[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.19.8 has been released
Hello all, We have released BASE 3.19.8 today. This is a bugfix release that among other things fixes the problems with BASE and Java 18 and higher. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.19.8=type Installation/upgrade instructions: 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.12.1 has been released
Hello all, We have released BASE 3.12.1 today. This is a bugfix release that fixes a critical bug in the annotation importer plug-in. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.12.1=type Installation/upgrade instructions: 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 -- ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.5 has been released
Hello all, We have released BASE 3.5 today. This is a new major release that is focusing on new features for filtering and annotations. Among other things: * It is possible to filter with OR logic in tables * Batch inhering annotations * Filtering on inherited annotation in tables * 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/latest/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/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.3 has been released
Hello all, We have released BASE 3.3! It is a new major release that includes several new features and enhancements. It may require some changes to the BASE server and/or and upgrade of the browser used to access BASE: * We now require Java 7 and Tomcat 7 on the server. If you are still using older versions, they should be upgraded before upgrading BASE. * The web interface has been reworked behind the scenes. Some (very old) browser may no longer work. It should be safe with IE 10 or a recent Firefox version. * The security in the web interface has been tightened in order to prevent cross-site scripting attacks. This can affect extensions. See the documentation for more information. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.3group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas -- ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.3-beta-2 has been released
A new beta-version of BASE 3.3 is now available for download. This fixes some minor issues since the last release. I don't expect any major issues to popup, but due to summer vacations a final BASE 3.3 release should not be expected until August or September. /Nicklas Original Message Subject: [basedb-devel] BASE 3.3-beta-1 has been released Date: Wed, 4 Jun 2014 09:52:30 +0200 From: Nicklas Nordborg nicklas.nordb...@med.lu.se Reply-To: BASE dev basedb-devel@lists.sourceforge.net To: BASE ML basedb-us...@lists.sourceforge.net, BASE dev basedb-devel@lists.sourceforge.net, basedb-annou...@lists.sourceforge.net Hello all, We have released BASE 3.3-beta-1 today! It is a new major release that includes several new features and enhancements. * We now require Java 7 and Tomcat 7 on the server. If you are still using older versions, they should be upgraded before upgrading BASE. * The web interface has been reworked behind the scenes. Some (very old) browser may no longer work. It should be safe with IE 10 or a recent Firefox version. * The security in the web interface has been tightened in order to prevent cross-site scripting attacks. This can affect extensions. See the documentation for more information. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.3group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/3.3-beta/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel -- 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.3-beta-1 has been released
Hello all, We have released BASE 3.3-beta-1 today! It is a new major release that includes several new features and enhancements. * We now require Java 7 and Tomcat 7 on the server. If you are still using older versions, they should be upgraded before upgrading BASE. * The web interface has been reworked behind the scenes. Some (very old) browser may no longer work. It should be safe with IE 10 or a recent Firefox version. * The security in the web interface has been tightened in order to prevent cross-site scripting attacks. This can affect extensions. See the documentation for more information. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.3group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/3.3-beta/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 3.0.1 has been released
Hello all, We have released BASE 3.0.1 today. It fixes a critical issue related to upgrading from BASE 2.17 to BASE 3. We recommend that all servers that has been upgraded are upgraded to BASE 3.0.1 as soon as possible. The issue doesn't affect fresh BASE 3.0 installations. More information at: http://base.thep.lu.se/ticket/1648 NOTE! Unlike other patch releases, this update requires that the 'updatedb.sh' script is executed. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.1group=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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Programmatic login using a token
On 2011-08-01 10:51, Pawel Sztromwasser wrote: Hi Nicklas, Thanks for the suggestions. Maybe I am missing something but wouldn't it be possible to send the username and password to the STS as part of the BASE login? Or, use an empty password string? I should have explained the use case better. It does not relate to the manual login to BASE using the web interface where one types in a username and password. For this we have already implemented and set up an authentication plugin that sends the username and password typed in by a user to the STS service for verification (just like you suggest). Now I am planning to enable programmatic access to BASE (via Web services) from another system that shares identity management (STS) with BASE. The idea is that the user that is logged in to any of these, has obtained a token and is able to access his/her resources in the other system without any further authentication, using only the token (single sign-on). In this federated authentication system one application will be able to automatically integrate resources available to a user in several distinct systems. Since the common authentication mechanism will be based on tokens, I don't expect an application to provide a username/password pair anytime when it needs to access resources hosted in a different system. Currently all the login methods in BASE are username/password oriented, but with the minor change I suggest, it could be easily extended to cover token-like objects as well. At least in programmatic access scenarios, but I can't see a need for any other. Ok, I understand that this is a bit different than the usual login procedure. But I think there is also already another possible way to solve this. It could be done in a similar way that we are doing with the job agents. They use a master user account with a known username+password that is used to login to BASE. The account should have the Act as another user permissions assigned to a role (eg. just as the Job agent role that is pre-installed in BASE). Then the SessionControl.impersonateLogin() can be used to login as any user without having to provide a password. You'll have to find the internal id of the user but that is more or less the same thing that is done in the diff for SessionControl that you posted in the original post. In any case, I am not sure that supplying a TokenAuthenticator object as a parameter to the login method is a good idea, since it would be very easy to to provide an implementation that just accept anything. I was thinking similarly, but how does it differ from supplying a login method in an authenticator plugin? That method could accept anything as well. Access to SessionControl.login(Token, TokenAuthenticator) operation in only from the code deployed together with BASE server (in my case in implementation of Web services deployed within BASE), so an environment that a BASE administrator should have full control over. The same as external authentication plugins. The difference is that the administrator sets up the authenticator to use in the configuration files and it is not possible for the calling code to change this. Ok, some mean code could probably get around this, so it is good to have control over the server environment. Despite this, I think the public BASE api shouldn't provide this kind of flexibility. I would prefer a solution where the administrator can setup exactly how the authentication should happen. /Nicklas -- 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.17 has been released
Hello all, We are happy to announce the release of BASE 2.17. This is a major release which include new functionality and enhancements as well as some bug fixes. Worth mentioning is the bioplate events feature which makes it possible to batch edit biomaterial on a bioplate. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.17group=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 -- Free Software Download: Index, Search Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] 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 ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] External authentication
On 2011-02-01 13:24, Pawel Sztromwasser wrote: Sorry, just noticed that you mentioned the ...basedb.util.JarClassLoader, not a regular Java class loader as I initially thought. Check the code for DataFileType.getValidator(): http://base.thep.lu.se/browser/tags/2.16.1/src/core/net/sf/basedb/core/DataFileType.java#L629 It is more or less something like that that you need. /Nicklas -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.16.1 has been released
Hello all, We are happy to announce the release of BASE 2.16. This is a bugfix release that fixes mostly minor bugs but also a critical problem that made it impossible to view reporter and raw data information in some places. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.16.1group=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 -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.16 has been released
Hello all, We are happy to announce the release of BASE 2.16. This is a major release which lots of new functionality and enhancements as well as some bug fixes For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.16group=type Installation/upgrade 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 -- Achieve Improved Network Security with IP and DNS Reputation. Defend against bad network traffic, including botnets, malware, phishing sites, and compromised hosts - saving your company time, money, and embarrassment. Learn More! http://p.sf.net/sfu/hpdev2dev-nov ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.15 has been released
Hello all, We are happy to announce the release of BASE 2.15. This is a major release which among other things include a new plug-in executor for running external analysis programs. The executor is highly configurable and extendable and it is intended that this should replace the old and inflexible wrapper for executing BASE 1 plug-ins. The new executor uses a new export/import format (BFS) which should be easier to use/parse than the old BASEfile format. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.15group=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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Tab2Mage exporter plugin
On 2010-02-05 10:07, Gildas Le Corguillé wrote: For the last point, I had to use the method RawBioAssay.setFileSet(). Which is implement in a newer BASE2Core than Tab2Mage_exporter previously used. But I don't know from which version of Base, this method appear ? Then if we propose my update, old version of base will show troubles. It appeared in BASE 2.5. We usually try to add a note in the javadoc for the api: http://base.thep.lu.se/chrome/site/latest/api/net/sf/basedb/core/RawBioAssay.html#getFileSet() Our policy for the Required BASE version for plug-ins is to specify the version that was used when testing. Even if it theoretically can be compiled against an older BASE version we really don't know if it works with that version. And since we don't have any resources to test with older BASE versions this usually means that all plug-ins will require the BASE version that was the current at the time the plug-in was released. If you, for example, tested your changes with BASE 2.14 it would mean that the new requirement is BASE 2.14. /Nicklas -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Setting active project via API
Woodbridge, Mark R wrote: Hi, I’m linking to experiments in BASE from another web application. This works fine, including automatically logging in, as long as the experiment belongs to the user’s active project. I’d like to ensure that the correct project is activated before the user clicks on the link. Does anyone know if I can get the relevant project id from an experiment id? There doesn’t seem to be an ExperimentInfo.getProject() method. There is no such method since an experiment can belong to more than one project. The web service API has very limited functionality. The functionality that currently exists was implemented to support some specific use cases (mainly related to downloading data files) for a project that we participated in. Using the regular BASE API you can find the projects by putting the experiment in a collection and then using a multi-permissions object: CollectionExperiment experiments = ... MultiPermissions mp = new MultiPermissions(experiments); ItemQueryProject q = mp.getProjects(); ListProject project = q.list(dc); The code is a bit awkward, but for some reason the obvious approach, Experiment.getProjectKey().getProjects(), is missing. /Nicklas -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Prompting for credentials
Olivier Lefevre wrote: Hi Nicklas, If you supply a URL like the one above BASE is going to ask you for a login and password. I assume you mean a screen like the attached. If so that is indeed what I get in my own local development instance but the production instance (not managed by me) occasionally returns a page with a PermissionDeniedException stack trace instead (screenshot also attached) and at other times the expected login screen, which is a bit confusing. I have never seen the stack trace behavious locally. The login screen is the prompt I am talking about. The stack trace is because trying to use the same session ID that is already used by a different user session. /Nicklas -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Prompting for credentials
Olivier Lefevre wrote: Out of curiosity, this error message implies that session IDs, once allocated, are tied to the remote ID the initial request came from. Is it a security feature? Yes, but a very simple one. The idea is to protect the server from someone guessing an ID that is in use. /Nicklas -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Prompting for credentials
Olivier Lefevre wrote: Is there a way to make BASE2 automatically prompt for credentials when a user who is not yet logged in clicks on a link pointing to a restricted-access resource? For instance the generic URL for an Experiment is http://localhost:8080/base2/views/experiments/index.jsp?ID=uidcmd=ViewItemitem_id=29 where uid is some hash. It seems one can use ID=0 as a magic value once the user is logged in but it fails the first time. What is the best way to handle this problem in the context of BASE2? I am not exactly sure what you are looking for... If you supply a URL like the one above BASE is going to ask you for a login and password. The value for ID (eg. 'uid' in the example) can be anything. There is nothing magic with ID=0, but the ID has to be a unique string per user session, so you can't just put a static link to the page within BASE. /Nicklas -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] ServicesUtil problem
Woodbridge, Mark R wrote: Hi, I might be misunderstanding the documentation but it appears that the Boolean flags that can be passed to the net.sf.basedb.info.QueryOptions constructor are ignored by net.sf.basedb.ws.server.ServicesUtil, as demonstrated by the failure of the following test: Thanks for reporting this. It seems like the query is already populated with some options (eg. Include.MINE is on by default). The ServicesUtil.getConfiguredItemQuery() is adding options that has been set to true, but is not removing options that has been set to false. We'll try to fix it in BASE 2.14.2: http://base.thep.lu.se/ticket/1445 /Nicklas -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.14 has been released
Hello all, We are happy to announce the release of BASE 2.14. This is a major release that among other things includes: * Performance enhancements related to annotation/experimental factor handling. * New plot functionality and more in experiment explorer. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.14group=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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.13 has been released
Hello all, We are happy to announce the release of BASE 2.13. The release fixes several bugs and adds some new features as well. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.13 Installation/upgrade instructions: 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Question about (To)Transferables
Olivier Lefevre wrote: Why don't *all* the BasicItem classes for which an info class exists implement ToTransferable? E.g., Annotation (doesn't) vs. Experiment (does). Just trying to understand the API. With annotations there is no one-to-one relationship between Annotation and AnnotationInfo. A single AnnotationInfo object can collect values from multiple Annotations. This is because annotations can be inherited and an item can have multiple parents with different annotation values. Also, is there a method somewhere connecting FooInfo classes to their Foo and vice-versa, maybe along the lines of Item.getItemClass()? For ToTransferable classes the toTransferable method or the type parameter provide the link (although not quite in the desired way) but for the others I draw a blank. No. /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] ServicesUtil not found
Olivier Lefevre wrote: My web service client (i.e., a child of AbstractRPCClient) references a custom class in a completely different package, which is is in its own jar under webapps/base2/WEB-INF/lib That class in turn references net.sf.basedb.ws.server.ServicesUtil Upon trying to run the service I got: java.lang.NoClassDefFoundError: net/sf/basedb/ws/server/ServicesUtil and I don't have enough experience with Axis or Tomcat to understand what is going on. Any suggestion? That is a server-side class and I don't know what you need to do with it on the client side. This class can't be used on the client-side since it would require a full BASE installation locally. The base2/WEB-INF/lib directory is only available on the server-side as well. So it is not a good idea to put custom client-side JAR files in there. It seems like you need to redesign your client side code if it depends on server side classes. A good starting point is the web services example that you can download from http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examples.webservices It should contain everything you need for developing client side web services. /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] ServicesUtil not found
The ServicesUtil and other classes in the net.sf.basedb.ws.server package
are not found in the WEB-INF/lib/ directory and thus can't be referenced from
classes that are there.
Axis has it's own class loader implementation and expects to find classes
in the WEB-INF/services/ directory in the form of *.aar files. There should
currently be only one file: core.aar. Classes in the .aar files can
reference/use any class that is found in WEB-INF/lib/ but not the other way
around.
I don't know if .aar files are visible to each other, but you can try to
put your custom file in WEB-INF/services/ directory and rename it to
end with .aar.
/Nicklas
lefev...@yahoo.com wrote:
Sorry, why did I write client? It was late, I should have slept
before posting. This happens in the service class. I have my own
utility class, which refers to ServicesUtil, and the service class
loads that utility class. The utility class can be loaded but not
ServicesUtil, which is odd since it *is* loaded in AbstractRPCService.
I have attached a minimal yet full example that can be deployed to
reproduce the problem (I have not attached the modified services.xml
because the mods there are obvious); the service and client classes
are in the appropriate jars (I just rebuild using ant), TestUtil in
its own jar under WEB-INF/lib. The bottom of the stack trace is
Caused by: java.lang.NoClassDefFoundError:
net/sf/basedb/ws/server/ServicesUtil
at com.acme.TestUtil.clinit(TestUtil.java:8)
at net.sf.basedb.ws.server.TestService.getResult(TestService.java:14)
... 25 more
Caused by: java.lang.ClassNotFoundException:
net.sf.basedb.ws.server.ServicesUtil
at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1387)
at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1233)
at java.lang.ClassLoader.loadClassInternal(Unknown Source)
... 27 more
There is nothing special about ServicesUtil, btw: attempting to
instantiate, say, TempFileDataSource, causes the same error. The
chain of references is net.sf.basedb.ws.server - com.acme -
net.sf.basedb.ws.server. Does the detour through another package
trigger some classloader complication?
A good starting point is the web services example that you can
download from [...]
Of course I studied the built-in examples first; I don't think I
could have so much as started otherwise. Still, I want to be able
to use custom classes on the server side. Why does (apparently)
everything have to be in the net.sf.basedb.ws.server package?
Thanks,
-- O.L.
=
package com.acme;
import net.sf.basedb.ws.server.ServicesUtil;
public class TestUtil {
// just to test whether ServicesUtil can be loaded
private static ServicesUtil util = new ServicesUtil();
public static String process(String x) {
return x.toUpperCase();
}
}
package net.sf.basedb.ws.server;
import net.sf.basedb.core.SessionControl;
import net.sf.basedb.ws.server.ServicesUtil;
import com.acme.TestUtil;
public class TestService extends AbstractRPCService {
public TestService() { }
public String getResult(String sid, String q) {
SessionControl sc = getSessionControl(sid);
return TestUtil.process(q);
}
}
package net.sf.basedb.ws.client;
import org.apache.axis2.AxisFault;
import com.acme.TestUtil;
public class TestClient extends AbstractRPCClient {
private final SessionClient session;
public TestClient(SessionClient session) {
super(session.getUrl(), Test, session.getServiceFactory());
this.session = session;
}
public String getResult(String q) throws AxisFault {
String sid = session.getId();
return invokeBlocking(getResult, String.class, sid, q);
}
}
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Re: [basedb-devel] ServicesUtil not found
Olivier Lefevre wrote: So it's a class loader issue. Thanks for the explanation. I'll find some arrangement that works; worst case is I just shove everything into net.sf.basedb.ws.server: it's my own code, so I can repackage it. While we are talking about design, I have another quick question: from the interop point of view, i.e., with non-Java clients in mind, isn't it asking for trouble to use complex data types from net.sf.basedb.info: shouldn't one stick to strings and other basic universal types instead? I don't see how it would be possible to return any structured information as simple strings. As far as I know it was no problem with perl. /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] ServicesUtil not found
Olivier Lefevre wrote: Re. the earlier problem, here is what I found: 1) custom classes in their own package and in their own jar under WEB-INF/lib: ClassNotFoundException 2) custom classes in their own package and in their own jar or aar under WEB-INF/services: ClassNotFoundException; note that in this case you must include a services.xml files (I used an empty one, i.e., just serviceGroup/) in the jar or aar file, otherwise Axis will complain about that as well 3) custom classes in their own package and in core.aar: works! 4) custom classes in net/sf/basedb/ws/server and therefore in core.aar: works but it is a last-resort option So I am reasonably happy with 4): the worst scenario is that you have to unpack and then repack third-party jars. I made some quick investigations as well and it seems like each .aar file has it's own class loader (created by Axis). The parent class loader is the regular Tomcat class loader which means that classes in an .aar file can only use classes that are in the same .aar file or classes in the WEB-INF/lib/ directory. Classes in the WEB-INF/lib/ directory can't use classes from any .aar file because those files are not known by the Tomcat class loader. This is described as a feature since it means that an .aar file can be replaced with a new version and deployed without having to restart the web application. So, since the ServicesUtil class is found in the core.aar file it means that it can only be used by other classes in core.aar. I don't see how it would be possible to return any structured information as simple strings. One could use JSON or even XML. I have heard the name JSON but didn't know that it had to do with web services. Regarding XML, everything is already sent as XML which is unwrapped and converted to Java objects by Axis. I have seen code examples (from the Axis tutorial) were the response is accessed as XML instead so I think that option is already available. Just because it is Java objects on the server side doesn't mean that it has to be the same objects on the client side (but it is convenient). /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Minor API questions
Olivier Lefevre wrote: Why aren't all the methods of ServiceUtil static since it has no state and why does that class sport a method with the signature ItemQueryT getConfiguredItemQuery(ItemQueryT query, QueryOptions qOpt) instead of void configuredItemQuery(ItemQueryT query, QueryOptions qOpt) since it does not return a new query but the original one? Just making sure I am not missing something. There is no special reason for it. /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Query tracing
Olivier Lefevre wrote: I am developing a service. How can I enable query tracing so that Query.list() appends the SQL or HQL form of the query to one of the Tomcat log files? My 'or' queries (Restrictions.or) seem to work ok but not my 'and' queries and I'd like to see what's going on. This can be enabled in the log4j.properties file which you find in the WEB-INF/classes folder. There are a lot of options but the one you are looking for is: log4j.logger.net.sf.basedb.core.query.ql=debug Just uncomment this and the HQL/SQL should be logged. If your query is a HQL query you may want the SQL Hibernate generates as well. This is controlled by log4j.logger.org.hibernate.SQL=debug. /Nicklas -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Query tracing
Olivier Lefevre wrote: Thanks. By the way, why were WHERE SQL clauses mapped to the unintuitive Restriction rather than Where, like ORDER was mapped to Order? Restrictions can appear in other places also. For example in queries with GROUP BY expression HAVING restriction /Nicklas -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.11.1 and BASE 2.12 released
Hello all, We are happy to announce the release of BASE 2.11.1 and of BASE 2.12. The first release is fixing some minor bugs in the 2.11 branch. BASE 2.12 includes the same (and more) bug fixes and a lot of new functionality as well. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.11.1 http://base.thep.lu.se/query?status=closedmilestone=BASE+2.12 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 -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, Big Spaceship. http://p.sf.net/sfu/creativitycat-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] External id for protocol
Pawel Sztromwasser wrote: Hi Nicklas, That was much quicker then I expected. Patch is attached here: http://base.thep.lu.se/ticket/1310 I just hope that I haven't missed too much lines while copy-pasting your code;) The code is looking good. I have not yet tested it but will do that as soon as I have some time left. Thanks a lot for fixing this. Is it ok for us to include it in the 2.12 release? We'll take care of fixing the database schema versions and other stuff related to upgrading. /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] External id for protocol
Pawel Sztromwasser wrote: Nicklas Nordborg wrote: Pawel Sztromwasser wrote: Hi Nicklas, That was much quicker then I expected. Patch is attached here: http://base.thep.lu.se/ticket/1310 I just hope that I haven't missed too much lines while copy-pasting your code;) The code is looking good. I have not yet tested it but will do that as soon as I have some time left. Thanks a lot for fixing this. Is it ok for us to include it in the 2.12 release? We'll take care of fixing the database schema versions and other stuff related to upgrading. Of course it is OK. I'll be happy if it is included. I have now tested it and it worked like a charm. I have committed the changes to the trunk. Thanks for the good work. /Nicklas -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.11 has been released
Hello all, We are happy to announce the release of BASE 2.11. This is a major release that has mainly targeted performance issues. There are several improvements in the analysis section and in plug-ins but also, for example, in the directory tree, which has been changed to only load subdirectories when a user browse to them (lazy loading). For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.11 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 -- ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Batch scan importer
Thanks for the code. I am not sure that I like that it creates a new image every time. I think it should at least check if there is already an image with the specified file. Is there a need for setting the other image properties (preview, format, description)? If so, it might be better to have a specific importer for images. /Nicklas Pawel Sztromwasser wrote: Hello BASE team, We really enjoy the set of batch uploading plugins and were doing a little training for our users in Bergen. Everything seemed great except that they couldn't link freshly created scans with image files. I read in the example spreadsheet that it is not supported and was very surprised since similar 'file attaching' works very nice for raw bioassays. I sat down, did some copy pasting from RawBioAssayImporter and after little edits it worked (source attached). I hope that you can make some use of it. All the best, Pawel -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Batch scan importer
Pawel Sztromwasser wrote: Mainly because image has no life on its own and also because there is actually no image list where one could run batch import. OK, there is a list of images for every scan, but image imports for each and every scan would be laborious. Ahh... yes, I didn't think of that. It doesn't make sense to have a standalone image importer. /Nicklas -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.10 has been released
ello all, We are happy to announce the release of BASE 2.10. This is a major release that adds several new features, for example a new Biomaterial LIMS system. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.10 Installation/upgrade instructions: 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 -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.9.3 has been released
We have now released BASE 2.9.3. This is a bug fix release that fixes some minor bugs. We expect this to be the last release in the 2.9.x branch. We hope to release BASE 2.10 next week. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.3 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html /Nicklas -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.9.2 has been released
We have now released BASE 2.9.2. This is a bug fix release that fixes some critical bugs in the Base1 plug-in executor only. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.2 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html /Nicklas -- Check out the new SourceForge.net Marketplace. It is the best place to buy or sell services for just about anything Open Source. http://p.sf.net/sfu/Xq1LFB ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.9.1 has been released
We have now released BASE 2.9.1. This is a bug fix release that among other things fixes several filtering-related bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.1 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html /Nicklas -- SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.9 has been released
Hello all, We are happy to announce the release of BASE 2.9. This is a major release that adds several new features and bugfixes. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9 IMPORTANT On important change is that BASE now requires an database that uses the UTF-8 character set. If the existing database doesn't have this it must be converted BEFORE upgrading to BASE 2.9. The upgrade instructions contains more information about this. 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.8.3 has been released
We have now released BASE 2.8.4, which is a bug fix release for some minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.8.4 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html /Nicklas - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Performance/delete issues on Postgres
Oh, I didn't know this. We are mainly working with MySQL which implicitly creates an index for every foreign key. I agree that indexes are certainly needed on the big tables. I guess we could make the 'updateindexes.sh' script check that each foreign key definition has an associated index. Right now it can only be used to check that indexes that have been explicitly defined really exists in the database. I'll add this for the 2.9 release. /Nicklas Pawel Sztromwasser wrote: Hello, I found something interesting regarding BASE2 performance on Postgres (we have 8.3 but I suppose it is valid for previous versions as well). Recently I was unable to delete ArrayDesign (Illumina Human 8Ref, no items connected to it, features imported), because database query was endless. I stopped it after 3 days and started similar on development installation (much, much smaller). It took almost 20h to complete. We started digging and found (among other similar) this: http://archives.postgresql.org/pgsql-admin/2006-02/msg00238.php In short, postgres does not create indexes on foreign keys by default. That has huge impact on performance when updating/deleting items from table that is referenced by other big table. In case above Features (that are deleted with ArrayDesign) are referenced by all RawData* tables. I created indexes on feature_id column in all of these tables and delete took less than a minute. That reminds me of another case where performance for postgres could be improved. When testing variuos kinds of jobs I noticed that concurent jobs creating root bioassayset took surprisingly long and did not scale well. That was due to sequential lookup in RawData* table on rawbioassay_id column. Creating index on that column improved performance by more than 50% (see: http://picasaweb.google.com/pawel.sztromwasser/Other#5257654388791782770). I know that indexes have drawbacks as well, but in cases above they are a huge advantage. Could these indexes be incorporated in updateDb/indexes scripts? If you know about any other possible places in BASE database where similar things may occur, let me know and I will test them. Best regards, Pawel - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.8.3 has been released
We have now released BASE 2.8.3. The release fixes two permission- related problems that may occur when using shared directories in a project and a few other minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.8.3 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html /Nicklas - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Webservices transport error: 411 Error: Length Required
Pawel Sztromwasser wrote:
Totally agree. That makes it much more flexible. Please, feel free to
change the code.
I have now implemented this feature in the trunk. There are several
possibilities to specify which 'ServiceFactory' to use. The easiest
is to use something like this when the application starts up:
Options opt = new Options();
opt.setProperty(HTTPConstants.CHUNKED, false);
ServiceFactory factory = new ConfigurableServiceFactory(opt);
Factories.setDefaultServiceFactory(factory);
The rest of the code can remain unchanged. Another option is to specify
the factory when you create the SessionClient object:
SessionClient session = new SessionClient(url, null, null, factory);
I have not seen any differences between having the HTTPConstants.CHUNKED
parameter true or false, so it would really be nice if you can verify
that the configurable factory is working.
/Nicklas
Pawel
Nicklas Nordborg wrote:
Thanks for the code. It was something like this that I had in mind. The
one thing I don't like is to pass the type as an 'int' parameter in the
constructor and having a switch statement that creates the actual object
to use. This makes it impossible for others to use their own
implementations of 'RPCServiceClientCreator'. Wouldn't it be better to
pass a 'RPCServiceClientCreator' directly to the constructor?
Eg.
protected AbstractRPCClient(
String url, String service,
RPCServiceClientCreator serviceCreator)
{
...
}
/Nicklas
Pawel Sztromwasser wrote:
Hi Nicklas,
I had some time and implemented the 'ServiceFactory' functionality.
Gzipped java files are attached. To summarize changes:
1) three new classes/interfaces were created (I put them in
net.sf.basedb.ws.client.added package):
a) RPCServiceClientCreator - interface containing RPCServiceClient
getService(String serviceUrl) method for creating RPCServiceClient objects
b) DefaultRPCServiceClientCreator - factory class implementing
interface above. It creates RPCServiceClient objects in the way they
were created in AbstractRPCClient.getService() method.
c) NoChunkRPCServiceClientCreator - the same as above but with CHUNK
option set to false.
2) AbstractRPCClient class uses own RPCServiceClientCreator object to
create objects in getService() method. Creator object is initialized in
constructor (type of creator is an argument of additional constructor).
The creator type can be chosen between values supported by
AbstractRPCClient, available as public static constants (currently only
DEFAULT_RPC_SERVICE_CLIENT and NO_CHUNK_RPC_SERVICE_CLIENT). If no
creator type is supplied, default one is used.
3) all the subclasses of AbstractRPCClient have additional constructor
with last argument being type of RPCServiceClientCreator which refers to
constructor in superclass. This makes possible to choose creator type
when programming BASE2 webservices clients.
I attached diffs.txt file which contains diff output on
net/sf/basedb/ws/client/ folders for my version and 2.7.1. Just thought,
it might be helpful.
I hope the code will be useful.
Best wishes,
Pawel
Nicklas Nordborg wrote:
Pawel Sztromwasser wrote:
Hello BASE developers,
We have been recently trying to enable retrieving some data from
BASE2 installation directly into our 'home made' analysis tool. We
use webservices for that and have to say that you are doing a great
job.
Thanks.
We are really looking forward to use them more extensively.
Recently, when I started testing the tool not only within the local
network I noticed that the webservice client does not switch off
chunking. It results in attached exception cascade. Chunking is on by
default in axis2 and some servers (i.e. our gateway to BASE which
apparently uses HTTP1.0 and not 1.1) have problems with it. The
remedy is to use
options.setProperty(HTTPConstants.CHUNKED, false);
in net.sf.basedb.ws.client.AbstractRPCClient.getService(). I don't
know what are the drawbacks of it, but that was the only way I could
run the services in our current setup (BASE2.6 accessible by
proxypass from exposed webserver). Could this option be set off by
default or configurable somewhere? Or maybe there is some other
workaround?
I am afraid that I am not very familiar with all possible options that
is available in the Axis API:s. There seems to be a lot of them and
their Javadoc is not very informative about what many of the options
are used for. The CHUNKED option seems to be related to the way HTTP
requests are made, but I have to admit that this is the first time I
have heard of it. This means that I probably know even less than you
about this.
I think that, in the future, there may be more requests about being
able to set other options. So, it may be better to think ahead and try
to figure out some way to be able to do this as easy as possible. With
the current BASE API the only workaround that doesn't involve
Re: [basedb-devel] intermittent hibernate errors when using BASE API
Bob MacCallum wrote: Hi Nicklas, I'll double check but I think we're sharing one DbControl across the whole webapp, so that will be the first place to look. This will definitely give you a lot of problems since a DbControl is not thread-safe. You may also run into memory problems since every item that has been loaded from the database will be stored in a cache. If you use one DbControl for everything you will end up with the entire database as Java objects in memory. In other words, every request to the web application needs it's own DbControl. /Nicklas Thanks for the hint. Will post back when I have a solution. cheers, Bob. Nicklas Nordborg writes: Bob MacCallum wrote: Quick follow up to: http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00316.html The problem seems to be triggered by concurrent access to our BASE-based web application (for example, me and googlebot). That doesn't bring me any closer to understanding what exactly is going on, but I thought I would share. I wonder if similar stacktraces occur on a busy multi-user BASE server? Are you sharing objects (eg. an ItemQuery, DbControl, etc.) between different threads? I think the problem can be caused by multiple threads that are accessing the same non-threadsafe object at the same time. /Nicklas - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.6.3 has been released
Hello all, We have now released BASE 2.6.3. The release is a bug fix release for some minor bugs only. We expect this to be the last release of the 2.6.x branch. 2.7.0 is scheduled for May 22, but may be released earlier if no more problems show up during testing. More information about the changes in 2.6.3: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.6.3 Download from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] setting annotation values programmatically
Micha Bayer wrote: Hi all, I am in the final throes of adding the custom interface to the tab2mage importer plugin but I have one more thing to do before it all works as specified, and that is to set values for the experimental factors on each of the raw bioassays added to the experiment so they can all be displayed in the experiment's detail view (at the moment I am just getting an empty list). I have been looking through the API and the dev docu for this but to no avail. Can anyone point me in the right direction here? I think the raw bioassays should probably be inheriting these values from the Sample objects they are linked to but I figure out how to a) add an annotation to a sample or any other item Annotatable item = ... AnnotationType at = ... Annotation a = item.getAnnotationSet().getAnnotation(at); // For a single annotation value a.setValue(...); // if it is multiple values a.setValues(...); b) how to let the bioassay inherit this programmatically. Annotatable child = ... Annotatable parent = ... AnnotationType at = ... Annotation a = parent.getAnnotationSet().getAnnotation(at); // To inherit a single annotation child.getAnnotationSet().inheritAnnotation(a); // To inherit all annotations child.getAnnotationSet().inheritAnnotationSet(parent.getAnnotationSet()); /Nicklas - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Integrating BASE to analysis packages
I have now checked in a foundation for the extension system in the trunk. It should be possible to start developing external extensions in the current state. A simple tutorial can be found at: http://base.thep.lu.se/chrome/site/trunk/html/developerdoc/extensions/extensions.html Note that you have to check out the trunk from our subversion server to be able to work with this. See http://base.thep.lu.se/wiki/DownloadPage There are also some Hello world extension examples to be found at: http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examples.extensions As usual, since this is non-released code, we can't make any guarantee of it's stability. In particular, don't install this in a production environment. Although we don't expect any major changes to the new extensions API, you should be prepared for minor changes to methods, classes, etc. at any time until the final 2.7 release. Currently, there are two extension points, one in the menu and one where the MeV Launcher is in the tree of bioassaysets in the analysis. Suggestions for other extension points can be posted to http://base.thep.lu.se/ticket/933 /Nicklas Nicklas Nordborg wrote: We agree with you, something more general is needed. We have discussed this issue several times and always postponed it, there is so many things to do. There is a very non-informative ticket related to this, http://base.thep.lu.se/ticket/436 but to be honest, to see the connection you need to join us in our coffee room. There is now more information in the ticket referenced above. The terminology has changed. We should should use the term extension instead of plug-in in order to avoid confusion with the existing plug-in system. We have decided to split the implementation in three parts: 1. Create the required infrastructure. This is what ticket 436 is about. 2. Implement a few extension points in the web client. This would cover the place were the Launch MeV button is located and a few other places. This is/will be described in ticket 933: http://base.thep.lu.se/ticket/933 3. Re-implement the Launch MeV functionality as an extension and remove it from the core distribution. This is described in ticket 932: http://base.thep.lu.se/ticket/932 Everything is currently only in the design phase. There are probably lots of details to work out. I'll soon start with some prototype code to see if the general idea works and if something needs to be changed. Comments are welcome. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Problem with multiple parameter values in PluginConfigurationImporter
I think this is a bug in the importer. I have created at ticket for this and will fix it in the 2.6.2 release. Can you upload the exported file that fails so we have something to test with? Use base/base as login/password. The ticket can be found here: http://base.thep.lu.se/ticket/970 /Nicklas Adam Ameur wrote: Hi, I'm using BASE2.4.6 and the PluginConfigurationExporter/Importer normally works fine for me, but the PCImporter fails to read configurations when parameters have multiple values. In such cases, the PCExporter seems to work fine and the parameter info in the xml file looks as in the example below (N parameter values in this example). parameter nameparamName/name labelparamLabel/label descriptionparamDesc/description classjava.lang.String/class valueparamValue1/value valueparamValue2/value ... valueparamValueN/value /parameter But the PCImporter fails and the stack trace looks somemthing like this: net.sf.basedb.core.BaseException: Found N values in parameter 'paramName'. Only 1 is allowed. at net.sf.basedb.plugins.PluginConfigurationImporter.doImport(PluginConfigurationImporter.java:340) at net.sf.basedb.plugins.PluginConfigurationImporter.run(PluginConfigurationImporter.java:226) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) at java.lang.Thread.run(Thread.java:613) Caused by: net.sf.basedb.core.InvalidDataException: Found N values in parameter 'paramName'. Only 1 is allowed. at net.sf.basedb.core.ParameterType.validate(ParameterType.java:248) at net.sf.basedb.core.PluginConfiguration.setParameterValuesInternal(PluginConfiguration.java:462) at net.sf.basedb.core.PluginConfiguration.setParameterValues(PluginConfiguration.java:430) at net.sf.basedb.plugins.PluginConfigurationImporter.setPluginConf(PluginConfigurationImporter.java:460) at net.sf.basedb.plugins.PluginConfigurationImporter.doImport(PluginConfigurationImporter.java:334) ... 4 more I think the problem could be that the parameter value multiplicity is not set properly. I don't know if this has been solved in later base versions, but I couldn't find any tickets about it. The fact that the PCExporter works suggests to me that the problem is not in the plugin configuration itself. What do you think about it? /Adam - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] extract Annotations from BioAssay: error connection closed
Alessandro De Stasio wrote:
Hi,
I'm writing a Fold Change Plugin. I need to extract all the Annotations
from a list of BioAssay.
So When I try:
...
DbControl dc = sc.newDbControl();
//From the input
BioAssaySet source = getSourceBioAssaySet(dc);
ListBioAssay bioAssays = (ListBioAssay)
job.getValues(bioAssays);
if(bioAssays!=null){
Iterator it = bioAssays.iterator();
while(it.hasNext()){
BioAssay bassay = (BioAssay) it.next();
AnnotationSet annSet = bassay.getAnnotationSet();
On bassay.getAnnotationSet() call, I have this Exception:
net.sf.basedb.core.ConnectionClosedException: The connection has been
closed.
at net.sf.basedb.core.DbControl.getItem(DbControl.java:718)
at net.sf.basedb.core.BioAssay.getAnnotationSet(BioAssay.java:185)
at
foldchange.src.net.sf.basedb.foldchangePlugin.FoldChangePlugin.run(FoldChangePlugin.java:170)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:108)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:487)
at java.lang.Thread.run(Thread.java:619)
An idea? Thanks in advance
Yes, the DbControl that the 'bassay' object was loaded with is closed
before the run() method on your plug-in is invoked. I was pretty sure
that this was documented somewhere but I can't find anything except a
single code example on
http://base.thep.lu.se/chrome/site/latest/html/developerdoc/plugin_developer/plugin_developer.analyse.html
I guess this is something that should be clearly stated somewhere since
it is a very common mistake, even among experienced developers. In any
case, the solution is simpe. Just reload the 'bassay' object with the
new DbControl. The safest way is to use:
bassay = BioAssay.getById(dc, bassay.getId());
before the 'bassay' object is used.
In your case you should be able to do
(if you change the iterator to IteratorBioAssay)
BioAssay bassay = BioAssay.getById(dc, it.next().getId());
/Nicklas
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[basedb-devel] Base 2.6.1 is released
Hello all, We have now released BASE 2.6.1. The release is a bugfix release, including some critical fixes for the BioAssaySetExporter and a potential out of memory problem. More information about the changes: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.6.1 Download from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Migration transfers deleted items
Pawel Sztromwasser wrote: We will be still testing migration for some time, because we haven't moved BASE1 to the new server yet. Some additional code was needed to move our local adaptations. They are supposed to be a part of 1.2.18 BASE1 release (if happens), so if anyone ever needs to migrate from that version, we might have the code. I don't know what is happening with 1.2.18. We have not been working with BASE 1 here in Lund for quite some time now. As far as I know, there is no longer any development going on for BASE 1. We are also working now on task of merging two (or more?) BASE1 installations into one BASE2, using migration package. Do you know of any issues that could be problematic in this case? I managed to run one migration after another (from different BASE1s), after minor code changes, but still need to check if some items do not clash somehow. There will be problems with all things that must be unique. Things that come to my mind are reporter ID:s, user logins, plug-in definitions and file names. The migration also creates a couple of roles and annotation types, which will be multiplied if running it more than once. Anyway, we are still working with migration so if anything serious pops up, I will let you know. Of course, if any of features I mentioned above is interesting for you Not really. We have finally done our own migration. we will be glad to contribute to the project. Great to hear. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Migration transfers deleted items
Pawel Sztromwasser wrote: Hi, While testing migration I found out that items deleted in BASE1 are migrated to BASE2. As I understand from documentation, BASE1 doesn't delete items from the database unless purgeDatabase.php script is executed. They are just flagged as deleted by setting remove value=2 (or 1 maybe). Those that have removed flag set to 1 are marked for deletion (something equivalent to moving to trashcan). Other items have removed=0. Migration code uses ResultSet.getBoolean() method to retrieve 'removed' value (which is smallint) and as I checked, it returns true only when removed==1. The consequence is that items marked for deletion go to trashcan as they suppose to, but those actually deleted get removed flag set to false and appear in BASE2 as not deleted. This could be due to postgres JDBC driver handling type mapping in different way than mysql driver, but I couldn't find any information on that. The quick solution is to run purgeDatabase.php before migration to remove deleted items from the database. I didn't know that. I simply assumed that the removed flag only could be 0 or 1. Kind of like in BASE2. In any case, the 2.6 release was the latest release of the migration program. It will still be included in future releases, but we will not test or actively maintain it anymore. The reason for this is that we are moving our servers to BASE 2, and at some time in the future we will not have a BASE 1 server to use for testing the migration. Should any remaining critical bugs appear we will of course assist in fixing it. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Base and baseplugins subversion repositories are moving
The baseplugins site has now been moved. The new subversion root url is: http://basesplugins.thep.lu.se/svn NOTE! The ip number of the baseplugins.thep.lu.se has been updated in our DNS to point to the new server. If your DNS system caches the old ip number you will not be able to reach the new site until the ip address has been updated in the DNS system. If you go to http://baseplugins.thep.lu.se and see a note about moving the server you are on the old site. If you can't see the note you are on the new site. The structure of the repository has changed a lot. You need to know the exact new location of a project when using the 'svn switch --relocate' command. Here is an outline of structure with the old paths in brackets: /plugins /base1 /se.lu.onk/trunk[/trunk/se/lu/onk] /se.lu.thep.wenni/trunk [/trunk/se/lu/thep/wenni] /base2 /net.sf.basedb.illumina/trunk [/trunk/net/sf/basedb/illumina] /se.lu.thep.affymetrix /trunk[/trunk/se/lu/thep/affymetrix] /tags [/tags/se/lu/thep/affymetrix] /uk.ac.ebi.tab2mage /trunk[/trunk/uk/ac/ebi/tab2mage] /branches /tab2mageimporter [/branches/uk_ac_ebi_Tab2MageImporter] /uk.ac.scri.batchimporter /trunk[trunk/uk/ac/scri/batchimporter] /webservices /se.lu.thep.webservices /trunk [/trunk/se/lu/thep/webservices_clients] You need to make two 'svn switch' commands to change your working copy to the new location. The first command will switch the repository location to the new server. This should be the same for everybody: svn switch --relocate http://lev.thep.lu.se/repository http://baseplugins.thep.lu.se/svn . Everything should be on one line. Don't forget the dot on the last line! The second command will point the working copy to the new location: svn switch http://baseplugins.thep.lu.se/svn/plugins/base2/net.sf.basedb.illumina/trunk Once again, everything should be on one line. The URL must of course be different for each project. Note to project managers! - Projects which has links on the wiki pages linking to files in the repository should make sure to update the links to point to the new locations. It is, for example, common practice to link to readme and installation information like this [source:/plugins/base2/net.sf.basedb.illumina/trunk/README README] We will not automatically fix links pointing to the old locations. /Nicklas Nicklas Nordborg wrote: We are planning to move the subversion repositories for the base and baseplugins site some time next week. The move is needed to simplify the administration of the various subversion repositories and trac sites. Right now, everything is located on too many different servers. The new subversion URL:s will be: BASE: http://base.thep.lu.se/svn BASE plugins: http://baseplugins.thep.lu.se/svn If you have checked out working copies of source code from the old locations there are two ways to handle the move: 1. Checkout a new working copy from the new location and delete the old working copy. Use this option only if you havn't made custom changes. 2. Use the 'svn switch --relocate' command. The syntax is: svn switch --relocate OLD_URL NEW_URL WORKING_COPY_PATH For example: cd base_working_copy_dir svn switch --relocate http://lev.thep.lu.se/repository/base http://base.thep.lu.se/svn . If you are using Eclipse the 'relocate' command can be found in the 'SVN Repository Exploring' perspective. In the list of repositories, right click on a root repository and choose the 'Relocate...' menu item. A popup wizard will be displayed. Click on Next and enter the new URL. The baseplugins repository will also be restructured as part of the server change. Instead of having /trunk, /tags and /branches at the root of the repository each subproject will now get their own /trunk, /tags and /branches. Here is an example: /trunk/se/lu/thep/affymetrix /tags/se/lu/thep/affymetrix/0.7 will change to: /se/lu/thep/affymetrix/trunk /se/lu/thep/affymetrix/tags/0.7 This change will make the baseplugins site easier to administrate and also makes it possible for each subproject to tag and branch as they wish. Note that this message is just to prepare everybody of the change. Nothing has been changed yet. The change will take place some time next week. We don't yet know the exact day but will send another message when the changes have been completed. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb
Re: [basedb-devel] Data Files in a RawBioAssay
Carl Mäsak wrote: I've now come far enough with my BASE2 web services client in Bioclipse that I dare show it to the eventual end user. Due to this, I have a couple of more specific questions: * How do I get the name of a data file contained in a RawBioAssay? You can't with the current web services implementation. It should not be hard to add support for it though. Contributions are welcome. * Somewhat relatedly, does the data model support several files of the same type in one RawBioAssay? I see no examples of this through the web client, and the signature of `downloadRawDataByType` suggests that it doesn't, but my end user mentioned that one sometimes wants to store, say, several .CEL files in one RawBioAssay. No. You can only have one file of each type. What is the use case for having more than one CEL file? A raw bioassay represents a SINGLE data set. * Also, is there a way to get information about the .cdf files through WS? They don't seem to be among the results of `getDataFileTypes`. Yes, the CDF file is part of the array design so you have to fetch that first. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] more trials with getting a web service client to work (Re: strange AxisFault exception when using the example in the docs (Re: Writing an external importer/exporter))
Carl Mäsak wrote: Since I last had my problems getting a web service client to work in mid-December, I've slowly come to the realisation that (1) I should be starting from the web service client examples provided on the home page, and (2) I should really use Java 1.6 and not Java 1.5, as I am now. Even so, I'm still having a bit of trouble getting a web service client to work properly. Given that I had a working prototype in October, before the switch to the new, permanent web services, this feels a bit discouraging. Any pointers towards a working client are appreciated. Nicklas (): All examples are included in the source download (is this what you downloaded?). To build the examples you need to do (from the root directory of the source download): ant package.examples This will build the examples, and put everything in the /examples/webservices directory. Read the README file for further instructions. I did this, and the build failed. Thought you might be interested: http://pastebin.com/m7d681d91 Seems like this is a problem with internal dependencies. Or in other words, the different BASE packages are compiled in incorrect order. Try 'ant dev' instead. This will compile everything. I also tried downloading the web service client example tar file from this page: http://base.thep.lu.se/wiki/DeveloperInformation http://www.thep.lu.se/~nicklas/base/examples/examplewebservices.tar.gz Running it on my own computer (somewhat predictably) produces an UnsupportedClassVersionError, since I'm running java 1.5.0_07. I cannot upgrade to 1.6 without upgrading my OS X version to 10.5. But from reading summaries of what's new in Java 1.6 -- foremost of which seems to be a better support for web services -- I suppose that the Java 1.6 dependency is not easily removed from the web service client code. Am I correct? If you are running Mac OS X you are out of luck. There is no Java 1.6 available yet for Mac. I think the problem is that the temporary example package that we put up on the web site is compiled with Java 1.6. We usually compile released packages with 1.5. It never happend in this case since all of us were really busy or on vacation. We'll fix this when we release 2.5.1. Running the client example on a collegue's computer equipped with Java 1.6 produces the following AxisFault exception: http://pastebin.com/f52f7b0dd The relevant settings in this case were: property name=services.url value=http://base2.thep.lu.se/demo/services; / property name=services.login value=base2 / property name=services.password value=base2 / What have I missed? No, but I think we have! The demo server is still running a 2.5beta version. It needs to be upgraded. We'll fix it as soon as possible. /Nicklas - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] BASE 2.5 beta has been released
We are happy to announce the release of BASE 2.5 beta. Since we normally don't release beta versions there are a few things that you need to be aware of. * The beta should be used for testing only. Don't install it on production servers. * Make a backup of the BASE database before installing the beta unless you are willing to risk data loss and/or corruption. * We can't guarantee that it will be possible to upgrade the beta version to the final 2.5 version. You can download this release from the usual download location http://base.thep.lu.se/wiki/DownloadPage. The reason that we are releasing a beta is that the 2.5 version contains many new features that affects central parts of BASE. By releasing a beta version we hope to get help with finding remaining bugs and issues related to the new features. The new features also affect plug-in developers and other developers programming against the BASE API. We also want to give those developers a chance to extend and modify their code to use the new features before the final 2.5 version is released. We don't expect any major changes to the API between the beta and the final release, unless a serious bug or design flaw is discovered. Here is a list of the most important features: * Made it possible to use files for storing raw data and array designs instead of importing it to the database. Previously this support was limited to the Affymetrix platform. Developers that are working on code that handles raw data and/or array designs should absolutely check the documentation to see what has changed. Most changes are backwards compatible, but there are some issues that may affect old code. Also note that in order to do anything with the data in the files special plug-ins are needed. So far, the only existing plug-ins are the RMAExpress and Plier plug-ins for the Affymetrix platform. Data from other platforms must still be imported into the database if you want to analyse it. For more info, see: - http://base.thep.lu.se/ticket/807 - http://base.thep.lu.se/ticket/721 * Added a few web services to the core BASE distribution. The web services are not compatible with the old prototype code in the webservices branch. For more info, see: - http://base.thep.lu.se/ticket/809 - http://base.thep.lu.se/ticket/492 * Automatic detection and installation of plug-ins is now supported. Plug-in installatation has been made easier. Now you can just drop the plug-in JAR file in a dedicated plug-in directory on the server. Then, use the auto-installation wizard to let BASE detect and install the plug-in(s). For this to work, the plug-in developer must have made certain preparations in the JAR file. For more info, see: - http://base.thep.lu.se/chrome/site/trunk/html/developerdoc/plugin_developer/plugin_developer.organize.html - http://base.thep.lu.se/ticket/364 * The update script that updates a 2.4.x installation to 2.5 is by far the most complex update script so far. We have tested it with test data and on the demo server. It would be very nice to get more reports from successful (or unsuccessful) updates. Remember that it is better to find bugs now than after the final 2.5 version has been released. Please download and try the beta and send us feedback. The final 2.5 release is scheduled to be released at December 6th. Happy BASEing, The Lund BASE team - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Index dropping fails with Postgres 7.3.19
Pawel Sztromwasser wrote: I investigated a bit and found out that this index in fact exists. I managed to drop it manually using psql with command: DROP INDEX dynamic.D21886Filtercolumn Command without schema name prefix (DROP INDEX D21886Filtercolumn) doesn't work. I checked the index dropping code and I found out that in net.sf.basedb.core.dbengine.PostgresDbEngine.getDropIndexSql() method code(line 120) creating 'drop index query' uses only index name without schema name prefix. That is why an exception is thrown. I didn't find anything about adding dynamic schema to users search_path in PostgreSql in Base2 requirements. Some of the code in the same 'problem causing' method adds schema prefix when dropping constraints, so I consider this issue as a bug. I think you are correct. The documentation for the method clearly mentions that it should generate SQL with the schema name included, but it doesn't. We'll fix it as soon as possible. The dropping of indexes is an important fix for performance but it doesn't affect the BASE application in any other way. With BASE 2.4.5 you will at least not get any more unwanted indexes on new experiments. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] JobAgents on multi-processor machine
Nicklas Nordborg wrote: I am taking this back to the mailing list in the hope that there is some Postgres expert that can shed some light on this. I found this http://www.thescripts.com/forum/thread174537.html It is about a rather old Postgres version (7.4). I am not sure if the same problem is still around. The problem is that when inserting data Postgres is locking all rows that are referenced by foreign keys. This means that if your five imports, for example, inserts data with references to the same reporter or feature on an array design, only one can proceed at a time. Actually, if this problem is still around in Postgres 8.2 I think this makes Postgres more or less unusable in a true multi-user setup. Since almost any data import or analysis plug-in will insert data and in many cases the new data will reference a reporter, an experiment or some other common item there is a high probability that only one job is able to proceed at a time. There is a tip about a DEFERRED mode that can overcome some limitations, but I am not very familiar with Postgres and don't really know how to set it. It would be good if there is a global server configuration option for this. Do you have the possibility to investigate this further? I did some investigation on my own. I can verify that the locking problem exists on Postgres 8.0.4. I tested this with only two jobs using the internal job queue and only one could work at a time. After installing Postgres 8.2.5 (which is the latest version) the locking problem disappeared. Checking the documentation on their website it seems like a new shared row-level lock mode has been introduced some time ago. This means that Postgres no longer has to use a write-lock which can only be held by one transaction at a time. So, unless some new information about this issue comes up I will not investigate this any more. Postgres users are encouraged to upgrade to Postgres 8.2.5. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] JobAgents on multi-processor machine
Paweł Sztromwasser wrote: All job agents were configured to run all installed plugins and Everyone group has access to them. In fact each of them is able to run a job, but only if no other job is running. I saw couple of times (on JobAgents tab in web UI), as 4 of jobs were assigned to (let's say) 3 agents and only one was progressing. Others were at 0% progress with status 'Executing: parsing headers...'. When the progressing one If a job is listed as 'Executing...' it is running. So it seems that your job agents have started more than one job after all. The status for each job is only updated in intervals about 10 seconds. This may make it seem like only one is progressing at a time. Especially if you have jobs that doesn't take much time to execute. For example if they take less than ten seconds the first status update will be 0% and the next 100%. If you check the started and ended time for each job you can get better timings and also see if they actually overlap or not. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] object attributes missing when API used from tomcat servlet
Bob MacCallum wrote: Only in ../../apache-tomcat-6.0.14/webapps/GEWebapp/WEB-INF/lib: biojava-ensembl.jar biojava.jar bytecode.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar gesol.jar GEWebapp.jar jstl.jar mysql-connector-java-3.0.10-stable-bin.jar standard.jar I figured out that mysql-connector-java-3.0.10-stable-bin.jar was both unnecessary and the **cause of this problem** It is not a good idea to have two versions of the same library in the classpath. That may cause very strange problems if one class is loaded from one version and another from the other version. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] File URL
Peter Mertens wrote: I searched in the base servlet code and the mev code, but i can't find how they manage the download. Could you provide more info? http://base.thep.lu.se/browser/trunk/src/clients/web/net/sf/basedb/clients/web/servlet/Download.java Line 89-123: Parse the request URL to find the session ID and the file path Line 125-147: Get the SessionControl and make sure that the user is logged in Line 148-156: Get the File object and find out the MIME type Line 157-159: Set response headers with MIME type, file name and file size Line 160-165: Send the file /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] hyb to l.extract (and onwards) with API
Hmmm... I was a bit puzzled at first... The query seemed to be a valid
query. However, I found that the problem is that the
creationEvent.sources is a Map collection where the LabeledExtract is
the key and the used quantity is the value part. Unfortunately it seems
like the expression creationEvent.sources only goes to the value part
(used quantity). That is why Hibernate complains with the error
could not resolve property: name of: component[usedQuantity,dummy]
Hibernate has an index() function which can be used to get to the key
part of the map (WHERE index(lbe) ...) but it seems like it only
retrieves the ID of the LabeledExtract and not the name and other
properties.
Now, all this can solved with a subquery magic using a custom-built
restriction. Replace the itemQuery.restrict() call with something like this:
itemQuery.restrict(
new Restriction()
{
public String toQl(Query query, DbControl dc)
{
return index(lbe) IN +
(SELECT l.id FROM LabeledExtractData l +
WHERE l.name = 'uci_tissues_fb_3.s1.e1.lbe1');
}
public Collection? extends QueryElement getChildren()
{
return null;
}
});
Of course, this needs to be polished up a bit to be used for real. If
you need to go up to samples you must do that in the subquery, but that
is easier:
WHERE l.parent.parent.name = ...
This assumes that you always use non-pooled items. If you have pooled
items nothing will work, since the number of hops to get to the sample
may be different for different paths. In that case you'll probably have
to start at the sample level and then follow each path down to the
hybridizations.
/Nicklas
Bob MacCallum wrote:
Hi,
The following isn't working, even though some very similar code in
net.sf.basedb.core.LabeledExtract works fine (I assume). I'm just restricting
on a hard-coded name at the moment for testing:
ItemQuerynet.sf.basedb.core.Hybridization itemQuery =
Hybridization.getQuery();
itemQuery.include(Include.SHARED);
itemQuery.setDistinct(true);
itemQuery.join(Hql.innerJoin(creationEvent.sources,
Item.LABELEDEXTRACT.getAlias()));
itemQuery.restrict(
Restrictions.eq(
Hql.property(Item.LABELEDEXTRACT.getAlias(), name),
Expressions.string(uci_tissues_fb_3.s1.e1.lbe1)
)
);
... = itemQuery.list(dc);
[java] Exception in thread main net.sf.basedb.core.BaseException:
could not resolve property: name of: component[usedQuantity,dummy] [SELECT
DISTINCT hyb FROM net.sf.basedb.core.data.HybridizationData hyb INNER JOIN
hyb.creationEvent.sources lbe WHERE (lbe.name =
:P1555286c83a454f1a9e048f5efbcde73)]
[java] at
net.sf.basedb.core.HibernateUtil.createQuery(HibernateUtil.java:1349)
[java] at
net.sf.basedb.core.AbstractEntityQuery.getMainHqlQuery(AbstractEntityQuery.java:349)
[java] at net.sf.basedb.core.ItemQuery.list(ItemQuery.java:93)
If I print out the query it looks like this
[java] ItemQuery: SELECT DISTINCT hyb.null FROM
net.sf.basedb.core.data.HybridizationData hyb INNER JOIN
creationEvent.sources lbe WHERE (lbe.name =
:P1555286c83a454f1a9e048f5efbcde73(uci_tissues_fb_3.s1.e1.lbe1))
Once we get this working, we want to join all the way to Sample - do you think
that will be possible?
many thanks,
Bob.
-
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Re: [basedb-devel] Getting normalized data out Base
Peter Mertens wrote: Dear list, again i have another question for you. I have developed a normalization plugin for Base. But now i want this normalized data back out of base to use it in another application. I wanted to do this using the webservices, since this is, according to me, the only way. Now i have 2 problems: First, the normalized data is not stored in a file but read into a table. Is there a way to also store it in a file and attach this to the raw bioassay. It would be better to attach it to the bioassay set. In any case it is currently not possible. We are working with a solution for this and it will be released in 2.5. See http://base.thep.lu.se/ticket/721 for more information. Second, the webservices are not able to handle this (downloading files other then cel and cdf), up till now. I'm willing to edit the services to make this service available. But then i need to get the location of the file that stores the normalized data. The web services was developed as a proof of concept. It was never intended to be used in real applications. Most of the functionality is hard-coded and the design (or lack of design) is not something to continue building on. The 2.5 release will hopefully include some sort of web services in the main branch. We are currently discussing what functionality to include as part of the web services. From user feedback the possibility to access files that are part of an experiment seems to be an important feature so there is a good possibility that this will be included. Any ideas to handle this? 1) Help us out with the web services implementation. But since details are a bit vague right now I don't know how to synchronize this with external developers. 2) Export the data from the database to a file. This can be done manually and fed to your application or by the use of a servlet and export plug-ins. See for example the code that MeV uses to download data directly from BASE: http://base.thep.lu.se/browser/trunk/src/clients/web/net/sf/basedb/clients/web/servlet/MevExport.java This code uses the BioAssaySetExporter in MeV mode. MeV uses the servlet like this: http://server.name/base2/plugins/org/tigr/microarray/mev/export?ID=SessionIDbioassayset_id=id where SessionId should be replaced with the current user's session ID and id with the id of the bioassayset to export data from. If your application can handle the MeV file format you can use the existing servlet, otherwise you need to create a new servlet and possible also a new export plug-in. 3) Well... wait for 2.5 and hope for the best... /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] How to delete a Job that is in Executing mode.
vegard nygaard wrote: I have some jobs I want to delete, but I am not allowed to. I think the reason is that they are still in Executing mode, according to the job list. In reality they are not executing, this is just old trial and error runs of plug-ins that apparently failed in unexpected ways. I can't find a way to remove them from the system or set their status to the appropriate Error. The safest possibility is to manually change the status flag to something else with your favourite database administration tool, and then delete them from the web interface in the normal way. The status codes can be found at: http://base.thep.lu.se/browser/trunk/src/core/net/sf/basedb/core/Job.java#L1406 /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Singel-item view stops working after adding annotations
Harald Stachelscheid wrote: Am Montag, 24. September 2007 schrieb Nicklas Nordborg: Harald Stachelscheid wrote: Hallo, after I add an annotation to an any type of item I get a blank window in the browser when I try to display the Single-item view. In contrast editing the item by ctrl+clicking the item in the list view works correctly and shows the added annotation. Any ideas to solve this problem? My configuration: BASE 2.4.1, Tomcat 5.5.23 and PostgreSQL 8.0.1. Can you check the Tomcat log file for information about errors? /Nicklas sorry just noticed that additionally to output in the .log-file the following is written to the catalina.out log: /Harald It seems to be a limitation in Postgres that we didn't know about and that Hibernate seems unable to help us with. Right now I don't have any workaround, other than to use MySQL instead of Postgres. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
[basedb-devel] Comments wanted about new feature in BASE 2.5: Store data in files instead of in the database
Hello all, We are currently working on the issue of keeping data (ie. raw data, array design data and possible analyzed data) in files instead of importing it into the database. It is alread possible to do that for Affymetrix experiments, but the solution can't be used to give the same functionality for other platforms. We have put together a few draft documents describing a possible design (database, API, etc...) to solve this issue in a more general way. In practice, it will be possible to let BASE store data for any platform. Using/analyzing the data will be a plug-in issue to 100% and is no longer a concern for the BASE core. So, anybody that is interested in checking this out can go to http://base.thep.lu.se/ticket/721. There are links to relevant documentation. If you have any comments or other ideas, please let us know. One thing we need help with is the list of pre-installed platforms. Anybody with knowledge of different platforms and what types of files they generate please tell us and we will try to add as much as possible to the standard BASE distribution. Prototype development has already started. We expect the design to be more or less finalized in a few weeks. Minor details may still be changed after that. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] Bug in how Base1PluginExecuter handles the stdin.txt file.
vegard nygaard wrote: When working with my BASE1 plug-in in BASE2 the Transformation page was suddenly broken. I think this happened when upgrading to 2.4 but I am not sure. After some investigation I found the reason to be that the stdin.txt file was missing in the database. It was not in the files table but a row in the anytoany table had it as a foreign key(non-existing), causing an error. My quick fix was to remove: dc.deleteItem(stdin); At line 685 in Base1PluginExecuter. Then stdin.txt got into the database and the transformation page showed nicely with link to the files. I have altered the Base1PluginExecuter my self and could accidentally caused this bug. The bug(s) existed before your changes. The file import seems to happen at too many places, and that is why it doesn't work properly. It may also affect other files, such as stdout.txt for example. Is it possible to get full root (or admin) privileges on the newest BASE2 test-installation in Lund to recreate bugs? No. Also I found another bug/feature: the leaveStdin/leaveStdout-flags did not seem to have any effect. The files were stored anyway. For my part this is ok. I think you are correct. I can't find any place in the code where the parameters are used. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] How to extend and overrideBioAssaySetExporterandBase1PluginExecuter?
vegard nygaard wrote: Hi. I have now modified my BASE2.4 code to the Abstract version, laid out earlier by Nicklas. I got it to work and it will do very well for my needs, that is if I understood what the plan really was. It would be nice if Lund put it into the next version. But verify that this was what you meant and modify it to fit your coding practice. And others might want different things done. Thanks for the code. I appreciate your effort, but I don't think it will be very useful for us (or anybody else). As far as I can tell the only real changes was to add the initBioAssaySetExporter() and exportBaseFileSectionNonStandard() methods. All other existing methods are still private and will not be available to subclasses for other developers. Moving the code from one class to another was what I meant. I think it requires a bit more hard work to decide what should go where and what should be public/protected/private. The AbstractPluginExecuter could, for example, be an abstract base class for all plug-ins with an execution pattern like this: 1. export data 2. start an external program that processes the data 3. import new data generated by the external program The actual format of exported/imported data should then go into the non-abstract subclasses. In this case, the Base1PluginExecuter exports a BASEFile (with the help of the BioAssaySetExporter), and imports BASEFile:s and other files. This is only one example of how it could be done. The first thing to do is to come up with and agree on a specification/design of the abstract classes. Maybe use the current plug-ins as a test bed for a simple prototype. Then, when everything seems to be working the real coding can begin. This is not a high-priority issue for us, so it would be great if we get help with specification, design and implementation. Since your changes are rather small another solution in your case is to keep a locally modified copy of BASE. If you do a subversion checkout your changes will be merged automatically when you do 'svn update' to get the a new version. The only thing to keep in mind is to only install released versions. Using the latest trunk will be too unstable. This should get you going until something better has been developed. A third option is to create non-plugin classes for reading and writing BASEFile:s, for example, BaseFileReader and BaseFileWriter. This is in the direction of separating functionality as suggested earlier by Gregory. If done right, the plug-in code will be much simplier, for example: writer = new BaseFileWriter(); writer.section(assay2rawdataset); writer.header(columns, id, rawdataset); ... writer.data(ba.getId(), rawBioAssayIds[0]); ... The writer/reader could also contain higher-level methods: ... writer.writeSectionSpots(BioAssaySet, and a lot more parameters) ... /Nicklas This is what I did. Made an AbstractBase1PluginExecuter that is almost the same as the old Base1PluginExecuter Modified Base1PluginExecuter so that it just contains what differs from my version Made VegardsBase1PluginExecuter; my version not to be included in a the Lund code. Just to show what I needed. Made an AbstractBioAssaySetExporter that is almost the same as the old BioAssaySetExporter Modified BioAssaySetExporter so it contains nothing. Made VegardsBioAssaySetExporter; my version not to be included in the Lund code. Just to show what I needed and not finished. Actually for my use, I did not have to abstract the BioAssaySetExporter, since it does nothing more that the abstract class. It is only my version that does a add-on. I abstracted it anyway in order to be compliant. The actual code change I did in the abstract classes was to isolate the change I needed and make a method that could be overridden by my class and others. I hope this was allowed or else I am in trouble. I don't think it works with attachments in this mailing list and I don't think I have any rights in the subversion to upload my code so I provide my files here: http://insilico.titan.uio.no/~vegardny/base2/VegardsBase1PluginExecuterModification.zip - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] How to extend and overrideBioAssaySetExporterand Base1PluginExecuter?
Gregory Vincic wrote: Hi, consider the possibility where future plugins would like to use code from both of the suggested Abstract classes - AbstractPluginExecuter - AbstractBioAssaySetExporter as you can only extend on of the abstract classes the problem remains. This is not a problem since one plug-in is an EXPORT plug-in and the other is an ANALYSIS plug-in. The plug-in API only allows a plug-in to be of one type. I suggest you try to separate the plugin code from the code that is useful elsewhere by putting them into separate classes. The Base1PluginExecuter is already using the BioAssaySetExporter. Actually, at first everything was part of the Base1PluginExecuter but the export part was moved out to it's own plug-in to make it possible to reuse the export code. In this case, the BioAssaySetExporter is used as a regular object and not as a plug-in: exporter = new BioAssaySetExporter(); exporter.exportBaseFileSerial(...); You have already done this in part by having the class FileUtil which in it's documentation states This class collects some useful methods for file and stream handling. This would be a good, if not great :-), place to put eg. - copy(..) - deleteDir(...) - emptyDir(...) from Base1PluginExecutor. Might be good candidates to be moved to FileUtil. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
Re: [basedb-devel] How to extend and override BioAssaySetExporterand Base1PluginExecuter?
Adam Ameur wrote: Hi, I would like to extend some methods in the Base1PluginExecuter for another purpose. I think we need to be careful about this. The Base1PluginExecuter and BioAssaySetExporter was designed and implemented to solve ONE specific problem: Being able to run plug-ins developed for BASE 1 under BASE 2. I can understand why people want to use the two classes for other but similar purposes since they contain a lot of useful code. Considering the historical changes (which has been large) in those two classes I don't think they are stable enough to make subclassing an appropriate solution in this case. Making methods 'public' or 'protected' instead of 'private' also means a future commitment to not change the contract of those methods (ie. method name, method parameters, return values, what they are supposed to do, etc...). The developers of the Affymetrix-related plug-ins, RMAExpress and Plier (http://lev.thep.lu.se/trac/baseplugins/wiki/se.lu.thep.affymetrix), faced almost the same problem. In this case, the RMAExpress plug-in was developed first. When development on the Plier plug-in started the developers realized that a lot of code was very similar and moved much code to an abstract base class: AbstractExternalBinaryPlugin I think a similar approach is a better solution also in the case of the Base1PluginExecuter and BioAssaySetExporter. That is, we should introduce the abstract classes AbstractPluginExecuter and AbstractBioAssaySetExporter. The hard part will be to decide what should go into the new abstract classes. The existing code will not take us all the way. I think we also need Vegard's and Adam's use cases to find a common pattern that can be used when designing the abstract classes. Other opinions on this matter and offers to help with the implementation are welcome. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
