Problems installing gd-ice-3.6.0.war

[Iñaki Sainz de Murieta]

Hi,

I'm trying to run the latest version (gd-ice-3.6.0.war) under glassfish 4.0. I have edited the database connection settings in the $ICE_HOME/WEB-INF/classes/hibernate.cfg.xml file, and seems I made it right because it does start to build the database (it creates 38 tables on my MySQL database). But the application deployment fails at a certain point returning the following error message:

Error occurred during deployment: Exception while loading the app : java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: java.lang.RuntimeException: org.jbei.ice.lib.utils.UtilityException: org.jbei.ice.controllers.common.ControllerException: org.jbei.ice.lib.dao.DAOException: Failed to get Configuration using key: STRAIN_STORAGE_ROOT

Does anybody have any idea what the problem can be or how to continue troubleshooting? Any known problems when using glassfish / mysql?

Thank you very much,

Iñaki.

[Hector Plahar]

Hello,

The project has a new home now at https://github.com/JBEI/ice. The latest version is actually 3.7.1 and you can find the war file on the continuous build system (http://registry-test.jbei.org:8111/) Click "Login as guest" and then artifacts on the master branch. The direct link for 3.7.1 is http://registry-test.jbei.org:8111/viewLog.html?buildId=232&tab=artifacts&buildTypeId=ice_Master.

Try that and see if it helps. Let me know if it doesn't.

Thanks,

Hector

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[Iñaki Sainz de Murieta]

Hi Hector,

Thanks for your quick answer. I have tried with the latest version you have pointed to, but I'm getting exactly the same outcome.

Any idea?

Thanks,

Iñaki.

[Hector Plahar]

I am tied up with another project now but I will try to reproduce it on my end later today. If there is a bug I should be able to issue a patch by tomorrow.

[Hector Plahar]

Unfortunately I was not able to reproduce the error. I was using a postgreSQL db though. I do not have a mySQL db handy just yet.

[Iñaki Sainz de Murieta]

Does it mean I should stick to using postgreSQL with ICE? Or can we expect MySQL support in near future?

[Hector Plahar]

MySQL support will be coming soon. I cannot give an accurate time estimate as to when to expect it though.

[Iñaki Sainz de Murieta]

Hi again,

Before the MySQL support arrives, I have tried to deploy the application using HSQLDB (under glassfish 4.0.), as it seems to be the default database engine for ICE. It keeps failing, with the following message:

Error occurred during deployment: Exception while loading the app : java.lang.IllegalStateException: ContainerBase.addChild: start: org.apache.catalina.LifecycleException: java.lang.RuntimeException: org.hibernate.AssertionFailure: null id in org.jbei.ice.lib.models.Storage entry (don't flush the Session after an exception occurs). Please see server.log for more details.

The settings I have changed in the configuration file $ICE_HOME/WEB-INF/classes/hibernate.cfg.xml must be correct, because it seems to connect to the database and starts to create some tables.

Any advice?

Thanks,

Iñaki.

[Hector Plahar]

I just issued a fix that should address this. (3.7.3). Let me know if you still have issues. The build system might take a couple of minutes to build the artifacts for that release (http://registry-test.jbei.org:8111/)

Thanks,

Hector.

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[Iñaki Sainz de Murieta]

Hi,

Now it works fine. Thank you very much.

Regards,

Iñaki.

PS. Please let me know after you publish a version compatible with MySQL.

[Iñaki Sainz de Murieta]

Hi again,

Question on BLAST: I've red at the end of this post that BLAST+ should be supported as of version 3.4. However, the ICE-JBEI installation page still asks to stick to the legacy BLAST. Which link should be the most up to date?

I'm also interested on how ICE-JBEI interacts with BLAST. Does it directly access the PostgreSQL / HSQLDB database, or rather keeping a parallel custom blast database with the DNA sequences information?

Thank you very much,

Iñaki.

[Hector Plahar]

The installation page is very outdated. I hope to have a new version up soon. BLAST+ is supported not legacy BLAST. You can download the BLAST+ package and point to the bin directory on the admin settings page.

The system maintains a separate blast database in a data directory also specified on the admin settings page.