Open Microscopy Environment

Hi,
The instructions about changing the binary repository location refer you to the instructions on reconfiguration which must be performed after any changes are made to property files. Is this reconfiguration step still necessary? If so, can someone explain how and where to perform this for a Windows installation? The reconfiguration commands don't make much sense to me:

Code: Select all

export JBOSS_HOME=~/Desktop/omero-3.0-Beta2.3/jboss-4.2.1.GA
java omero deploy

Thanks

As the page indicates at the top, that is legacy documentation for Beta3.2. Have you looked at the page on the main OME website linked from that Trac page?

http://www.openmicroscopy.org/site/supp ... repository

Oh, I should have noticed that large "3.2 ONLY" at the top of the page.
In my defence, I was taken to that page from the current Windows installation instructions.

If you have chosen a non-standard OmeroBinaryRepository location above, be sure to configure the omero.data.dir property. When using C:\ style file paths it is necessary to "escape" the backslashes. For example:

Thanks

Ah, thanks for pointing that out! Links have been fixed on both the install pages.

I've finally had a go at moving the binary repository but have run into trouble.
After stopping the omero server, setting the new location and moving the repository contents there, the server doesn't start again from the "omero admin start" command - it times out after 5 minutes. OMERO.master is shown as started in Windows Services but I can't connect with a client.

I'm trying to move the repository from the default location to a mapped network drive for which the logged in user (domain account with local admin rights) has full control security permissions. Moving the repository back to the default location gets everything working again. Do I need to change the "Log on As" settings for the omero service so that it can access the mapped drive or something like that?
Thanks

In order to debug that we'll need the output of bin/omero config get and the contents of var/log/Blitz-0.log.

Hi
I noticed that a couple of typos I made whilst trying to enter the omero config set omero.data.dir command ended up in etc\grid\config.xml but I've tidied them up and now omero config get returns (amongst other things e.g. my ldap settings)

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omero.data.dir=R:\\OMERO

I've moved the contents of the original repository location at c:\OMERO to that folder.

This is the log file of the most recent attempt to start the server

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2010-09-01 15:16:47,586 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2010-09-01 15:16:50,148 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2010-09-01 15:16:53,318 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2010-09-01 15:16:53,350 WARN  [ate.search.store.DirectoryProviderHelper] (      main) Index directory not found, creating: 'R:\OMERO'
2010-09-01 15:16:53,350 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2010-09-01 15:16:53,350 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:/C:/omero_dist/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:/C:/omero_dist/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: could not init listeners
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:409)
   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)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/C:/omero_dist/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:/C:/omero_dist/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: could not init listeners
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:586)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
   at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048)
   at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397)
   ... 3 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'ome.server' defined in URL [jar:file:/C:/omero_dist/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: could not init listeners
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:281)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 16 more
Caused by: 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: could not init listeners
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141)
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273)
   ... 25 more
Caused by: 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: could not init listeners
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1308)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1067)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:562)
   at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:871)
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:423)
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
   at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:105)
   at ome.system.OmeroContext.<init>(OmeroContext.java:98)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
   at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
   at java.lang.reflect.Constructor.newInstance(Unknown Source)
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
   ... 27 more
Caused by: 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: could not init listeners
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
   at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:600)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:140)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:984)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:888)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:479)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 47 more
Caused by: 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: could not init listeners
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1403)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:450)
   at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 59 more
Caused by: org.hibernate.HibernateException: could not init listeners
   at org.hibernate.event.EventListeners.initializeListeners(EventListeners.java:205)
   at org.hibernate.cfg.Configuration.getInitializedEventListeners(Configuration.java:1396)
   at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1385)
   at org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:954)
   at org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:855)
   at org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:774)
   at org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:211)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1460)
   at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1400)
   ... 66 more
Caused by: org.hibernate.search.SearchException: Unable to initialize: FullText
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProvider(DirectoryProviderFactory.java:132)
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProviders(DirectoryProviderFactory.java:63)
   at org.hibernate.search.impl.SearchFactoryImpl.initDocumentBuilders(SearchFactoryImpl.java:404)
   at org.hibernate.search.impl.SearchFactoryImpl.<init>(SearchFactoryImpl.java:119)
   at org.hibernate.search.event.ContextHolder.getOrBuildSearchFactory(ContextHolder.java:30)
   at org.hibernate.search.event.FullTextIndexEventListener.initialize(FullTextIndexEventListener.java:79)
   at org.hibernate.event.EventListeners$1.processListener(EventListeners.java:198)
   at org.hibernate.event.EventListeners.processListeners(EventListeners.java:181)
   at org.hibernate.event.EventListeners.initializeListeners(EventListeners.java:194)
   ... 74 more
Caused by: org.hibernate.search.SearchException: Unable to create index directory: R:\OMERO for index FullText
   at org.hibernate.search.store.DirectoryProviderHelper.makeSanityCheckedDirectory(DirectoryProviderHelper.java:117)
   at org.hibernate.search.store.DirectoryProviderHelper.getVerifiedIndexDir(DirectoryProviderHelper.java:100)
   at org.hibernate.search.store.FSDirectoryProvider.initialize(FSDirectoryProvider.java:40)
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProvider(DirectoryProviderFactory.java:129)
   ... 82 more


Ahar,

the OMERO server logs on as "LocalService" unless you change the "Log on as" settings. If the permissions of "R:\\OMERO" require it, do try changing this and restarting OMERO.master.

Let us know how things go.
~Josh

Hi,
I changed the "Log on as" to the user with full control over the mapped network drive but it didn't make a difference. The server only worked with the repository on the C: drive.

Can you check if the "Log on as" value stuck? The value may have gotten reset by a subsequent call to bin\omero admin start. If that is the case, to make sure the value sticks, it's necessary to set "omero.windows.user". An example of this is in the QUICKSTART.bat:

http://trac.openmicroscopy.org.uk/omero/browser/trunk/docs/QUICKSTART.bat#L96

This is similar to passing -u "username" to bin\omero admin start. However, the use of the parameter is closely tied to your rights, and so it may require some back and forth before we get it to work.

If possible, include the output from the console if you have any trouble getting it to work.

If the "Log on as" value is as you expect, are you getting the same error as before?

Cheers,
~Josh.