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From: Muench, J. E <jm...@fr...> - 2017-12-09 00:40:18
|
I'm working with a well-established BASE-based installation. One of our goals has been to move the build into CI. I have switched from ant to gradle without too much difficulty, although needed to call xdoclet from a spawned ant task. Given that JPA annotations are now the recommended mapping mechanism for Hibernate, I wondered if you had ever looked into migrating from xdoclet to JPA annotation? It is something we're considering, and would appreciate knowing if there are major issues with that migration. Also, I'm happy to share how to build in gradle, if anyone is interested. Thanks! Joanna Muench Software Engineering Hutch Data Commonwealth O 206.667.2320 jm...@fr... |
|
From: Nicklas N. <nic...@me...> - 2017-11-23 10:24:46
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2017-06-07 11:24:08
|
Hello all, We have released BASE 3.11.1 today. This is a bugfix release that fixes some old and new bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.11.1&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2017-05-16 06:21:21
|
On 2017-05-15 23:32, Tyree Lush wrote: > Good evening, > > I was wondering if someone could confirm whether the BASE software can > be installed on a virtual server with full functionality. If it does and > there are specs that are mandatory, could that be provided? BASE should work just fine on a virtual server. Specs depends a lot on number of users and amount of data you are putting in. The amount of memory assigned to Tomcat is typically the most critical. For testing purposes 1GB should be enough and for a production installation maybe 4GB. Note that you'll need memory for the OS and database as well. Hope this helps. /Nicklas |
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From: Tyree L. <ty...@ho...> - 2017-05-15 21:32:23
|
Good evening, I was wondering if someone could confirm whether the BASE software can be installed on a virtual server with full functionality. If it does and there are specs that are mandatory, could that be provided? Thank you very much! Tyree |
|
From: Nicklas N. <nic...@me...> - 2017-05-10 11:08:41
|
Hello all, We have released BASE 3.11 today. This is a new major release which mostly consists of improvements related to project-specific annotations that was introduced in the previous BASE relase. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.11&group=type&groupdesc=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 |
|
From: Nicklas N. <nic...@me...> - 2017-04-28 11:52:55
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2017-01-31 14:55:23
|
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&group=type&groupdesc=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 |
|
From: Nicklas N. <nic...@me...> - 2016-11-24 07:23:36
|
Hello all, We have released BASE 3.9.2 today. It is mainly a fix for an upgrade problem that may cause an upgrade from BASE 3.7 to BASE 3.8 to fail. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.9.2&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2016-08-23 11:19:14
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Bob M. <r.m...@im...> - 2016-08-08 14:29:24
|
Thank you Nicklas, that works in four steps no problems at all. On Mon, Aug 8, 2016 at 8:42 AM, Nicklas Nordborg <nic...@me... > wrote: > > Upgrading several BASE versions in one go is not really something that > is supported. Usually we only test the update script between one version > and the next. The 119->120 change belongs to BASE 3.5 and it seems like > it fails due to changes that was made in BASE 3.7. > > The BASE versions 3.5, 3.6 and 3.7 all contain several database changes > so I would recommend that at least those upgrades are made one step at a > time. The 3.8 and 3.9 versions are not making any major changes to the > database so I think it should be possible to go directly from 3.7 to 3.9. > > /Nicklas > > > On 2016-08-05 15:28, Bob MacCallum wrote: > > Dear BASE guys, > > > > I got the error below with updatedb.sh > > > > I've had a look at Update.java and I'm afraid the hibernate stuff is > > outside my comfort zone... > > > > Please could you let me any further information you need to diagnose? > > cheers, > > Bob > > > > > > [72%] --Creating platforms... > > [73%] --Creating news... > > [75%] Database initialised successfully. > > [75%] Updating database... > > [75%] --Updating schema version: 118 -> 119... > > [77%] --Updating schema version: 119 -> 120...14:06:22,779 ERROR > > Update:1313 - updateToSchemaVersion120: FAILED > > org.hibernate.exception.SQLGrammarException: could not execute statement > > at > > org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert( > SQLExceptionTypeDelegate.java:63) > > at > > org.hibernate.exception.internal.StandardSQLExceptionConverter.convert( > StandardSQLExceptionConverter.java:42) > > at > > org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert( > SqlExceptionHelper.java:109) > > at > > org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert( > SqlExceptionHelper.java:95) > > at > > org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate( > ResultSetReturnImpl.java:207) > > at > > org.hibernate.engine.query.spi.NativeSQLQueryPlan.performExecuteUpdate( > NativeSQLQueryPlan.java:194) > > at > > org.hibernate.internal.SessionImpl.executeNativeUpdate( > SessionImpl.java:1373) > > at > > org.hibernate.internal.SQLQueryImpl.executeUpdate(SQLQueryImpl.java:373) > > at net.sf.basedb.core.Update.updateToSchemaVersion120( > Update.java:1280) > > at net.sf.basedb.core.Update.updateDatabase(Update.java:465) > > at net.sf.basedb.install.InitDB.main(InitDB.java:86) > > Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: > > Unknown column 'removed' in 'field list' > > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native > Method) > > at > > sun.reflect.NativeConstructorAccessorImpl.newInstance( > NativeConstructorAccessorImpl.java:62) > > > > > > > > ------------------------------------------------------------ > ------------------ > > > > > > > > _______________________________________________ > > The BASE general discussion mailing list > > bas...@li... > > unsubscribe: send a mail with subject "unsubscribe" to > > bas...@li... > > > > > ------------------------------------------------------------ > ------------------ > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... > |
|
From: Nicklas N. <nic...@me...> - 2016-08-08 07:58:24
|
Upgrading several BASE versions in one go is not really something that is supported. Usually we only test the update script between one version and the next. The 119->120 change belongs to BASE 3.5 and it seems like it fails due to changes that was made in BASE 3.7. The BASE versions 3.5, 3.6 and 3.7 all contain several database changes so I would recommend that at least those upgrades are made one step at a time. The 3.8 and 3.9 versions are not making any major changes to the database so I think it should be possible to go directly from 3.7 to 3.9. /Nicklas On 2016-08-05 15:28, Bob MacCallum wrote: > Dear BASE guys, > > I got the error below with updatedb.sh > > I've had a look at Update.java and I'm afraid the hibernate stuff is > outside my comfort zone... > > Please could you let me any further information you need to diagnose? > cheers, > Bob > > > [72%] --Creating platforms... > [73%] --Creating news... > [75%] Database initialised successfully. > [75%] Updating database... > [75%] --Updating schema version: 118 -> 119... > [77%] --Updating schema version: 119 -> 120...14:06:22,779 ERROR > Update:1313 - updateToSchemaVersion120: FAILED > org.hibernate.exception.SQLGrammarException: could not execute statement > at > org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63) > at > org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42) > at > org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109) > at > org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:95) > at > org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:207) > at > org.hibernate.engine.query.spi.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:194) > at > org.hibernate.internal.SessionImpl.executeNativeUpdate(SessionImpl.java:1373) > at > org.hibernate.internal.SQLQueryImpl.executeUpdate(SQLQueryImpl.java:373) > at net.sf.basedb.core.Update.updateToSchemaVersion120(Update.java:1280) > at net.sf.basedb.core.Update.updateDatabase(Update.java:465) > at net.sf.basedb.install.InitDB.main(InitDB.java:86) > Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: > Unknown column 'removed' in 'field list' > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) > at > sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... > |
|
From: Bob M. <r.m...@im...> - 2016-08-05 13:29:01
|
Dear BASE guys,
I got the error below with updatedb.sh
I've had a look at Update.java and I'm afraid the hibernate stuff is
outside my comfort zone...
Please could you let me any further information you need to diagnose?
cheers,
Bob
[72%] --Creating platforms...
[73%] --Creating news...
[75%] Database initialised successfully.
[75%] Updating database...
[75%] --Updating schema version: 118 -> 119...
[77%] --Updating schema version: 119 -> 120...14:06:22,779 ERROR
Update:1313 - updateToSchemaVersion120: FAILED
org.hibernate.exception.SQLGrammarException: could not execute statement
at
org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63)
at
org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:95)
at
org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:207)
at
org.hibernate.engine.query.spi.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:194)
at
org.hibernate.internal.SessionImpl.executeNativeUpdate(SessionImpl.java:1373)
at
org.hibernate.internal.SQLQueryImpl.executeUpdate(SQLQueryImpl.java:373)
at net.sf.basedb.core.Update.updateToSchemaVersion120(Update.java:1280)
at net.sf.basedb.core.Update.updateDatabase(Update.java:465)
at net.sf.basedb.install.InitDB.main(InitDB.java:86)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
Unknown column 'removed' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
|
|
From: Nicklas N. <nic...@me...> - 2016-06-09 12:46:36
|
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&group=type&groupdesc=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 |
|
From: Bob M. <r.m...@im...> - 2016-05-12 11:25:43
|
Thanks Nicklas, Most awesome! On Thu, May 12, 2016 at 12:02 PM, Nicklas Nordborg < nic...@me...> wrote: > On 2016-05-12 12:24, Bob MacCallum wrote: > > Dear BASE developers, > > > > It's really great that Experiments can have annotations now (I know, > > already for several years...). > > > > Would it be possible to add these as configurable columns in Experiment > > list view? > > Yes, it is possible. It should have been included from the start, but > for some reason it was overlooked. > > > I can add the Trac ticket if you remind me privately of the login info. > > I created a ticket: http://base.thep.lu.se/ticket/2005 > > /Nicklas > > > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data > untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... > |
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From: Nicklas N. <nic...@me...> - 2016-05-12 11:03:22
|
On 2016-05-12 12:24, Bob MacCallum wrote: > Dear BASE developers, > > It's really great that Experiments can have annotations now (I know, > already for several years...). > > Would it be possible to add these as configurable columns in Experiment > list view? Yes, it is possible. It should have been included from the start, but for some reason it was overlooked. > I can add the Trac ticket if you remind me privately of the login info. I created a ticket: http://base.thep.lu.se/ticket/2005 /Nicklas |
|
From: Bob M. <r.m...@im...> - 2016-05-12 10:24:50
|
Dear BASE developers, It's really great that Experiments can have annotations now (I know, already for several years...). Would it be possible to add these as configurable columns in Experiment list view? I can add the Trac ticket if you remind me privately of the login info. many thanks, Bob |
|
From: Nicklas N. <nic...@me...> - 2016-04-27 06:34:05
|
Hello all, We have released BASE 3.8 today. This is a new major release which among other things include a major performance improvement in the Annotation batch importer plug-in and several other enhancements related to annotations. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.8&group=type&groupdesc=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 |
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From: Nicklas N. <nic...@me...> - 2016-04-22 12:13:30
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2016-03-07 09:14:21
|
Hello all, We have released BASE 3.7.1 today. This is a bugfix release that fixes a few minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.7.1&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2016-01-11 14:02:42
|
Hello all, We have released BASE 3.7 today. This is a new major release which among other things introduces a 'Kit' item for keeping track of chemicals and other things used in the lab. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.7&group=type&groupdesc=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 |
|
From: Nicklas N. <nic...@me...> - 2015-11-25 10:19:37
|
Hello all, We have released BASE 3.6.3 today. This is a bugfix release that includes a fix for a critical permission issue related to projects and some other minor fixes and improvements. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.6.3&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2015-11-12 08:35:42
|
Hello all, We have released BASE 3.6.2 today. This is a bugfix release that fixes some critical permission issues related to accessing raw data and reporters. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.6.2&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2015-10-19 07:39:56
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Hello all, We have released BASE 3.6.1 today. This is a bugfix release that fixes a critical issue with some JSP files that could not be compiled. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.6.1&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2015-10-08 07:22:29
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Hello all,
We have released BASE 3.6 today. This is a new major release that
has been focused on giving more control over experimental factor values
to the owner of the experiment.
* Experimental factors are now stored as part of the experiment
instead of as part of the raw bioassays. This is useful when
sharing raw data between users and projects.
* It is possible to clone annotations from parent items instead
of just inheriting them. This is useful for protecting downstream
analysis from updates to the original annotations.
Also note that BASE 3.6 now requires Java 8 and Tomcat 8. Java and
Tomcat should be updated before updating BASE.
For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.5&group=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
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