce the release of BASE 3.2. It is a new major
release that includes several new features and enhancements.

   * Several new extension possibilities in table listings,
 the item overview and other places.

   * A new parent/child structure for derived bioassays that makes
 it possible to merge bioassays from multiple physical bioassays.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] Change BASE's HTML title

2012-08-20 Thread Nicklas Nordborg
On 2012-08-20 17:09, Paulo Nuin wrote:
 Hi

 I have a quick question on configuring BASE's HTML page title. In the
 server we have installed now it appears

 BASE 3.1.1 @ unknown

 I found the jsp pages in the www directory but it is not clear to me
 where this title is coming from. I was able to add a value to the
 title variable in the jsp, but the unknown still appears.

The title is generated from the current BASE version and the name of the 
computer it is installed on. I have never seen the string 'unknown' 
there. Usually, if the computer doesn't have a name the title will be 
something like: 'BASE x.y.z @ 127.0.0.1' or 'BASE x.y.z @ localhost'

Maybe it is an indication that there is no network connection...

Or maybe the computer's name is 'unknown'?

/Nicklas


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Re: [base] Change BASE's HTML title

2012-08-20 Thread Nicklas Nordborg
On 2012-08-20 18:56, Paulo Nuin wrote:
 Hi

 The computer has a name under /etc/HOSTNAME running SuSE, and network is fine.

Check Tomcat's log file if there are any error messages. The name is set 
to 'unknown' if the name can't be retrieved from the system.

/Nicklas


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[base] BASE 3.1.2 has been released

2012-07-31 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.1.2 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.1.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] MeV: export bioassay set to TDMS file error

2012-06-14 Thread Nicklas Nordborg
On 2012-06-07 08:52, Nicklas Nordborg wrote:
 On 2012-06-05 22:52, Steven Charles Fan wrote:
 Running base v3.1.1 with mev-launcher-1.9 binary (current base version
 and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
 bioassays to a TDMS file for analysis in MeV and got a unnamed error
 with the following stack trace:
 ...
 Is this a user error I can do something about or have I stumbled upon
 a bug?

 I can confirm that this is indeed a bug. Until a fix has been released,
 the workaround is to use the 'Clone reporters' function on the
 experiment view page.

I have now release a new version of the MeV plug-in (1.10). It fixes 
this bug and also update MeV to 4.8.1. It can be downloaded from:

http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev

/Nicklas

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Re: [base] MeV: export bioassay set to TDMS file error

2012-06-07 Thread Nicklas Nordborg
On 2012-06-05 22:52, Steven Charles Fan wrote:
 Running base v3.1.1 with mev-launcher-1.9 binary (current base version
 and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
 bioassays to a TDMS file for analysis in MeV and got a unnamed error
 with the following stack trace:
...
  Is this a user error I can do something about or have I stumbled upon 
a bug?

I can confirm that this is indeed a bug. Until a fix has been released, 
the workaround is to use the 'Clone reporters' function on the 
experiment view page.

 The following is unrelated, but I was wondering if reporters were best
 imported from a gpr file or GAL file or if there is a difference. I was
 also wondering if there was a way to update biological annotations
 automatically from SGD.

It shouldn't really matter since the only reporter information in gpr 
and gal files are the reporter id. Annotations need to come from a 
different source. I do not know what SGD is, but in any case there is no 
function to update annotations automatically from any external source. 
It must be done manually by exporting and importing files.

 Oh and a (possible) bug notice: in the *Genepix raw data cy5/cy3
 (cy5/cy3) import configuration* for the *raw bioassay import from file*,
 I had to change *Rgn Rsuperscipt 2* to *Rgn R2* to get it to work with
 my grp extension genepix files.

It's not really a bug. The data files we have all have R² (superscript). 
My guess is that it depends on the Genepix software version and/or 
settings in the software.

/Nicklas

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[base] BASE 3.1.1 has been released

2012-03-29 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.1.1 today. This is a bugfix release that
fixes a possibly critical issue with access permission to annotation
values and a few other minor issues.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.1.1group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.1 has been released

2012-03-19 Thread Nicklas Nordborg
Hello all,

We are happy to announce the release of BASE 3.1. It is a new major 
release that among other things include:

  * A new and improved user interface
  * Possibility to clone reporter information to a local copy
per experiment
  * A migration script for moving a BASE installation from MySQL
to PostgreSQL

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.1group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage


/Nicklas

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[base] BASE 3.0.4 has been released

2012-03-05 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.0.4 today. This is a bugfix
release that fixes a few minor bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0.4group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.0.3 has been released

2012-02-22 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.0.3 today. This is a bugfix
release that fixes an annoying Internet Explorer issue
with popup windows.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0.3group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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[base] BASE 3.0.2 has been released

2012-01-25 Thread Nicklas Nordborg
Hello all,

We have released BASE 3.0.2 today. This is a bugfix
release that fixes a few minor bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage


/Nicklas

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Re: [base] Dealing wiht duplicate spots

2011-11-22 Thread Nicklas Nordborg
On 2011-11-21 21:32, Nantel Andre wrote:


 We don't have any regular users yet since we are still figuring out
 how it works. I am doing everything from my administrator account.

Have you created a file format configuration for the files you are 
using? This is done in Administrate - Plug-ins  Extensions - Plug-in 
configurations. Create a new configuration for the 'Raw data importer' 
plug-in and use the 'Test with file' function to get regular 
expressions, etc. correct.

 Anyway that's all the time I can give to this problem until later
 this week. This whole process has been much much more difficult than
 we expected. Please don't take this the wrong way but it might be a
 problem for your team as well if you ever hope to expand on your user
 base. It's not like we're new at this, we've been using microarrays
 since 1999 but I was getting tired of sending thousands of dollars to
 Agilent every year.

Setting up a BASE server is not trivial. We have recently set up a new 
BASE installation for a project here and I guess we have spent several 
months just setting up lab procedures, data import procedures, and also 
made some customizations to BASE in order to further streamline the data 
entry.

We don't have an explicit goal to get more users. We are primarily using 
BASE at our own site to solve our own problems. The Illumina extension 
package is an example of that. Unfortunately, we don't have the 
resources to develop things targeted for other platforms than what we 
are using ourselves. This doesn't mean that BASE can't be used with 
other platforms, but in order to get the most out of BASE one need to 
invest time and maybe also resources for customization. In may 
experience at least a week would be needed for initial testing and 
prototyping and then maybe a couple of months for setting up a 
production-ready server, formalizing lab and data handling procedures, 
developing custom plug-ins and extensions, etc.

/Nicklas

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Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 17:08, Nantel Andre wrote:
 Greetings,

 We are currently trying to integrate BASE into our lab and writing the
 necessary plug-ins to import normalized data from ImaGene. Let's just
 say that the lack of documentation has been challenging.

 Right now we are trying to figure out how to deal with duplicate spots.
  From the GenePix examples in the Base2 server we see cases of raw
 biosassays wtih [raw] columns defined by the unique spot coordinates as
 well as “rep‘ columns containing the duplicated GeneID classifiers. Any
 suggestions on how to do this?

What do you mean with a duplicate spots? Physically a spot is a spot and 
there can of course only be one on a given position. However there is 
nothing in BASE that prevents two or more spots from referencing the 
same gene/reporter. Then there are some platforms (for example Illumina 
BeadArrays) that doesn't have spots in the classical meaning. In this 
case one need to construct a unique feature id for each spot 
equivalent that one wants to measure. In the Illumina case, the unique 
ID is provided by the Illumicode column in the data files. This value 
is then mapped to gene/reporter annotations via a BGX file, and the 
importer is also calculating means, etc for all entries with the same 
Illumicode value. See 
http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina for more 
information about how the Illumina platform has been implemented.

I don't know what kind of data files that are generated by the ImaGene 
platform, so it is hard to advice on exactly how to the same thing for 
ImaGene.

/Nicklas

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Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 19:23, Nantel Andre wrote:
 That issue goes beyond the ImaGene format. When doing contact
 printing of microarrays it is still fairly common to spot the same
 probe 2 or more times as shown in the example here
 (http://www.digitalapoptosis.com/2005/10/12/dna-microarray/).

 It is also very common for commercial arrays (Agilent for example) to
 have multiple copies of their control spots.

I wouldn't call that duplicate spots. They are different spots on 
different coordinates that just happen to have the same reporter/gene. 
The importer should import those as two separate entries and it is then 
up to down-stream analysis if they should be merged into a single value 
and what kind of average method to use for merging.


 We'll take a look at the Illumina plug-ins but I'm sure that there is
 a more elegant solution.

Does the ImaGene data file have spot coordinates in the data files or 
not? If not, then the Illumina case might be useful, but not otherwise.

  What were are trying to do is,
 theoretically, simple since our data is already
 background-substracted and normalized (ImaGene does a perfectably
 acceptable job in doing that). We have two collums with ch1 and ch2
 normalized intensities in Log2 and a Flag column showing spots that
 have to be filtered out. We were hoping to use BASE to help up
 organize our experiments before sending them off to MeV.

 In the Base2 demo server, the demoHyb1 bioassay is similar to our
 situation. When I open that item and click on the Raw data tab, It
 appears  that the spot coordinate were imported and then used to
 produce columns entitled [Rep] Name and [Rep] ID that clearly come
 from duplicate spots. That's what we are trying to replicate.

The demo data set is a GenePix data set and for each spot the file 
contains the coordinates, reporter id and a lot of measured intensities 
and other values. So if your data is similar to this, then I think you 
don't need any special new importer. Use the generic Raw data flat file 
importer and make sure to map spot coordinates, reporter id and 
intensity columns that are in your data files.

Maybe you can post a few lines from the files you are working with so I 
don't have to guess...

/Nicklas

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Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 20:31, Nantel Andre wrote:
 On 2011-11-21, at 2:13 PM, Nicklas Nordborg wrote:

 The demo data set is a GenePix data set and for each spot the file
 contains the coordinates, reporter id and a lot of measured intensities
 and other values. So if your data is similar to this, then I think you
 don't need any special new importer. Use the generic Raw data flat file
 importer and make sure to map spot coordinates, reporter id and
 intensity columns that are in your data files.

 Maybe you can post a few lines from the files you are working with so I
 don't have to guess...

 Here is our data format. We never got the generic importer working even
 after updating the raw-data-types.xml file to our version of the Imagene
 files. When we try to use that, we get a no plug-in error.

This is usually due to lack of permission for the logged in user. Make 
sure that the file format configuration has been shared properly.

The file seems to be equivalent to and contain information that is very 
similar to GenePix files. I don't see any reason why the generic raw 
data importer shouldn't work in this case.

/Nicklas

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[base] BASE 3.0 has been released

2011-11-02 Thread Nicklas Nordborg
Hello all,

We are happy to announce the release of BASE 3.0. It is a new major
release that contains a lost of new functionality, including (but not
limited to):

 * Support for RNAseq experiments
 * A subtype feature for classifying generic items
 * Easier installation of plug-ins and extensions

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0group=type

NOTE!

Upgrading is supported from BASE 2.17 only. Older BASE versions must be
upgraded to BASE 2.17 before trying to upgrade to BASE 3.

BASE 3 is not binary-compatible with BASE 2. This means that existing
plug-ins/extensions may not work until updated versions are available.
We'll start releasing BASE 3-compatible versions for many of the
plug-in/extensions packages found on http://baseplugins.thep.lu.se later
today and tomorrow.

Changes to the batch item importer plug-ins may require that users
update their file templates and file format configurations.

There is more information about this in the upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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

2011-10-26 Thread Nicklas Nordborg
On 2011-10-25 19:36, Pawel Sztromwasser wrote:

 That I didn't know. So when no column mapping is provided for a
 property, the project default is used (since the property is regarded as
 not initialized, and not null). I also like the expression solution in
 column mappings. It has an advantage over a plugin parameter because it
 allows to select particular properties to apply default values to.

I have created a ticket for this: http://base.thep.lu.se/ticket/1642

/Nicklas


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

2011-10-26 Thread Nicklas Nordborg
On 2011-10-25 19:36, Pawel Sztromwasser wrote:
 I like one-click fix-it buttons (one is available for inheriting
 annotations if I am not mistaken), and they would definitely speed up
 work with BASE removing some of the repetitive interactions. If it is
 possible to include them in the roadmap for 3.1, that would be
 excellent. The sooner the better:)

And another one: http://base.thep.lu.se/ticket/1643

I put it in BASE Future release milestone since it feels like a big 
change and we already have a few big things to do in BASE 3.1

/Nicklas

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

2011-10-26 Thread Nicklas Nordborg
On 2011-10-25 13:34, Bob MacCallum wrote:

 +1 for annotatable experiments

http://base.thep.lu.se/ticket/1644

/Nicklas

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

2011-10-25 Thread Nicklas Nordborg
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 as
 default in an active project? I did a quick test and it didn't work, so
 I thought I could suggest it. This way setting project properties
 upfront would save some work latter when editing the batch-import
 spreadsheets.
 I can imagine that in some cases it is not desired to set default
 properties automatically, so maybe a plugin configuration option to use
 project defaults would suffice. When updating with 'use defaults' option
 set, the plugin should overwrite existing properties.

The batch importers doesn't really care about project default values. 
It is handled entirely by the core code which has a contract to set 
default values when creating new items, but only if no explicit value 
has been set.

The key issue here is that if a column is mapped in the batch importers 
an empty value is considered as an explicit request to set the value to 
null, and the core will not use the default value. In other words, when 
using the batch importers the project default values are only used for 
unmapped columns.

There are also a lot of changes in this area in BASE 3. It is now for 
example, possible to have more than one default value and the core tries 
to match everything depending on the subtype of an item.

So, I don't really know what is the best solution here... Maybe, instead 
of using hard column mappings (eg. \Protocol\) we could add support 
for expressions. Something like =default() would always select the 
project default value, or =defaultIfNull('Protocol') select the mapped 
protocol if a value is specified, but uses the default if the column is 
empty.

 The second suggestion is also about the project default properties. We
 appreciate the nice and very useful links in the experiment
 overview/validator that help correct the experiment, and we saw a need
 for a new one(s). When an item is missing a protocol/software/hardware
 (or similar), the link could help in setting the default value in the
 active project. Or even suggest doing it for all the items of the same
 type having the property missing. This would be an awesome option
 allowing to fix the experiment quickly when one forgot to set the
 defaults in advance.

The fix it links can currently only provide a link that opens an edit 
dialog. The user must do the change manually. Automatic fixes would 
really nice and could probably be done for several other problems as 
well. It is not straight-forward to implement since we'll probably have 
to keep track of a lot more information related to each suggested fix.

Maybe we could define some kind of 'FixIt' interface and then use a 
'FixItFactory' to provide actual implementations. Seems like something 
for BASE 3.1 or later...

/Nicklas

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[base] BASE 3.0-beta has been released

2011-10-12 Thread Nicklas Nordborg
Hello all,

Today we are happy to announce the release of BASE 3.0-beta. If all goes
well the final 3.0 release is expected within the near future.

This release should contain all new functionality that is needed for
supporting sequencing experiments with expression like data, but there
may still be some bugs to fix.

Do not use this release on a production server. It is not certain that
upgrading to the final 3.0 release will be possible. Upgrading existing
servers will be possible from BASE 2.17 only. The beta release should be
able to upgrade both MySQL- and PostgreSQL- backed installations.

The 3.0 release is not binary-compatible with BASE 2. This means that
existing plug-ins/extensions may not work until updated versions are
available. There is more information about this in the upgrade instructions.

The user and administrator documentation should be up to date, but the
developer documentation is still not 100% complete. We will try to
answer questions and help with problems on the mailing list.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.0-beta/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] Anyone using BASE with PostgreSQL?

2011-09-30 Thread Nicklas Nordborg
On 2011-09-30 12:09, Pawel Sztromwasser wrote:
 Hi Nicklas,

 Our backup procedure is from before-WAL-times so it does not use WAL.
 Currently we make daily dumps which are stored if different from the
 previous one (based on md5). Not much help for the things that you asked
 for, sorry.

Ok. Thanks anyway.

/Nicklas

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[base] Anyone using BASE with PostgreSQL?

2011-09-29 Thread Nicklas Nordborg
Hello,

We are thinking about migrating our BASE production server from MySQL to 
PostgreSQL. The major reason is that PostgreSQL seems to have a lot more 
interesting solutions for backup. We are particularly interested in the 
WAL archiving solution. Possible combined with a warm standby server 
which can then be used for SQL dumps without disturbing the main server.

We have a similar procedure for MySQL but it is not a continuous 
backup in the first step and the SQL dump is taking far too long time.

So, if anyone has any experience with PostgreSQL we would love to hear 
about your experience.

There is also a ticket related to the MySQL-PostgreSQL migration on our 
website (http://base.thep.lu.se/ticket/1630). Any comments about that 
are also welcome.

Thanks,
   Nicklas

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Re: [base] Anyone using BASE with PostgreSQL?

2011-09-29 Thread Nicklas Nordborg
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 the backup though, if you were interested.

Thanks for the reply. It's good to hear that you are happy with 
PostgreSQL. It's actually quite hard to find someone that isn't...

In any case, if it's not too much trouble it would be nice to hear what 
your techs have to say.

/Nicklas

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Re: [base] base 3 RNAseq overview

2011-09-27 Thread Nicklas Nordborg
On 2011-09-26 22:19, Bob MacCallum wrote:
 Hi Nicklas et al,

 I've been scanning the 3.0 alfa documentation and have seen how
 biomaterials are handled with respect next gen (with the new library
 type).

 However, I can't see how raw data and analysis works.  Do the concepts
 of reporters and array designs still apply? I'm happy to install and
 play but first I would greatly appreciate a few sentences of
 explanation.  Apologies if I missed this previously on the mailing
 list.

I don't think you missed anything because that part is not implemented 
in the alpha release. The ongoing work more or less follows the ideas 
that you posted in http://base.thep.lu.se/ticket/1153 a few years ago. 
For 1) we are providing a GTF importer that creates a virtual array 
design referencing the genes/transcripts that is of interest.

3a is the main choice so far. Everything done outside BASE can however 
be tracked and intermediate result files can be uploaded and stored. The 
derived bioassay item replaces scan and it is now also possible to 
have multiple steps of derived bioassays before a raw bioassay is 
created. In theory, it would be possible to implement BASE plug-ins to 
do the analysis here also, but in practice it is not so easy because of 
the large amount of data that is generated and the processing time 
required to analyze it. I don't know much about the details here, but in 
the end Cufflinks (http://cufflinks.cbcb.umd.edu/) is generating one 
output file per sample containing a count (fpkm) that should be usable 
as the expression level. This can be imported as a raw bioassay.

We have some ideas to create a specialized kind of job agent that 
follows a scripted path of analysis programs to run and then report to 
BASE what has been done and upload some of the results files. We have 
not started on this yet and there is no real time plan either. I guess 
it will be rather site-specific to begin with, since much depend on 
details about file storage areas, computational clusters, etc.

We'll keep the Generic platform for microarray experiments and add a 
new platform for sequencing experiments, but that's mostly cosmetics and 
a way for plug-ins to hide/show themselves depending on the context.

Hope this answers some of your questions. We'll try to release a new 
version (beta?) in about two weeks if we can get the desired 
functionality in place.

/Nicklas

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[base] BASE 3.0-alfa has been released

2011-09-15 Thread Nicklas Nordborg
Hello all,

Today we are happy to announce the relase of BASE 3.0-alfa. If all goes 
well the final 3.0 release is expected in a couple of months. This 
release contains major changes which are mainly targeted at supporting 
sequencing experiments with expression like data.

Do not use this release on a production server. It is not certain that 
upgrading to the final 3.0 release will be possible. Upgrading existing 
servers will be possible from BASE 2.17 only. This alfa release can't be 
used to upgrade if PostgreSQL is used. This will be fixed before the 
final 3.0 release.

The 3.0 release is not binary-compatible with BASE 2. This means that 
existing plug-ins/extensions may not work until updated versions are 
available. There is more information about this in the upgrade instructions.

Note that since this is an alfa-version, there are features and 
functionality that are still missing and/or not working as expected. The 
documentation is not up to date in many places and information about 
many of the new features is missing. We will try to answer questions and 
help with problems on the mailing list.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.0group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/3.0-alfa/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] uploading files

2011-09-09 Thread Nicklas Nordborg
On 2011-09-09 09:48, Line Agledal wrote:
 Tried to upload files to my project in BASE, but I only get an empty
 window when using the upload tab. Is this a bug or am I doing something
 wrong?

It's hard to tell, since you don't include any information about your 
environment. It would be useful with information about your BASE 
version, browser, etc. It is also possible that there is some error 
messages in Tomcat's log files.

/Nicklas

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Re: [base] uploading files

2011-09-09 Thread Nicklas Nordborg
On 2011-09-09 11:24, Line Agledal wrote:
 Thanks. My storage quota is now increased and that fixed it.

Ok, it seems like the error message about the quota doesn't show up for 
some reason. Don't know why that happens. Will try to fix this in the 
next BASE release: http://base.thep.lu.se/ticket/1622

Thank for reporting this.

/Nicklas


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Re: [base] Tab2Mage Importer configuration

2011-08-01 Thread Nicklas Nordborg
It seems like the Tab2MageImporter claims that it supports 
configurations when in reality it doesn't.

The plug-in should be started from the experiment page and all 
parameters should be supplied as part of the job definition.

/Nicklas

On 2011-07-15 04:50, Irina 264 wrote:
 Dear team,

 Could you help,
 when I try to configure Tab2MageImporter I have following error:

 *Unexpected error*

 *java.lang.NullPointerException on page /base2/common/plugin/index.jsp*


   

 *Version*

   

 BASE 2.17.2 (build #5659; schema #90)

 *Web server*

   

 Apache Tomcat/6.0.29

 *Database Server*

   

 MySQL 5.0.77

 *Database Dialect*

   

 org.hibernate.dialect.MySQLInnoDBDialect

 *JDBC Driver*

   

 com.mysql.jdbc.Driver (version 5.1)

 *Java runtime*

   

 OpenJDK Runtime Environment (1.6.0_17-b17), Sun Microsystems Inc.
 http://java.sun.com/

 *Operating system*

   

 Linux amd64 2.6.18-194.17.4.el5

 *Memory*

   

 Total: 810.3 MB
 Free: 627.2 MB
 Max: 1.8 GB

 *Browser*

   

 Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; .NET CLR
 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
 3.5.30729; InfoPath.2; .NET4.0C)

 *Error message*

   

 *Stack trace*

   

 java.lang.NullPointerException

 ...at
 PluginConfigurationRequest.getRequestInformation(PluginConfigurationRequest.java:139)

 ...at org.apache.jsp.common.plugin.index_jsp.getJspPage(index_jsp.java:85)

 ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:294)

 ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

 ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

 ...at
 org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:377)

 ...at
 org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)

 ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)

 ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

 ...at 
 org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

 ...at 
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

 ...at 
 net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)

 ...at 
 org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

 ...at 
 org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

 ...at 
 org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)

 ...at 
 org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)

 ...at 
 org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

 ...at 
 org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

 ...at 
 org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

 ...at 
 org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)

 ...at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)

 ...at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)

 ...at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:774)

 ...at 
 org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703)

 ...at 
 org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:896)

 ...at 
 org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)

 ...at java.lang.Thread.run(Thread.java:636)


 Why this happend?

 Kind regards,
 Irina



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Re: [base] Save to BASE function in the MeV gui

2011-06-27 Thread Nicklas Nordborg
On 2011-06-24 05:50, Irina 264 wrote:
 Dear team,

 The idea to analyse data in MeV is great. I successfully transferred
  data to MeV, analyzed it and used ‘save to BASE’ function to create
 new child bioassays set. However, new created bioassays are the copy
 of the original one. I don’t have possibility to transfer the
 analysis result to the BASE even simple filtering and create a new
 bioassay set. Please tell me what I missed, what the point created
 new child bioassay set if it is duplicate the previous?

 Is it possible to transfer result of analysis as Ch1 column in
 bioassay set, or it is only attached analysis file, which I can use
 with MeV only? Please help me, I need the result of analysis to
 further steps.

The point is that the file saved from MeV is attached to the bioassay
set and that it is possible to re-start MeV using the same file again.

You don't have to create a new child bioassay set in BASE when you do
this, but if you do you can choose if the child should keep the same
data from the parent or not. The idea of actually importing data to the
BASE database has been discussed but was never implemented.

/Nicklas


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[base] BASE 2.17.2 has been released

2011-06-17 Thread Nicklas Nordborg
Hello all,

We are happy to announce the release of BASE 2.17.2. This is a bugfix
release that fixes a few minor bugs.

For a complete list of changes, see:
http://base.thep.lu.se/query?status=closedmilestone=BASE+2.17.2group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

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Re: [base] Tab2Mage exporter plugin

2011-06-13 Thread Nicklas Nordborg
On 2011-06-13 08:51, Irina 264 wrote:
 I upgrade BASE, but have anothe error message:

 Error: [EXPORT FAILED: Experiment - Experiment[id=27; name=Agilent
 IFNalpha time course] do not have a rawbiosay specified].

Add raw bioassays to your experiment.

/Nicklas

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Re: [base] Tab2Mage exporter plugin

2011-06-13 Thread Nicklas Nordborg
On 2011-06-13 09:17, Irina 264 wrote:
 Thanks, thay already there!

Have you checked that the owner of the raw bioassays is the same as the 
owner of the experiment or that everything is shared to the same project 
which must also be the active project?

/Nicklas

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Re: [base] Tab2Mage exporter plugin

2011-06-10 Thread Nicklas Nordborg
This was fixed in BASE 2.16.1 (http://base.thep.lu.se/ticket/1553). I 
suggest that you upgrade.


On the other hand... the Tab2Mage plug-in may require that you specify 
labeled extracts, extracts, samples and biosources or it may not work.

/Nicklas

On 2011-06-10 08:17, Irina 264 wrote:
 Dear team,

 I am working on ‘Tab2Mage exporter’ plugin. I created Agilent experiment
 and Validate it with following message:


   java.lang.NullPointerException on page
   /base2/common/overview/index.jsp

 *Version*

   

 BASE 2.16.0 (build #5472; schema #88)

 *Web server*

   

 Apache Tomcat/6.0.29

 *Database Server*

   

 MySQL 5.0.77

 *Database Dialect*

   

 org.hibernate.dialect.MySQLInnoDBDialect

 *JDBC Driver*

   

 com.mysql.jdbc.Driver (version 5.1)

 *Java runtime*

   

 OpenJDK Runtime Environment (1.6.0_17-b17), Sun Microsystems Inc.
 http://java.sun.com/

 *Operating system*

   

 Linux amd64 2.6.18-194.17.4.el5

 *Memory*

   

 Total: 924.8 MB
 Free: 607.6 MB
 Max: 1.8 GB

 *Browser*

   

 Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0; .NET CLR
 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
 3.5.30729; InfoPath.2; .NET4.0C)

 *Error message*

   

 *Stack trace*

   


 Version   BASE 2.16.0 (build #5472; schema #88)
 Web serverApache Tomcat/6.0.29
 Database Server   MySQL 5.0.77
 Database Dialect  org.hibernate.dialect.MySQLInnoDBDialect
 JDBC Driver   com.mysql.jdbc.Driver (version 5.1)
 Java runtime  OpenJDK Runtime Environment (1.6.0_17-b17), Sun
 Microsystems Inc. http://java.sun.com/
 Operating system  Linux amd64 2.6.18-194.17.4.el5
 MemoryTotal: 924.8 MB
 Free: 607.6 MB
 Max: 1.8 GB
 Browser   Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0;
 .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
 3.5.30729; InfoPath.2; .NET4.0C)
 Error message 
 Stack trace


 Version   BASE 2.16.0 (build #5472; schema #88)
 Web serverApache Tomcat/6.0.29
 Database Server   MySQL 5.0.77
 Database Dialect  org.hibernate.dialect.MySQLInnoDBDialect
 JDBC Driver   com.mysql.jdbc.Driver (version 5.1)
 Java runtime  OpenJDK Runtime Environment (1.6.0_17-b17), Sun
 Microsystems Inc. http://java.sun.com/
 Operating system  Linux amd64 2.6.18-194.17.4.el5
 MemoryTotal: 924.8 MB
 Free: 607.6 MB
 Max: 1.8 GB
 Browser   Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0;
 .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
 3.5.30729; InfoPath.2; .NET4.0C)
 Error message 
 Stack trace


 Version   BASE 2.16.0 (build #5472; schema #88)
 Web serverApache Tomcat/6.0.29
 Database Server   MySQL 5.0.77
 Database Dialect  org.hibernate.dialect.MySQLInnoDBDialect
 JDBC Driver   com.mysql.jdbc.Driver (version 5.1)
 Java runtime  OpenJDK Runtime Environment (1.6.0_17-b17), Sun
 Microsystems Inc. http://java.sun.com/
 Operating system  Linux amd64 2.6.18-194.17.4.el5
 MemoryTotal: 924.8 MB
 Free: 607.6 MB
 Max: 1.8 GB
 Browser   Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0;
 .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
 3.5.30729; InfoPath.2; .NET4.0C)
 Error message 
 Stack trace   


 java.lang.NullPointerException
 ...at 
 net.sf.basedb.util.overview.validator.LabeledExtractValidator.postValidateFolder(LabeledExtractValidator.java:122)
 ...at 
 net.sf.basedb.util.overview.node.NodeFactory.postValidateFolder(NodeFactory.java:224)
 ...at 
 net.sf.basedb.util.overview.loader.BasicItemNodeLoader.postValidateFolder(BasicItemNodeLoader.java:134)
 ...at 
 net.sf.basedb.util.overview.loader.LabeledExtractLoader.createReverseNode(LabeledExtractLoader.java:230)
 ...at 
 net.sf.basedb.util.overview.loader.LabeledExtractLoader.createReverseNode(LabeledExtractLoader.java:104)
 ...at 
 net.sf.basedb.util.overview.loader.AutoChildNodeLoader.createReverseNode(AutoChildNodeLoader.java:95)
 ...at 
 net.sf.basedb.util.overview.loader.HybridizationLoader.loadReverseChildNodes(HybridizationLoader.java:187)
 ...at 
 net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfItemNode(AbstractNodeLoader.java:126)

 ...at 
 net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:112)
 ...at 
 net.sf.basedb.util.overview.loader.AutoChildNodeLoader.loadChildNodes(AutoChildNodeLoader.java:121)
 ...at 
 net.sf.basedb.util.overview.loader.AutoChildNodeLoader.createReverseNode(AutoChildNodeLoader.java:96)
 ...at 
 net.sf.basedb.util.overview.loader.ScanLoader.loadReverseChildNodes(ScanLoader.java:171)
 ...at 
 net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfItemNode(AbstractNodeLoader.java:126)
 ...at 
 net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:112)
 ...at 
 

Re: [base] Tab2MageExporter

2011-05-25 Thread Nicklas Nordborg
On 2011-05-26 07:24, Irina 264 wrote:
 Dear team,

 I install Tab2MageExporter plugin into /base/plugins directory and
 addition copy Tab2MageExporter.jar and ebi-plugins-utils.jar into
 /base/www/WEB-INF/lib directory

Never install the same jar file in two locations. It can result in 
random failures.


 I have an error message, when I export Experiment with Tab2Mage exporter:

 *View job -- Run plugin: Tab2Mage exporter*

 *Status*

   

 Error:

 *Stack trace*

 java.lang.NullPointerException
 at uk.ac.ebi.nugo.plugins.Tab2MageExporter.run(Tab2MageExporter.java:354)
 at
 net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
 at
 net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
 at java.lang.Thread.run(Thread.java:636)

 Could you, please, tell me what is wrong or what I missed?


I recommend that you use the Experiment overview first to ensure that 
there are no error messges and warnings. Select your experiment from the 
list and then go to the Overview tab and click on the Validate 
button. The Tab2Mage exporter assumes that your experiment includes a 
lot of information all the way up to BioSource items.

The exception in your case seems to come from not having specified a 
scan for the raw bioassay.

/Nicklas


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Re: [base] Error: GC overhead limit exceeded

2011-05-23 Thread Nicklas Nordborg
It's difficult to say something about out of memory errors. 2GB should 
be more than enough. Have you verified in the Help - About - 
Configuration dialog that you really have 2GB?

/Nicklas

On 2011-05-23 04:03, Irina 264 wrote:
 Dear Team,

 I run Illumina plugin and had error: Java heap space. I have increased
 CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem:

 Error: GC overhead limit exceeded

 View job -- Run plugin: Illumina raw data importer

 java.lang.OutOfMemoryError: GC overhead limit exceeded
 at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182)
 at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198)
 at
 org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898)
 at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327)
 at
 org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254)
 at
 org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123)
 at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66)
 at net.sf.basedb.core.RawDataBatcher.init(RawDataBatcher.java:263)
 at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104)
 at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119)
 at
 net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520)
 at
 net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691)
 at
 net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468)
 at
 net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
 at
 net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
 at java.lang.Thread.run(Thread.java:636)

 Did I gave too much memory?

 Regards,
 Irina



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