[base] Unable to view BioMaterials items after upgrade to 2.3.2
Hello All, I've attempted an upgrade of my base-2.2.2 installation with base-2.3.2 multiple times, but each time I am unable to view items listed in the BioMaterials table using the Samples, Extracts, or Label Extracts web pages. Almost all the icons for managing items on these pages are missing as well, such the ones that say New, Delete, Restore, Share, etc., as well as the preset filter, number of records to see, etc. The Samples page has one little stub of an icon for "New". If I click this I can bring up the New Sample dialog box and create a sample that is written to the MySQL BioMaterials table, but the new item fails to show up on the Samples page. My installation is pretty standard (Red Hat 3.4.6-8, apache-tomcat-5.5.20, MySQL-server-standard-5.0.27-0, jdk 1.6.0). I have been following the documentation instructions to the letter, using updatedb.sh and updateindexes.sh, and I edited base.config to match my system. Prior to the upgrade, I had modified the extended-properties.xml and raw-data-types.xml files, but they worked fine with 2.2.2. Any ideas on what could be going wrong? Thanks, Jim Collett James R. Collett, Ph.D. Systems Biology Fellow Battelle Memorial Institute Pacific Northwest National Laboratory - 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/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Unable to view BioMaterials items after upgrade to 2.3.2
Collett, James R wrote: > Hello All, > > I've attempted an upgrade of my base-2.2.2 installation with base-2.3.2 > multiple times, but each time I am unable to view items listed in the > BioMaterials table using the Samples, Extracts, or Label Extracts web > pages. Almost all the icons for managing items on these pages are > missing as well, such the ones that say New, Delete, Restore, Share, > etc., as well as the preset filter, number of records to see, etc. The > Samples page has one little stub of an icon for "New". If I click this > I can bring up the New Sample dialog box and create a sample that is > written to the MySQL BioMaterials table, but the new item fails to show > up on the Samples page. > > My installation is pretty standard (Red Hat 3.4.6-8, > apache-tomcat-5.5.20, MySQL-server-standard-5.0.27-0, jdk 1.6.0). I > have been following the documentation instructions to the letter, using > updatedb.sh and updateindexes.sh, and I edited base.config to match my > system. Prior to the upgrade, I had modified the extended-properties.xml > and raw-data-types.xml files, but they worked fine with 2.2.2. > > Any ideas on what could be going wrong? I think it is the same problem as described in http://base.thep.lu.se/ticket/682 If the suggested workarounds doesn't fix the problem there is probably an error message in the Tomcat logfile. /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/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Unable to view BioMaterials items after upgrade to 2.3.2
Hi James, Option 2 on that ticket (http://base.thep.lu.se/ticket/682) works quite well for me. Especially if your application/installation is not particularly gaining any substantial features of mysql 5.0.27. So migrating to a lower Mysql version should be ok. Do remember to backup your data though. However, if your machine has a massive memory capability then go for option 3. ¬Dominic Collett, James R wrote: > Hello All, > > I've attempted an upgrade of my base-2.2.2 installation with base-2.3.2 > multiple times, but each time I am unable to view items listed in the > BioMaterials table using the Samples, Extracts, or Label Extracts web > pages. Almost all the icons for managing items on these pages are > missing as well, such the ones that say New, Delete, Restore, Share, > etc., as well as the preset filter, number of records to see, etc. The > Samples page has one little stub of an icon for "New". If I click this > I can bring up the New Sample dialog box and create a sample that is > written to the MySQL BioMaterials table, but the new item fails to show > up on the Samples page. > > My installation is pretty standard (Red Hat 3.4.6-8, > apache-tomcat-5.5.20, MySQL-server-standard-5.0.27-0, jdk 1.6.0). I > have been following the documentation instructions to the letter, using > updatedb.sh and updateindexes.sh, and I edited base.config to match my > system. Prior to the upgrade, I had modified the extended-properties.xml > and raw-data-types.xml files, but they worked fine with 2.2.2. > > Any ideas on what could be going wrong? > > Thanks, > > Jim Collett > > James R. Collett, Ph.D. > Systems Biology Fellow > Battelle Memorial Institute > Pacific Northwest National Laboratory > > - > 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/ > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] - 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/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
