Open Microscopy Environment

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

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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.

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.

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

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,

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

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

Cheers

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

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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

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

Wow, I just found the problem!

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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...

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

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...
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,