[base] BASE 3.19.9 has been released
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: 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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.19.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.19 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.18.2 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.18.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.18 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.17.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.17 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.16.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.16 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.15.2 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.15.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.15 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.14.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.14 and BASE 3.13.1 has been released
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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.13 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.12.3 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.12.2 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.12 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
Re: [base] xdoclet in ant build
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.11.2 has been relased
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.11.1 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
Re: [base] Question about BASE
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.11 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.10.1 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.10 has been released
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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.9.1 has been released
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 -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.9 has been released
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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.8 has been released
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 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.7.2 has been released
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 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.7.1 has been released
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 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://makebettercode.com/inteldaal-eval ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.7 has been released
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 -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311=/4140 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.6.3 has been released
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 -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551=/4140 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.6 has been released
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 -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.5.3 has been released
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 -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.5.2 has been released
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 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.5.1 has been released
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 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.5-beta-1 has been released
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 -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.4.2 has been released
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 -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.4.1 has been released
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 -- Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Files with FTP locations only
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 -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] array design GTF import - not 9 columns
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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] reseting root password
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 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 3.2 installation on Mac OS 10.6 server
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
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 -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=5127iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.2.3 has been released
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 -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.2.2 has been released
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 -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.2.1 has been released
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 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Error on Biomaterials LIMS
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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Schema
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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] DataQuery.order(...) 2.x API question
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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] DataQuery.order(...) 2.x API question
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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Setting up a new root bioassay set
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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Can BASE (v2.12.1) import files directly from the server it's running on?
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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://ad.doubleclick.net/clk;258768047;13503038;j? http://info.appdynamics.com/FreeJavaPerformanceDownload.html ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.2 has been released
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Change BASE's HTML title
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Change BASE's HTML title
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.1.2 has been released
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] MeV: export bioassay set to TDMS file error
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] MeV: export bioassay set to TDMS file error
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.1.1 has been released
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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.1 has been released
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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.0.4 has been released
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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.0.3 has been released
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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.0.2 has been released
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 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Dealing wiht duplicate spots
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 -- 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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Dealing wiht duplicate spots
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 -- 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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Dealing wiht duplicate spots
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 -- 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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Dealing wiht duplicate spots
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 -- 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 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.0 has been released
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 -- RSA#174; Conference 2012 Save $700 by Nov 18 Register now#33; http://p.sf.net/sfu/rsa-sfdev2dev1 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Project defaults in batch-import and experiment validator
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 -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Project defaults in batch-import and experiment validator
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 -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] MO terms (annotations) for experiments
On 2011-10-25 13:34, Bob MacCallum wrote: +1 for annotatable experiments http://base.thep.lu.se/ticket/1644 /Nicklas -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.0-beta has been released
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 -- 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. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Anyone using BASE with PostgreSQL?
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 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2dcopy2 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] Anyone using BASE with PostgreSQL?
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 -- 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. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Anyone using BASE with PostgreSQL?
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 -- 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. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 3.0-alfa has been released
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 -- Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] uploading files
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 -- Why Cloud-Based Security and Archiving Make Sense Osterman Research conducted this study that outlines how and why cloud computing security and archiving is rapidly being adopted across the IT space for its ease of implementation, lower cost, and increased reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] uploading files
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 -- Why Cloud-Based Security and Archiving Make Sense Osterman Research conducted this study that outlines how and why cloud computing security and archiving is rapidly being adopted across the IT space for its ease of implementation, lower cost, and increased reliability. Learn more. http://www.accelacomm.com/jaw/sfnl/114/51425301/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Tab2Mage Importer configuration
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 -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Save to BASE function in the MeV gui
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 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 2.17.2 has been released
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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Tab2Mage exporter plugin
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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Tab2Mage exporter plugin
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 -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Tab2Mage exporter plugin
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
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 -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Error: GC overhead limit exceeded
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 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] reporters on MergeBioAssay plug-in
On 2011-05-20 09:04, Irina 264 wrote: Hi Nicklas, Thanks for the quick reply. I run RMAExpress with Affy data, then I done filtering with equal size of arrays afterwards. Then I run MergeBioAssay (with Base1pluginExecuter) to find average between replicates (grouping assays by control and treatment with method ‘arithmetic mean of intensity) and have this error message: “Error: Raw data for raw data type: Affymetrix is not stored in the database.” When I use Agilent data, i have no problems. Did I explain better? Yes... but I still have no idea why the error about raw data is coming up... As far as I know the Merge BioAssay plug-in doesn't use raw data for the calculations. It would be useful to get a complete stacktrace of the error in order to locate the source of the problem. Do you get the error while you are configuring the job? If so you should be able to display more error information by clicking on the little [+] icon in the configuration wizard. Or, if you get the error while the plug-in is running, there is a Stack trace tab in the job dialog. /Nicklas -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] reporters on MergeBioAssay plug-in
Thanks for the stacktrace. It seems to be a bug in the
Base1PluginExecuter plug-in. It is trying to remap the raw data
associations after the bioassays have been merged. Obviously, this is
not possible if there is no raw data stored in the first place. The
Base1PluginExecuter need to be fixed with a check for this case.
I have created a ticket for this fix to be included with the BASE 2.17.2
release. Unfortunately there is no workaround.
http://base.thep.lu.se/ticket/1610
/Nicklas
On 2011-05-20 10:12, Irina 264 wrote:
from Stack trace tab:
View job -- Run plugin: Base1PluginExecuter
javascript:Main.openTabControlHelp('7a1ebdaa616cc46f',%20'main',%20'null')
Name Run plugin: Base1PluginExecuter
Description
Priority 5 (1 = highest, 10 = lowest)
StatusError: Raw data for raw data type: Affymetrix is not stored in
the database.
Percent complete
unknown
100%
Created 2011-05-20 18:10:30
Scheduled 2011-05-20 18:11:10
Started 2011-05-20 18:11:28
Ended 2011-05-20 18:11:42
Running time 14 seconds
Serververa097.its.monash.edu.au
Job agent /- none -/
User Irina Rusinova
ExperimentE-GEOD-6257
PluginBase1PluginExecuter (version 2.16.0)
Configuration MergeBioAssay
net.sf.basedb.core.BaseException: Raw data for raw data type: Affymetrix
is not stored in the database.
at
net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261)
at
net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510)
at
net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346)
at
net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471)
at
net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774)
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)
Date: Fri, 20 May 2011 09:21:12 +0200
From: nick...@thep.lu.se
To: basedb-users@lists.sourceforge.net
Subject: Re: [base] reporters on MergeBioAssay plug-in
On 2011-05-20 09:04, Irina 264 wrote:
Hi Nicklas,
Thanks for the quick reply.
I run RMAExpress with Affy data, then I done filtering with equal size
of arrays afterwards.
Then I run MergeBioAssay (with Base1pluginExecuter) to find average
between replicates (grouping assays by control and treatment with
method
‘arithmetic mean of intensity) and have this error message: “Error: Raw
data for raw data type: Affymetrix is not stored in the database.”
When I use Agilent data, i have no problems.
Did I explain better?
Yes... but I still have no idea why the error about raw data is coming
up... As far as I know the Merge BioAssay plug-in doesn't use raw data
for the calculations. It would be useful to get a complete stacktrace of
the error in order to locate the source of the problem.
Do you get the error while you are configuring the job? If so you should
be able to display more error information by clicking on the little [+]
icon in the configuration wizard.
Or, if you get the error while the plug-in is running, there is a Stack
trace tab in the job dialog.
/Nicklas
--
What Every C/C++ and Fortran developer Should Know!
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Read this article and learn how Intel has extended the reach of its
next-generation tools to help Windows* and Linux* C/C++ and Fortran
developers boost performance applications - including clusters.
http://p.sf.net/sfu/intel-dev2devmay
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developers boost
Re: [base] reporters on MergeBioAssay plug-in
On 2011-05-20 03:46, Irina 264 wrote: Dear team, I am working with MergeBioAssay plug-in. I created a formula for reporterID using rep(‘id’) as expression, because other reporter parameters (Name or ExternalID) don’t work. However, when I run MergeBioAssay with Affy dataset I have an error message: “Error: Raw data for raw data type: Affymetrix is not stored in the database.” I don't see how this error message can be coming from the Merge BioAssay plug-in. Can you explain better what you are doing when you get that error message. Eg. which menus, buttons, etc. you click on to get there? Could you help me, what is better way to solve it: to add Affy data format to the raw-data-types.xml or you have another idea? Affymetrix raw data should never be added to the database. There are too many data points for this to work satisfactory. You'll have to rely on other plug-ins for getting the data into the database. See for example http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix /Nicklas -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 2.17.1 has been released
Hello all, We are happy to announce the release of BASE 2.17.1. 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+2.17.1group=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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
On 2011-03-11 18:13, Thomas Person wrote: Ok, I guess I'm missing something in the configuration of the plugin, for all the plugins associated with the Base1PluginExecuter. If i simply create the plugin under the Base1PluginExecuter but then not configure it, then I am given the option under the drop down to run it when attempting Run an analysis plugin but it does not function as it hasn't been configured. Oh... I guess we have to look into that. Unconfigured plug-in shouldn't really be in that list. But once i do configure it, with the proper file and path to the run command. the option to run the plugin in the drop down under run an analysis plugin disappears as an option to run. We have checked the installation procedure of the VirtualArray plug-in and it turns out that the configuration file that is used is incorrect. The problem with the 'descr' field has already been fixed but there are two more issues: * The 'geneAverages' setting should be '1', not '0'. * The 'minChannels' setting should be '1', not '2'. Fortunately both settings can be changed in the web gui. Start the configuration wizard for the VirtualArray plug-in. In the first step, make sure to NOT select a file. This will take you to a second step where you can change the value for the two parameters mentioned above. The 'geneAverages' setting is called 'Average on reporters' in the wizard. Hope this works better. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
On 2011-03-10 20:58, Jari Häkkinen wrote: Also, Virtual array works only on 2-channel data. I was never involved in the development of this plug-in so maybe I am missing something obvious I had a quick lock at the code (http://baseplugins.thep.lu.se/browser/plugins/base1/se.lu.onk.VirtualArray/trunk/src/virtualarray/VirtualArray.java) and I can't see anything in it that depends on the number of channels. As far as I can tell it is simply copying the input intensities to the output without change. The only difference is that it assigns negative position numbers. Actually I don't see any point in running the VirtualArray at all. All intensity data afterwards will be exactly the same as it was before. The only change is that position numbers are different, and as a side-effect of that the connection to raw data is lost. But... maybe I am missing something obvious... Anyone knows more about this? In any case, since there is not any dependency on the number of channels in the code, it should be safe to change 'minChannels 2' to 'minChannels 1' in the pluginVirtualArray.base file. Or (easier) directly by reconfiguring the plug-in in the web interface. There should be an option for this setting in the second step (leave the file field empty in the first step). /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
On 2011-03-08 22:28, Thomas Person wrote: Howdy All, I'm attempting to install the Virtual Array 1.1 plugin on my Base 2.15 server. I get two sets of errors. ( I was able to install the Center-2.1 Plugin with no error). Thanks for the report. I can verify that the VirtualArray plug-in can't be installed as is. There seems to be a bug in BASE that is related to the 'descr' field in the 'pluginVirtualArray.base' file. This file has a space instead of a tab character between the 'descr' and the rest of the line. Please change the space to a tab and then re-try the installation. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] BASE 2.16.2 has been released
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 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 -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Illumina Bead Summary importer
On 2011-02-11 23:23, Thomas Person wrote: Howdy all, I'm still having issues with the Illumina Plug in, When running the job the summary window gives: Bead Summary importer Executing: New raw bioassay -parsed 93094 lines in 2 files Preparing database for import... Then eventually crashes with OutOfMemoryErrror: Java heap space. I've tried upping Xmx up to 2gb under CATALINA_OPTS. and setting the Illumina Bead Summary importer plugin max memory to 1gb, but still no luck. Thanks in advance for your help, This seems strange. 2Gb should be more than enough. The memory setting on the plug-in is only used when running on a a job agent but even 1Gb should be enough. Our test data set is about the same size as your data set and when I made a test today the memory usage peeked at 300Mb. Please check the information in Help - About - Configuration to verify your memory settings. /Nicklas -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE: Pinpoint memory and threading errors before they happen. Find and fix more than 250 security defects in the development cycle. Locate bottlenecks in serial and parallel code that limit performance. http://p.sf.net/sfu/intel-dev2devfeb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] update issue from 2.14.0 to 2.16.1
On 2010-11-24 15:10, Olivier Lefevre wrote: I guess we really should change the compilation to use '-target 1.6' Or simply omit it. In general I can think of few scenarios where you'd want to target an older VM than the one you are working with (one reason might be compiler fixes that were not back-ported): that invites the sort of errors the OP ran into, unless the developer is extremely careful not to use any of the newer functionality. I investigated the history of this a bit further and the story is like this: BASE 2.5 only worked with java 1.5 but not with 1.6 due to some issues with webservices. We were developing with 1.5. We started to use java 1.6 for development during BASE 2.6 but still wanted to keep support for java 1.5 since no Mac version of 1.6 existed (we had two developers using Mac). This is when the target 1.5 was added to the build. BASE 2.7 dropped official support for java 1.5 but nobody though of changing the target attribute. I have done this today so it will be fixed in the next BASE release. /Nicklas -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Formula/plugins
On 2010-11-25 04:39, Irina 264 wrote: Dear team, I used plugins and created Formulas for dataset analysis and its work only with each dataset (bioassay) separately; What do you mean with this? What plug-in did you use? What are the formulas? the result is column (Ch1). Is it possible to make analysis (for example quantile normalization of 3 bioassays, or formula to find mean between bioassay1 (Ch1))and bioassay2 (Ch1)). When i used 3 bioassays for normalization i have result again only one column Ch1 but 3 times longer and analysis was done for each bioassay separately. Did I missed something or I have to develop plugin to operate between bioassays? I am not sure I understand what you have done and what you want to do. Can you please explain in more detail? The Lowess and median-ratio normalization that is shipped with BASE only works with 2-channel data so I am not sure which plug-in you have used. /Nicklas -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] update issue from 2.14.0 to 2.16.1
On 2010-11-23 21:22, Olivier Lefevre wrote: That line of code (IntensityFormula.java:91) was changed in 2.16 so it is not so strange. I meant I was surprised that this 1.5 VM didn't immediately reject classes obviously compiled against 1.6. Did you use the -target 1.5 option in compilation? Ahh... yes actually we have that.. I have tried to investigate why and it seems to be related with BASE version around 2.5-2.7 (http://base.thep.lu.se/ticket/899). There was a period when we had to support java 1.5 even though we used java 1.6 for development. Since that is no longer the case I guess we really should change the compilation to use '-target 1.6'. Thanks for pointing it out. /Nicklas -- Increase Visibility of Your 3D Game App Earn a Chance To Win $500! Tap into the largest installed PC base get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
