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From: Nicklas N. <nic...@me...> - 2014-12-04 09:30:45
|
Hello all, We have released BASE 3.3.4 today. It fixes a single minor bug related to classloading of extensions. We have also released BASE 3.4-beta-1. 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+3.3.3&group=type http://base.thep.lu.se/query?milestone=BASE+3.4&group=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 |
From: Nicklas N. <nic...@me...> - 2014-11-17 07:24:35
|
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+3.3.3&group=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 |
From: Nicklas N. <nic...@me...> - 2014-10-22 17:09:16
|
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+3.3.2&group=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 |
From: Nicklas N. <nic...@me...> - 2014-09-26 11:33:48
|
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+3.3.1&group=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 |
From: Nicklas N. <nic...@me...> - 2014-09-09 05:57:59
|
On 2014-09-05 12:30, Bob MacCallum wrote: > Hello BASE devs and users, > > I didn't post this to the users list because I'm 99% sure there isn't a > GUI way to add/remove inherited annotations (in our case inheriting > annots from BioSources to Physical Bioassays). But please correct me if > I'm wrong, Nicklas. There is no GUI for doing batch modifications, you'll have to do it for one item at a time. > We're doing a bit of a spring clean and would like to re-inherit annots > for a few hundred hybs - as a one-off event but we don't really want to > get RSI through the GUI ;-) > > Does anyone have/know of some code that NickH and I could modify for our > purpose (just to save some time). The only place I can think of is the feature that let's you inherit annotations to all raw bioassays in an experiment. Basically it calls AnnotationSet.autoInherit() (http://base.thep.lu.se/browser/tags/3.3/src/core/net/sf/basedb/core/AnnotationSet.java#L869) for each raw bioassay in the experiment and passing in the set of annotation types selected as "experimental factors". It doesn't remove or replace existing inherited annotations. /Nicklas |
From: Bob M. <r.m...@im...> - 2014-09-05 10:30:42
|
Hello BASE devs and users, I didn't post this to the users list because I'm 99% sure there isn't a GUI way to add/remove inherited annotations (in our case inheriting annots from BioSources to Physical Bioassays). But please correct me if I'm wrong, Nicklas. We're doing a bit of a spring clean and would like to re-inherit annots for a few hundred hybs - as a one-off event but we don't really want to get RSI through the GUI ;-) Does anyone have/know of some code that NickH and I could modify for our purpose (just to save some time). many thanks, Bob |
From: Nicklas N. <nic...@me...> - 2014-08-18 11:54:42
|
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+3.3&group=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 |
From: Nicklas N. <nic...@me...> - 2014-06-26 08:39:53
|
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 <nic...@me...> Reply-To: BASE dev <bas...@li...> To: BASE ML <bas...@li...>, BASE dev <bas...@li...>, <bas...@li...> 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+3.3&group=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 ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ basedb-devel mailing list bas...@li... https://lists.sourceforge.net/lists/listinfo/basedb-devel |
From: Nicklas N. <nic...@me...> - 2014-06-04 07:53:29
|
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+3.3&group=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 |
From: Nicklas N. <nic...@me...> - 2013-09-09 08:02:12
|
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+3.2.3&group=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 |
From: Nicklas N. <nic...@me...> - 2013-04-10 09:42:46
|
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+3.2.2&group=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 |
From: Nicklas N. <ni...@th...> - 2012-12-13 10:08:37
|
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+3.2.1&group=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 |
From: Nicklas N. <ni...@th...> - 2012-09-13 09:11:04
|
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+3.2&group=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 |
From: Nicklas N. <ni...@th...> - 2012-07-31 09:17:38
|
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+3.1.2&group=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 |
From: Nicklas N. <ni...@th...> - 2012-03-29 09:43:59
|
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+3.1.1&group=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 |
From: Nicklas N. <ni...@th...> - 2012-03-19 09:30:27
|
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+3.1&group=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 |
From: Nicklas N. <ni...@th...> - 2012-03-05 08:56:47
|
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+3.0.4&group=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 |
From: Nicklas N. <ni...@th...> - 2012-02-22 11:13:22
|
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+3.0.3&group=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 |
From: Nicklas N. <ni...@th...> - 2012-01-25 13:25:56
|
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+3.0.2&group=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 |
From: Pawel S. <Paw...@bc...> - 2011-11-22 14:15:40
|
I think 3 will be the best. That way I could submit changes easily, and everyone could get access to versioned code Pawel On 22/11/11 14:44, Nicklas Nordborg wrote: > On 2011-11-22 13:50, Pawel Sztromwasser wrote: >> Hi Nicklas, >> >> I guess the MageTab export plugin is ready for submission. I followed >> instructions for plugin developers >> (http://baseplugins.thep.lu.se/wiki/PluginSubmitReq), so all the >> documentation bits should be in place. How could I send you the bundle? >> Would you provide a repository dir to park the source? > There are basically three options: > > 1. Submit the packages binary and source files to us (me) off the > mailing list together with the rest of the information and we will > create a simple information page (see for example: > http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie) for the plug-in. > > 2. We can give you a login and password for our Trac environment and you > can do everything above yourself. > > 3. All in 2 plus that we also setup a subversion repository for the > source code in case you are interested in that. > > >> The plugin works with BASE2, but we'll start looking at BASE3 soon, and >> as part of preparations for migration I will port the plugin to BASE3. > It's great to hear! > > /Nicklas > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > basedb-devel mailing list > bas...@li... > https://lists.sourceforge.net/lists/listinfo/basedb-devel |
From: Nicklas N. <ni...@th...> - 2011-11-22 13:45:02
|
On 2011-11-22 13:50, Pawel Sztromwasser wrote: > Hi Nicklas, > > I guess the MageTab export plugin is ready for submission. I followed > instructions for plugin developers > (http://baseplugins.thep.lu.se/wiki/PluginSubmitReq), so all the > documentation bits should be in place. How could I send you the bundle? > Would you provide a repository dir to park the source? There are basically three options: 1. Submit the packages binary and source files to us (me) off the mailing list together with the rest of the information and we will create a simple information page (see for example: http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie) for the plug-in. 2. We can give you a login and password for our Trac environment and you can do everything above yourself. 3. All in 2 plus that we also setup a subversion repository for the source code in case you are interested in that. > The plugin works with BASE2, but we'll start looking at BASE3 soon, and > as part of preparations for migration I will port the plugin to BASE3. It's great to hear! /Nicklas |
From: Pawel S. <Paw...@bc...> - 2011-11-22 12:50:50
|
Hi Nicklas, I guess the MageTab export plugin is ready for submission. I followed instructions for plugin developers (http://baseplugins.thep.lu.se/wiki/PluginSubmitReq), so all the documentation bits should be in place. How could I send you the bundle? Would you provide a repository dir to park the source? The plugin works with BASE2, but we'll start looking at BASE3 soon, and as part of preparations for migration I will port the plugin to BASE3. Pawel |
From: Nicklas N. <ni...@th...> - 2011-11-10 08:09:12
|
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 at: http://base.thep.lu.se/ticket/1648 NOTE! Unlike other patch releases, this update requires that the 'updatedb.sh' script is executed. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.1&group=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 |
From: Nicklas N. <ni...@th...> - 2011-11-02 10:08:46
|
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+3.0&group=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 |
From: Nicklas N. <ni...@th...> - 2011-10-12 13:45:56
|
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+3.0&group=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 |