Instalation problems - omero 4.1.1 (Blitz errors)

[rubenalves]

Hi everyone,
I've got that tricky info/error messages on my Blitz log:

Code: Select all

2009-12-10 19:24:12,359 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2009-12-10 19:24:12,425 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2009-12-10 19:24:12,430 ERROR [                ome.services.blitz.Entry] (      main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/RAID/omero_4.1.1/lib/server/blitz.jar!/beanRefContext.xml]: Cannot resolve reference to bean 'ome.server' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/RAID/omero_4.1.1/lib/server/server.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionManager' defined in class path resource [ome/services/sec-primitives.xml]: Cannot resolve reference to bean 'executor' while setting bean property 'executor'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'executor' defined in class path resource [ome/services/services.xml]: Cannot resolve reference to bean 'sessionFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [ome/services/hibernate.xml]: Invocation of init method failed; nested exception is org.hibernate.HibernateException: Unable to initialize: FullText
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:410)
   at ome.system.OmeroContext.getInstance(OmeroContext.java:203)
   at ome.services.blitz.Entry.start(Entry.java:203)
   at ome.services.blitz.Entry.main(Entry.java:121)



Did someone understand that kind of error? I just don't get it - Did someone can help me to follow a new way to solve this problem.

[cxallan]

Hi Ruben,

This implies one simple error but I'll need to see the entire log please. You can attach it here compressed if that's easiest.

[jmoore]

My guess would be that the directory pointed to by the "omero.data.dir" configuration property doesn't exist.

[rubenalves]

Back to "war" against that server!
I've been a little busy at work (and xmas things...), but now I'm back with this OMERO server.
Thanks to both of you for your help. Let's see...

@cxallan: Do you want something specific? Or all the startup logs are just fine?
@jmoore: I've just checked the "omero.data.dir" property, everything seems OK.
-> omero.data.dir=/RAID0/omero_4.1.1/REPOSITORIES/

Cheers,

[jmoore]

Blitz-0.log would be a good place to start.

[rubenalves]

Hello, thanks for your fast reply.
I've uploaded the Blitz-0.log like you said.

Cheers

[jmoore]

At the end of your log there's this error:

Code: Select all

Caused by: org.hibernate.search.SearchException: Cannot write into index directory: /RAID/omero_4.1.0/


which says the server is trying to find a different omero.data.dir directory from the one you mentioned ("/RAID0/omero_4.1.1/...") . Did you move the directory? Where did you change the configuration to point to ".../4.1.1/..."? i.e. are you using "bin/omero config set" or modifying "default.xml"?

Hope that's of use.
~Josh

[rubenalves]

So strange... in fact I've begun my journey in with this new version of Omero 4 few days before the 4.1.1. After installing all (compiling Ice etc...), I've moved 4.1.0 to 4.1.1 by removing everything and installing a fresh new 4.1.1
I can't explain this error .... Is the Blitz configuration outside the omero folder?

Cheers

[rubenalves]

Wow, I just found the problem!

Code: Select all

root@omero:/home/omero/.java/.userPrefs/omero/prefs/default# cat prefs.xml
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE map SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<map MAP_XML_VERSION="1.0">
  <entry key="omero.data.dir" value="/RAID/omero_4.1.0/"/>
  <entry key="omero.db.name" value="omero_psql"/>
  <entry key="omero.db.pass" value="myClearPassword"/>
  <entry key="omero.db.user" value="omero_db_user"/>
</map>
root@omero:/home/omero/.java/.userPrefs/omero/prefs/default#


Let's remove this, and try again...
note: I'm really surprised to see my PostgreSQL password in this XML file...

[rubenalves]

And the problem continues...
It seems that it should be a error between Blitz and Postgres. If configured omero.properties like this:

Code: Select all

...
omero.db.authority=export.openmicroscopy.org
omero.db.version=OMERO4.1
omero.db.patch=0
omero.db.host=localhost
omero.db.port=5432
omero.db.name=omero_psql
omero.db.user=omero_db_user
omero.db.pass=myClearPassword
omero.db.poolsize=10
omero.db.driver=org.postgresql.Driver
omero.db.dialect=org.hibernate.dialect.PostgreSQLDialect
omero.security.filter.bitand=(int8and(permissions,%s) = %s)
omero.security.password_provider=chainedPasswordProvider
omero.security.default_permissions=rw----
....


By the way, I've uploaded the new Blitz-0.log.

Cheers,