Re: [basedb-devel] How to extend and override BioAssaySetExporterand Base1PluginExecuter?

2007-08-29 Thread Nicklas Nordborg
Adam Ameur wrote: Hi, I would like to extend some methods in the Base1PluginExecuter for another purpose. I think we need to be careful about this. The Base1PluginExecuter and BioAssaySetExporter was designed and implemented to solve ONE specific problem: Being able to run plug-ins

Re: [basedb-devel] How to extend and overrideBioAssaySetExporterand Base1PluginExecuter?

2007-09-03 Thread Nicklas Nordborg
Gregory Vincic wrote: Hi, consider the possibility where future plugins would like to use code from both of the suggested Abstract classes - AbstractPluginExecuter - AbstractBioAssaySetExporter as you can only extend on of the abstract classes the problem remains. This is not a

Re: [basedb-devel] Bug in how Base1PluginExecuter handles the stdin.txt file.

2007-09-05 Thread Nicklas Nordborg
vegard nygaard wrote: When working with my BASE1 plug-in in BASE2 the Transformation page was suddenly broken. I think this happened when upgrading to 2.4 but I am not sure. After some investigation I found the reason to be that the stdin.txt file was missing in the database. It was not in

Re: [basedb-devel] How to extend and overrideBioAssaySetExporterandBase1PluginExecuter?

2007-09-05 Thread Nicklas Nordborg
vegard nygaard wrote: Hi. I have now modified my BASE2.4 code to the Abstract version, laid out earlier by Nicklas. I got it to work and it will do very well for my needs, that is if I understood what the plan really was. It would be nice if Lund put it into the next version. But verify that

[basedb-devel] Comments wanted about new feature in BASE 2.5: Store data in files instead of in the database

2007-09-21 Thread Nicklas Nordborg
Hello all, We are currently working on the issue of keeping data (ie. raw data, array design data and possible analyzed data) in files instead of importing it into the database. It is alread possible to do that for Affymetrix experiments, but the solution can't be used to give the same

Re: [basedb-devel] Singel-item view stops working after adding annotations

2007-09-24 Thread Nicklas Nordborg
Harald Stachelscheid wrote: Am Montag, 24. September 2007 schrieb Nicklas Nordborg: Harald Stachelscheid wrote: Hallo, after I add an annotation to an any type of item I get a blank window in the browser when I try to display the Single-item view. In contrast editing the item by ctrl

Re: [basedb-devel] Getting normalized data out Base

2007-09-27 Thread Nicklas Nordborg
Peter Mertens wrote: Dear list, again i have another question for you. I have developed a normalization plugin for Base. But now i want this normalized data back out of base to use it in another application. I wanted to do this using the webservices, since this is, according to me, the

Re: [basedb-devel] How to delete a Job that is in Executing mode.

2007-09-27 Thread Nicklas Nordborg
vegard nygaard wrote: I have some jobs I want to delete, but I am not allowed to. I think the reason is that they are still in Executing mode, according to the job list. In reality they are not executing, this is just old trial and error runs of plug-ins that apparently failed in unexpected

Re: [basedb-devel] hyb to l.extract (and onwards) with API

2007-10-04 Thread Nicklas Nordborg
Hmmm... I was a bit puzzled at first... The query seemed to be a valid query. However, I found that the problem is that the creationEvent.sources is a Map collection where the LabeledExtract is the key and the used quantity is the value part. Unfortunately it seems like the expression

Re: [basedb-devel] File URL

2007-10-08 Thread Nicklas Nordborg
Peter Mertens wrote: I searched in the base servlet code and the mev code, but i can't find how they manage the download. Could you provide more info? http://base.thep.lu.se/browser/trunk/src/clients/web/net/sf/basedb/clients/web/servlet/Download.java Line 89-123: Parse the request URL to

Re: [basedb-devel] object attributes missing when API used from tomcat servlet

2007-10-26 Thread Nicklas Nordborg
Bob MacCallum wrote: Only in ../../apache-tomcat-6.0.14/webapps/GEWebapp/WEB-INF/lib: biojava-ensembl.jar biojava.jar bytecode.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar gesol.jar GEWebapp.jar jstl.jar mysql-connector-java-3.0.10-stable-bin.jar standard.jar

Re: [basedb-devel] JobAgents on multi-processor machine

2007-10-31 Thread Nicklas Nordborg
Paweł Sztromwasser wrote: All job agents were configured to run all installed plugins and Everyone group has access to them. In fact each of them is able to run a job, but only if no other job is running. I saw couple of times (on JobAgents tab in web UI), as 4 of jobs were assigned to (let's

Re: [basedb-devel] JobAgents on multi-processor machine

2007-11-01 Thread Nicklas Nordborg
Nicklas Nordborg wrote: I am taking this back to the mailing list in the hope that there is some Postgres expert that can shed some light on this. I found this http://www.thescripts.com/forum/thread174537.html It is about a rather old Postgres version (7.4). I am not sure if the same

Re: [basedb-devel] Index dropping fails with Postgres 7.3.19

2007-11-05 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: I investigated a bit and found out that this index in fact exists. I managed to drop it manually using psql with command: DROP INDEX dynamic.D21886Filtercolumn Command without schema name prefix (DROP INDEX D21886Filtercolumn) doesn't work. I checked the index

[basedb-devel] BASE 2.5 beta has been released

2007-11-07 Thread Nicklas Nordborg
We are happy to announce the release of BASE 2.5 beta. Since we normally don't release beta versions there are a few things that you need to be aware of. * The beta should be used for testing only. Don't install it on production servers. * Make a backup of the BASE database before

Re: [basedb-devel] more trials with getting a web service client to work (Re: strange AxisFault exception when using the example in the docs (Re: Writing an external importer/exporter))

2008-01-11 Thread Nicklas Nordborg
Carl Mäsak wrote: Since I last had my problems getting a web service client to work in mid-December, I've slowly come to the realisation that (1) I should be starting from the web service client examples provided on the home page, and (2) I should really use Java 1.6 and not Java 1.5, as I am

Re: [basedb-devel] Data Files in a RawBioAssay

2008-01-30 Thread Nicklas Nordborg
Carl Mäsak wrote: I've now come far enough with my BASE2 web services client in Bioclipse that I dare show it to the eventual end user. Due to this, I have a couple of more specific questions: * How do I get the name of a data file contained in a RawBioAssay? You can't with the current web

Re: [basedb-devel] Base and baseplugins subversion repositories are moving

2008-02-29 Thread Nicklas Nordborg
to readme and installation information like this [source:/plugins/base2/net.sf.basedb.illumina/trunk/README README] We will not automatically fix links pointing to the old locations. /Nicklas Nicklas Nordborg wrote: We are planning to move the subversion repositories for the base and baseplugins

Re: [basedb-devel] Migration transfers deleted items

2008-03-14 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Hi, While testing migration I found out that items deleted in BASE1 are migrated to BASE2. As I understand from documentation, BASE1 doesn't delete items from the database unless purgeDatabase.php script is executed. They are just flagged as deleted by setting

Re: [basedb-devel] Migration transfers deleted items

2008-03-17 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: We will be still testing migration for some time, because we haven't moved BASE1 to the new server yet. Some additional code was needed to move our local adaptations. They are supposed to be a part of 1.2.18 BASE1 release (if happens), so if anyone ever needs to

[basedb-devel] Base 2.6.1 is released

2008-03-25 Thread Nicklas Nordborg
Hello all, We have now released BASE 2.6.1. The release is a bugfix release, including some critical fixes for the BioAssaySetExporter and a potential out of memory problem. More information about the changes: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.6.1 Download from:

Re: [basedb-devel] extract Annotations from BioAssay: error connection closed

2008-03-31 Thread Nicklas Nordborg
Alessandro De Stasio wrote: Hi, I'm writing a Fold Change Plugin. I need to extract all the Annotations from a list of BioAssay. So When I try: ... DbControl dc = sc.newDbControl(); //From the input BioAssaySet source = getSourceBioAssaySet(dc);

Re: [basedb-devel] Integrating BASE to analysis packages

2008-04-02 Thread Nicklas Nordborg
. Currently, there are two extension points, one in the menu and one where the MeV Launcher is in the tree of bioassaysets in the analysis. Suggestions for other extension points can be posted to http://base.thep.lu.se/ticket/933 /Nicklas Nicklas Nordborg wrote: We agree with you, something more

Re: [basedb-devel] Problem with multiple parameter values in PluginConfigurationImporter

2008-04-02 Thread Nicklas Nordborg
I think this is a bug in the importer. I have created at ticket for this and will fix it in the 2.6.2 release. Can you upload the exported file that fails so we have something to test with? Use base/base as login/password. The ticket can be found here: http://base.thep.lu.se/ticket/970

Re: [basedb-devel] setting annotation values programmatically

2008-04-11 Thread Nicklas Nordborg
Micha Bayer wrote: Hi all, I am in the final throes of adding the custom interface to the tab2mage importer plugin but I have one more thing to do before it all works as specified, and that is to set values for the experimental factors on each of the raw bioassays added to the experiment so

[basedb-devel] BASE 2.6.3 has been released

2008-05-09 Thread Nicklas Nordborg
Hello all, We have now released BASE 2.6.3. The release is a bug fix release for some minor bugs only. We expect this to be the last release of the 2.6.x branch. 2.7.0 is scheduled for May 22, but may be released earlier if no more problems show up during testing. More information about the

Re: [basedb-devel] intermittent hibernate errors when using BASE API

2008-08-05 Thread Nicklas Nordborg
for the hint. Will post back when I have a solution. cheers, Bob. Nicklas Nordborg writes: Bob MacCallum wrote: Quick follow up to: http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00316.html The problem seems to be triggered by concurrent access to our BASE

Re: [basedb-devel] Webservices transport error: 411 Error: Length Required

2008-08-20 Thread Nicklas Nordborg
Pawel Nicklas Nordborg wrote: Thanks for the code. It was something like this that I had in mind. The one thing I don't like is to pass the type as an 'int' parameter in the constructor and having a switch statement that creates the actual object to use. This makes it impossible

[basedb-devel] BASE 2.8.3 has been released

2008-10-15 Thread Nicklas Nordborg
We have now released BASE 2.8.3. The release fixes two permission- related problems that may occur when using shared directories in a project and a few other minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.8.3 As usual, the program can

Re: [basedb-devel] Performance/delete issues on Postgres

2008-10-16 Thread Nicklas Nordborg
Oh, I didn't know this. We are mainly working with MySQL which implicitly creates an index for every foreign key. I agree that indexes are certainly needed on the big tables. I guess we could make the 'updateindexes.sh' script check that each foreign key definition has an associated index.

[basedb-devel] BASE 2.8.3 has been released

2008-10-27 Thread Nicklas Nordborg
We have now released BASE 2.8.4, which is a bug fix release for some minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.8.4 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade

[basedb-devel] BASE 2.9 has been released

2008-11-26 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.9. This is a major release that adds several new features and bugfixes. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9 IMPORTANT On important change is that BASE now requires

[basedb-devel] BASE 2.9.1 has been released

2008-12-18 Thread Nicklas Nordborg
We have now released BASE 2.9.1. This is a bug fix release that among other things fixes several filtering-related bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.1 As usual, the program can be downloaded from:

[basedb-devel] BASE 2.9.2 has been released

2009-01-08 Thread Nicklas Nordborg
We have now released BASE 2.9.2. This is a bug fix release that fixes some critical bugs in the Base1 plug-in executor only. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.2 As usual, the program can be downloaded from:

[basedb-devel] BASE 2.9.3 has been released

2009-02-19 Thread Nicklas Nordborg
We have now released BASE 2.9.3. This is a bug fix release that fixes some minor bugs. We expect this to be the last release in the 2.9.x branch. We hope to release BASE 2.10 next week. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.3 As usual,

[basedb-devel] BASE 2.10 has been released

2009-02-24 Thread Nicklas Nordborg
ello all, We are happy to announce the release of BASE 2.10. This is a major release that adds several new features, for example a new Biomaterial LIMS system. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.10 Installation/upgrade instructions:

Re: [basedb-devel] Batch scan importer

2009-03-12 Thread Nicklas Nordborg
Thanks for the code. I am not sure that I like that it creates a new image every time. I think it should at least check if there is already an image with the specified file. Is there a need for setting the other image properties (preview, format, description)? If so, it might be better to have

Re: [basedb-devel] Batch scan importer

2009-03-12 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Mainly because image has no life on its own and also because there is actually no image list where one could run batch import. OK, there is a list of images for every scan, but image imports for each and every scan would be laborious. Ahh... yes, I didn't think of

[basedb-devel] BASE 2.11 has been released

2009-03-30 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.11. This is a major release that has mainly targeted performance issues. There are several improvements in the analysis section and in plug-ins but also, for example, in the directory tree, which has been changed to only load

Re: [basedb-devel] External id for protocol

2009-05-19 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Hi Nicklas, That was much quicker then I expected. Patch is attached here: http://base.thep.lu.se/ticket/1310 I just hope that I haven't missed too much lines while copy-pasting your code;) The code is looking good. I have not yet tested it but will do that as

Re: [basedb-devel] External id for protocol

2009-05-19 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Nicklas Nordborg wrote: Pawel Sztromwasser wrote: Hi Nicklas, That was much quicker then I expected. Patch is attached here: http://base.thep.lu.se/ticket/1310 I just hope that I haven't missed too much lines while copy-pasting your code;) The code is looking

[basedb-devel] BASE 2.11.1 and BASE 2.12 released

2009-05-27 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.11.1 and of BASE 2.12. The first release is fixing some minor bugs in the 2.11 branch. BASE 2.12 includes the same (and more) bug fixes and a lot of new functionality as well. For a complete list of changes, see:

Re: [basedb-devel] Query tracing

2009-06-08 Thread Nicklas Nordborg
Olivier Lefevre wrote: I am developing a service. How can I enable query tracing so that Query.list() appends the SQL or HQL form of the query to one of the Tomcat log files? My 'or' queries (Restrictions.or) seem to work ok but not my 'and' queries and I'd like to see what's going on. This

Re: [basedb-devel] Query tracing

2009-06-08 Thread Nicklas Nordborg
Olivier Lefevre wrote: Thanks. By the way, why were WHERE SQL clauses mapped to the unintuitive Restriction rather than Where, like ORDER was mapped to Order? Restrictions can appear in other places also. For example in queries with GROUP BY expression HAVING restriction /Nicklas

Re: [basedb-devel] Minor API questions

2009-06-09 Thread Nicklas Nordborg
Olivier Lefevre wrote: Why aren't all the methods of ServiceUtil static since it has no state and why does that class sport a method with the signature ItemQueryT getConfiguredItemQuery(ItemQueryT query, QueryOptions qOpt) instead of void configuredItemQuery(ItemQueryT query, QueryOptions

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
Olivier Lefevre wrote: My web service client (i.e., a child of AbstractRPCClient) references a custom class in a completely different package, which is is in its own jar under webapps/base2/WEB-INF/lib That class in turn references net.sf.basedb.ws.server.ServicesUtil Upon trying to run the

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
The ServicesUtil and other classes in the net.sf.basedb.ws.server package are not found in the WEB-INF/lib/ directory and thus can't be referenced from classes that are there. Axis has it's own class loader implementation and expects to find classes in the WEB-INF/services/ directory in the form

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
Olivier Lefevre wrote: So it's a class loader issue. Thanks for the explanation. I'll find some arrangement that works; worst case is I just shove everything into net.sf.basedb.ws.server: it's my own code, so I can repackage it. While we are talking about design, I have another quick

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
Olivier Lefevre wrote: Re. the earlier problem, here is what I found: 1) custom classes in their own package and in their own jar under WEB-INF/lib: ClassNotFoundException 2) custom classes in their own package and in their own jar or aar under WEB-INF/services:

Re: [basedb-devel] Question about (To)Transferables

2009-06-18 Thread Nicklas Nordborg
Olivier Lefevre wrote: Why don't *all* the BasicItem classes for which an info class exists implement ToTransferable? E.g., Annotation (doesn't) vs. Experiment (does). Just trying to understand the API. With annotations there is no one-to-one relationship between Annotation and AnnotationInfo.

[basedb-devel] BASE 2.13 has been released

2009-08-31 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.13. The release fixes several bugs and adds some new features as well. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.13 Installation/upgrade instructions:

[basedb-devel] BASE 2.14 has been released

2009-10-22 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.14. This is a major release that among other things includes: * Performance enhancements related to annotation/experimental factor handling. * New plot functionality and more in experiment explorer. For a complete list of changes,

Re: [basedb-devel] ServicesUtil problem

2009-12-10 Thread Nicklas Nordborg
Woodbridge, Mark R wrote: Hi, I might be misunderstanding the documentation but it appears that the Boolean flags that can be passed to the net.sf.basedb.info.QueryOptions constructor are ignored by net.sf.basedb.ws.server.ServicesUtil, as demonstrated by the failure of the

Re: [basedb-devel] Prompting for credentials

2009-12-14 Thread Nicklas Nordborg
Olivier Lefevre wrote: Is there a way to make BASE2 automatically prompt for credentials when a user who is not yet logged in clicks on a link pointing to a restricted-access resource? For instance the generic URL for an Experiment is

Re: [basedb-devel] Prompting for credentials

2009-12-15 Thread Nicklas Nordborg
Olivier Lefevre wrote: Hi Nicklas, If you supply a URL like the one above BASE is going to ask you for a login and password. I assume you mean a screen like the attached. If so that is indeed what I get in my own local development instance but the production instance (not managed by

Re: [basedb-devel] Prompting for credentials

2009-12-15 Thread Nicklas Nordborg
Olivier Lefevre wrote: Out of curiosity, this error message implies that session IDs, once allocated, are tied to the remote ID the initial request came from. Is it a security feature? Yes, but a very simple one. The idea is to protect the server from someone guessing an ID that is in use.

Re: [basedb-devel] Setting active project via API

2010-01-06 Thread Nicklas Nordborg
Woodbridge, Mark R wrote: Hi, I’m linking to experiments in BASE from another web application. This works fine, including automatically logging in, as long as the experiment belongs to the user’s active project. I’d like to ensure that the correct project is activated before the

Re: [basedb-devel] Tab2Mage exporter plugin

2010-02-05 Thread Nicklas Nordborg
On 2010-02-05 10:07, Gildas Le Corguillé wrote: For the last point, I had to use the method RawBioAssay.setFileSet(). Which is implement in a newer BASE2Core than Tab2Mage_exporter previously used. But I don't know from which version of Base, this method appear ? Then if we propose my

[basedb-devel] BASE 2.15 has been released

2010-04-20 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.15. This is a major release which among other things include a new plug-in executor for running external analysis programs. The executor is highly configurable and extendable and it is intended that this should replace the old and

[basedb-devel] BASE 2.16 has been released

2010-11-03 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.16. This is a major release which lots of new functionality and enhancements as well as some bug fixes For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.16group=type Installation/upgrade

[basedb-devel] BASE 2.16.1 has been released

2010-11-21 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.16. This is a bugfix release that fixes mostly minor bugs but also a critical problem that made it impossible to view reporter and raw data information in some places. For a complete list of changes, see:

Re: [basedb-devel] External authentication

2011-02-01 Thread Nicklas Nordborg
On 2011-02-01 13:24, Pawel Sztromwasser wrote: Sorry, just noticed that you mentioned the ...basedb.util.JarClassLoader, not a regular Java class loader as I initially thought. Check the code for DataFileType.getValidator():

[basedb-devel] BASE 2.16.2 has been released

2011-02-18 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.16.2. This is a bugfix release that fixes a few non-critical bugs and is the last 2.16.x release before BASE 2.17 For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.16.2group=type

[basedb-devel] BASE 2.17 has been released

2011-02-23 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.17. This is a major release which include new functionality and enhancements as well as some bug fixes. Worth mentioning is the bioplate events feature which makes it possible to batch edit biomaterial on a bioplate. For a complete list

[basedb-devel] 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:

Re: [basedb-devel] Programmatic login using a token

2011-08-01 Thread Nicklas Nordborg
On 2011-08-01 10:51, Pawel Sztromwasser wrote: Hi Nicklas, Thanks for the suggestions. Maybe I am missing something but wouldn't it be possible to send the username and password to the STS as part of the BASE login? Or, use an empty password string? I should have explained the use case

[basedb-devel] 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

[basedb-devel] 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

[basedb-devel] BASE 3.0.1 has been released

2011-11-10 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.1 today. It fixes a critical issue related to upgrading from BASE 2.17 to BASE 3. We recommend that all servers that has been upgraded are upgraded to BASE 3.0.1 as soon as possible. The issue doesn't affect fresh BASE 3.0 installations. More information

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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

[basedb-devel] 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

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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

[basedb-devel] BASE 3.3-beta-2 has been released

2014-06-26 Thread Nicklas Nordborg
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-devel@lists.sourceforge.net To: BASE ML basedb-us...@lists.sourceforge.net, BASE dev basedb-devel

[basedb-devel] 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

[basedb-devel] 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

[basedb-devel] BASE 3.5 has been released

2015-04-21 Thread Nicklas Nordborg
Hello all, We have released BASE 3.5 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 *

[basedb-devel] 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

[basedb-devel] 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

[basedb-devel] 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

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] BASE 3.12.1 has been released

2018-04-03 Thread Nicklas Nordborg
Hello all, We have released BASE 3.12.1 today. This is a bugfix release that fixes a critical bug in the annotation importer plug-in. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.12.1=type Installation/upgrade instructions:

[basedb-devel] 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:

[basedb-devel] 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

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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:

[basedb-devel] 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

[basedb-devel] 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:

[basedb-devel] BASE 3.19.1 has been released

2021-12-14 Thread Nicklas Nordborg via basedb-devel
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:

[basedb-devel] BASE 3.19.8 has been released

2023-04-21 Thread Nicklas Nordborg via basedb-devel
Hello all, We have released BASE 3.19.8 today. This is a bugfix release that among other things fixes the problems with BASE and Java 18 and higher. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.19.8=type Installation/upgrade instructions:

[basedb-devel] BASE 3.19.9 has been released

2023-06-07 Thread Nicklas Nordborg via basedb-devel
Hello all, We have released BASE 3.19.9 today. This is a bugfix release that mainly fixes a few annotation-related issues. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.19.9=type Installation/upgrade instructions: