Open Microscopy Environment

Hello,

I'm a developer with the CellProfiler project looking to add an OMERO interface to CellProfiler 2.0. Someone at OME was kind enough to set me up with an account on the demo server, but I sense that I will need to be running a server of my own in order to really play with the OMERO Python API. Unfortunately, I'm having an extremely difficult time trying to setup OMERO server on my machine. Here goes:

Platform:
Mac OS X 10.5, 32bit Intel

Currently installed:
OMERO clients Beta 4.2.2
Ice-3.3.1 (via binary)
Ice Python extension (built from source)
PostgreSQL 8.3.10 server (via macports)
Java 1.6.0_03-p3
Python 2.5.4

Following the instructions on http://www.openmicroscopy.org/site/supp ... stallation get me to the point where I can start the server, and yet I am unable to actually connect to it via OMERO.insight or by using the Python API:

Code: Select all

>>> import omero
>>> c = omero.client()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/afraser/Desktop/omero/lib/python/omero/__init__.py", line 23, in client
    return omero.clients.BaseClient(*args, **kwargs)
  File "/Users/afraser/Desktop/omero/lib/python/omero/clients.py", line 122, in __init__
    self._initData(id)
  File "/Users/afraser/Desktop/omero/lib/python/omero/clients.py", line 224, in _initData
    self.__ic = Ice.initialize(id)
  File "/opt/Ice-3.3/python/Ice.py", line 340, in initialize
    communicator = IcePy.Communicator(args, data)
Ice.EndpointParseException: exception ::Ice::EndpointParseException
{
    str = ssl  -p 4064 -h <"omero.host" not set>
}
>>>

Where can I set omero.host?

Also in omero.properties, I have:

Code: Select all

omero.db.host=localhost
omero.db.port=5432
omero.db.name=omero
omero.db.user=omero
omero.db.pass=omero

Isn't this the information that I should set in Insight when logging in? When I try to use these settings I get "Failed to log onto OMERO. Please check the port or try again later."... I also tried port 4064 and 4080 Previously I was getting password errors, so it seems that I've taken a step backward somehow.

Any help would be much appreciated.
-Adam

Okay so I did a grep for omero.host and found a file ~/Desktop/omero/lib/etc/ice.config with:

Code: Select all

omero.host=localhost

My guess is that this is where ice should be looking for omero.host, but it doesn't seem to be.

Oh, I should also add that I have the following at the end of my .bash_profile:

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# Postgres
export PATH=/opt/local/lib/postgresql83/bin/:$PATH
alias pgstart="sudo su postgres -c 'pg_ctl -D /Users/afraser/postgres -l /Users/afraser/postgres
/logfile start'"
alias pgstop="sudo su postgres -c 'pg_ctl -D /Users/afraser/postgres stop -m fast'"
alias pgstatus="sudo su postgres -c 'pg_ctl status -D /Users/afraser/postgres'"

# Ice
export ICE_HOME=/opt/Ice-3.3
export PATH=$PATH:$ICE_HOME/bin
export PYTHONPATH=$ICE_HOME/python:$PYTHONPATH
export DYLD_LIBRARY_PATH=$ICE_HOME/lib:$DYLD_LIBRARY_PATH

# OMERO
export PYTHONPATH=/Users/afraser/Desktop/omero/lib/python:$PYTHONPATH


Hi Adam,

afraser wrote:I'm a developer with the CellProfiler project looking to add an OMERO interface to CellProfiler 2.0.

This is great news, there has certainly been a good deal of interest from our users to have the CellProfiler interface upgraded from 1.x to 2.x.

Code: Select all

using the Python API:

>>> import omero
>>> c = omero.client()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/afraser/Desktop/omero/lib/python/omero/__init__.py", line 23, in client
    return omero.clients.BaseClient(*args, **kwargs)
  File "/Users/afraser/Desktop/omero/lib/python/omero/clients.py", line 122, in __init__
    self._initData(id)
  File "/Users/afraser/Desktop/omero/lib/python/omero/clients.py", line 224, in _initData
    self.__ic = Ice.initialize(id)
  File "/opt/Ice-3.3/python/Ice.py", line 340, in initialize
    communicator = IcePy.Communicator(args, data)
Ice.EndpointParseException: exception ::Ice::EndpointParseException
{
    str = ssl  -p 4064 -h <"omero.host" not set>
}
>>>

Where can I set omero.host?


You can set the host directly on the client object if you'd like:

Code: Select all

client = omero.client("localhost")


To use a configuration file (as outlined in etc/ice.config), you'll need to either set ICE_HOME in your environment, or pass ["--Ice.Config=your_config_file"] to the omero.client constructor.

However, if you're also not having luck logging in with Insight, then none of these code changes will make much difference. Could you possibly send us the output of:

Code: Select all

bin/omero admin diagnostics


Thanks,
~Josh

Josh,

Thanks for your reply.

This is great news, there has certainly been a good deal of interest from our users to have the CellProfiler interface upgraded from 1.x to 2.x.

I'm glad to hear this, and would be very interested to hear if there are any suggestions for improving upon the interface. It would be very helpful if I could speak/chat with someone who could help me better understand OMERO and where it has potential for a CP interface.

As for my questions: using omero.client('localhost') got me one step further, but I'm now apparently running into permissions issues when trying to create a session:

Code: Select all

>>> client.createSession('omero', 'omero')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/afraser/Desktop/omero/lib/python/omero/clients.py", line 443, in createSession
    prx = self.getRouter(self.__ic).createSession(username, password, ctx)
  File "/opt/Ice-3.3/python/Glacier2_Router_ice.py", line 107, in createSession
    return _M_Glacier2.Router._op_createSession.invoke(self, ((userId, password), _ctx))
Glacier2.PermissionDeniedException: exception ::Glacier2::PermissionDeniedException
{
    reason = internal server error
}

Here are some possibly relevant permissions:

Code: Select all

afraser$ ls -al /OMERO/
total 0
drwxr-xr-x   3 afraser  admin   102 Jan 14 13:56 .
drwxrwxr-t  40 root     admin  1428 Jan 14 13:46 ..
drwxr-xr-x   4 afraser  admin   136 Jan 14 13:56 FullText

afraser$ ls -al ~/Desktop/omero
total 536
drwxr-xr-x@ 12 afraser  CHARLES\domain users     408 Jan 14 13:50 .
drwx------+ 19 afraser  CHARLES\domain users     646 Jan 18 07:22 ..
... trimmed ...
-rw-r--r--   1 afraser  CHARLES\domain users  243192 Jan 14 13:50 OMERO4.2__0.sql
drwxr-xr-x@  6 afraser  CHARLES\domain users     204 Dec  6 05:16 bin
drwxr-xr-x@  3 afraser  CHARLES\domain users     102 Dec  6 05:16 docs
drwxr-xr-x@ 22 afraser  CHARLES\domain users     748 Dec  6 05:16 etc
drwxr-xr-x@  5 afraser  CHARLES\domain users     170 Jan 14 10:36 include
drwxr-xr-x@  9 afraser  CHARLES\domain users     306 Dec  6 05:16 lib
drwxr-xr-x@  6 afraser  CHARLES\domain users     204 Dec  6 05:16 sql
drwxr-xr-x   5 afraser  CHARLES\domain users     170 Jan 14 13:55 var

afraser$ ls -al /opt/Ice-3.3.1/
total 264
drwxr-xr-x@  17 afraser  CHARLES\domain users    578 Jan  6 16:02 .
drwxr-xr-x    7 root     wheel                   238 Jan  7 13:29 ..
... trimmed ...
drwxr-xr-x@  37 afraser  CHARLES\domain users   1258 Mar 23  2009 bin
drwxr-xr-x@   8 afraser  CHARLES\domain users    272 Mar 23  2009 config
drwxr-xr-x@  14 afraser  CHARLES\domain users    476 Jan  6 16:09 include
drwxr-xr-x@  49 afraser  CHARLES\domain users   1666 Mar 23  2009 lib
drwxr-xr-x@ 109 afraser  CHARLES\domain users   3706 Jan 10 11:30 python
drwxr-xr-x@  10 afraser  CHARLES\domain users    340 Jan  6 16:09 slice

afraser$ ls -al /opt/local/lib/postgresql83
total 10472
drwxr-xr-x   59 root  admin     2006 Dec 13 12:26 .
... trimmed ...

Here's the diagnostics output:

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afraser$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
       
Commands:   java -version                  1.6.0     (/Users/afraser/soylatte/bin/java -- 2 others)
Commands:   python -V                      2.5.4     (/Library/Frameworks/Python.framework/Versions/Current/bin/python -- 2 others)
Commands:   icegridnode --version          3.3.1     (/opt/Ice-3.3/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/opt/Ice-3.3/bin/icegridadmin)
Commands:   psql --version                 8.3.10    (/opt/local/lib/postgresql83/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        inactive (disabled)
Server:     DropBox                        inactive (disabled)
Server:     FileServer                     active (pid = 80861, enabled)
Server:     Indexer-0                      inactive (disabled)
Server:     MonitorServer                  inactive (disabled)
Server:     OMERO.Glacier2                 active (pid = 80865, enabled)
Server:     OMERO.IceStorm                 active (pid = 80868, enabled)
Server:     Processor-0                    activating (enabled)
Server:     Repository-1                   error: node `repo' couldn't be reached:
the node is not active
Server:     Tables-0                       inactive (disabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /Users/afraser/Desktop/omero/var/log exists

Log files:  Blitz-0.log                    50.0 KB       errors=3    warnings=4   
Log files:  DropBox.log                    4.0 KB        errors=6    warnings=3   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  45.0 KB       errors=2    warnings=13 
Log files:  MonitorServer.log              1.0 KB        errors=2    warnings=0   
Log files:  OMEROweb.log                   0.0 KB       
Log files:  Processor-0.log                477.0 KB      errors=134  warnings=938
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     1.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.58 MB

Parsing Blitz-0.log:[line:104] Did you create your omero.data.dir? E.g. /OMERO

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/opt/local/lib/postgresql83/bin/:/opt/local/bin:/opt/local/sbin:/Users/afraser/soylatte/bin:/opt/subversion/bin:/Library/Frameworks/Python.framework/Versions/Current/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/mysql/bin:/opt/Ice-3.3/bin
Environment:ICE_HOME=/opt/Ice-3.3         
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=/opt/Ice-3.3/lib:

OMERO data dir: '/OMERO'   Exists? True   Is writable? True
OMERO.web status... [NOT STARTED]


Regarding specifying a config file: At this point, I'm pretty much interested only in running with defaults so I can get up and running. However, I do have ICE_HOME set (mentioned in my first post). So would I have to copy ~/Desktop/omero/lib/etc/ice.config to ICE_HOME and modify it from there?

...sorry to dump so much info, I've been banging my head against this for too long. Just getting Ice and Ice Python installed took me ages. I'm dying to start hacking at the API. Speaking of which, are there any example datasets that I could play with?

Thanks again for your attention,
Adam

Hey Adam,

afraser wrote:I'm glad to hear this, and would be very interested to hear if there are any suggestions for improving upon the interface. It would be very helpful if I could speak/chat with someone who could help me better understand OMERO and where it has potential for a CP interface.

Sure. Do you have any timeline/documentation on your current plans?

{
reason = internal server error
}

So, this basically means your server's not working. Looking below...

Here's the diagnostics output:

Code: Select all

afraser$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta4.2.2-r8718-Beta4.2-b56
================================================================================
       
Commands:   java -version                  1.6.0     (/Users/afraser/soylatte/bin/java -- 2 others)
Commands:   python -V                      2.5.4     (/Library/Frameworks/Python.framework/Versions/Current/bin/python -- 2 others)
Commands:   icegridnode --version          3.3.1     (/opt/Ice-3.3/bin/icegridnode)
Commands:   icegridadmin --version         3.3.1     (/opt/Ice-3.3/bin/icegridadmin)
Commands:   psql --version                 8.3.10    (/opt/local/lib/postgresql83/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        inactive (disabled)
...
Log dir:    /Users/afraser/Desktop/omero/var/log exists

Log files:  Blitz-0.log                    50.0 KB       errors=3    warnings=4 
...


The main Java service, Blitz, did not start properly. Could you possibly attach the var/log/Blitz-0.log file (which has 3 errors in it)?

Regarding specifying a config file: At this point, I'm pretty much interested only in running with defaults so I can get up and running. However, I do have ICE_HOME set (mentioned in my first post). So would I have to copy ~/Desktop/omero/lib/etc/ice.config to ICE_HOME and modify it from there?

That shouldn't be necessary. The only configuration that is necessary is omero.host, omero.user and omero.pass. When working from Python, this suffices:

Code: Select all

import omero
c = omero.client(omero_host)
s = c.createSession(omero_user, omero_pass);


...sorry to dump so much info, I've been banging my head against this for too long. Just getting Ice and Ice Python installed took me ages. I'm dying to start hacking at the API. Speaking of which, are there any example datasets that I could play with?

No worries, it's what we're here for. If you have any specific issues with Ice, we'd certainly like to hear them. Just be sure to let us know which OS, etc.

As for datasets, there aren't any downloads at the moment, since typically people are bringing their data to us. But I'll bring it up at our next team meeting and let you know.

Cheers,
~Josh.

Sure. Do you have any timeline/documentation on your current plans?

Sure thing, I just sent you a PM with details.

As for datasets, there aren't any downloads at the moment, since typically people are bringing their data to us. But I'll bring it up at our next team meeting and let you know.

Hrm, that's unfortunate. Not only would example data be massively helpful for me, it would probably be helpful for first time users who want to get a feel for how the system works and what they can use it for.

Anyway, here's Blitz-0.log:

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2011-01-14 13:56:26,491 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2011-01-14 13:56:37,515 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2011-01-14 13:56:53,204 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2011-01-14 13:56:53,257 WARN  [ate.search.store.DirectoryProviderHelper] (      main) Index directory not found, creating: '/OMERO/FullText'
2011-01-14 13:56:53,260 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2011-01-14 13:56:53,285 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:/Users/afraser/Desktop/omero/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:/Users/afraser/Desktop/omero/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:/Users/afraser/Desktop/omero/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:/Users/afraser/Desktop/omero/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:/Users/afraser/Desktop/omero/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(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   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: /OMERO/FullText for index FullText
   at org.hibernate.search.store.DirectoryProviderHelper.makeSanityCheckedDirectory(DirectoryProviderHelper.java:117)
   at org.hibernate.search.store.DirectoryProviderHelper.getVerifiedIndexDir(DirectoryProviderHelper.java:102)
   at org.hibernate.search.store.FSDirectoryProvider.initialize(FSDirectoryProvider.java:40)
   at org.hibernate.search.store.DirectoryProviderFactory.createDirectoryProvider(DirectoryProviderFactory.java:129)
   ... 82 more
2011-01-18 11:53:47,516 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2011-01-18 11:53:51,406 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2011-01-18 11:53:59,423 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Found location in errorTimes: -1
2011-01-18 11:53:59,423 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Removing 0 from errorTimes
2011-01-18 11:53:59,423 WARN  [ome.services.db.SelfCorrectingDataSource] (      main) Registering error with list: Current size: 0
2011-01-18 11:53:59,423 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Sleeping for 0 then retry: 1
2011-01-18 11:53:59,424 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Found location in errorTimes: -1
2011-01-18 11:53:59,424 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Removing 0 from errorTimes
2011-01-18 11:53:59,424 WARN  [ome.services.db.SelfCorrectingDataSource] (      main) Registering error with list: Current size: 1
2011-01-18 11:53:59,424 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Sleeping for 1000 then retry: 2
2011-01-18 11:54:00,426 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Found location in errorTimes: -1
2011-01-18 11:54:00,426 INFO  [ome.services.db.SelfCorrectingDataSource] (      main) Removing 0 from errorTimes
2011-01-18 11:54:00,426 WARN  [ome.services.db.SelfCorrectingDataSource] (      main) Registering error with list: Current size: 2
2011-01-18 11:54:00,442 ERROR [ome.services.db.SelfCorrectingDataSource] (      main) Failed to acquire connection after retries=3
java.sql.SQLException: unable to get a connection from pool of a PoolingDataSource containing an XAPool of resource 70d1e0d0-980d-4581-9094-aa027a8c5576 with 0 connection(s) (0 still available)
   at bitronix.tm.resource.jdbc.PoolingDataSource.getConnection(PoolingDataSource.java:109)
   at org.springframework.jdbc.datasource.DelegatingDataSource.getConnection(DelegatingDataSource.java:83)
   at ome.services.db.SelfCorrectingDataSource.call(SelfCorrectingDataSource.java:102)
   at ome.services.db.SelfCorrectingDataSource.callWithRetries(SelfCorrectingDataSource.java:75)
   at ome.services.db.SelfCorrectingDataSource.getConnection(SelfCorrectingDataSource.java:59)
   at org.springframework.jdbc.datasource.DataSourceUtils.doGetConnection(DataSourceUtils.java:113)
   at org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy$TransactionAwareInvocationHandler.invoke(TransactionAwareDataSourceProxy.java:214)
   at $Proxy46.getMetaData(Unknown Source)
   at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:116)
   at org.hibernate.cfg.Configuration.buildSettingsInternal(Configuration.java:2163)
   at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2159)
   at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1383)
   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)
   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)
   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)
   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(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
   at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:107)
   at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:273)
   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)
   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)
   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: java.sql.SQLException: unable to connect to non-XA resource org.postgresql.Driver
   at bitronix.tm.resource.jdbc.lrc.LrcXADataSource.getXAConnection(LrcXADataSource.java:82)
   at bitronix.tm.resource.jdbc.PoolingDataSource.createPooledConnection(PoolingDataSource.java:167)
   at bitronix.tm.resource.common.XAPool.createPooledObject(XAPool.java:200)
   at bitronix.tm.resource.common.XAPool.grow(XAPool.java:310)
   at bitronix.tm.resource.common.XAPool.getInPool(XAPool.java:289)
   at bitronix.tm.resource.common.XAPool.getConnectionHandle(XAPool.java:72)
   at bitronix.tm.resource.common.XAPool.getConnectionHandle(XAPool.java:58)
   at bitronix.tm.resource.jdbc.PoolingDataSource.getConnection(PoolingDataSource.java:105)
   ... 83 more
Caused by: org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
   at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123)
   at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
   at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:124)
   at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
   at org.postgresql.jdbc3.Jdbc3Connection.<init>(Jdbc3Connection.java:24)
   at org.postgresql.Driver.makeConnection(Driver.java:386)
   at org.postgresql.Driver.connect(Driver.java:260)
   at bitronix.tm.resource.jdbc.lrc.LrcXADataSource.getXAConnection(LrcXADataSource.java:79)
   ... 90 more
Caused by: java.net.ConnectException: Connection refused
   at java.net.PlainSocketImpl.socketConnect(Native Method)
   at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
   at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
   at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
   at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
   at java.net.Socket.connect(Socket.java:519)
   at java.net.Socket.connect(Socket.java:469)
   at java.net.Socket.<init>(Socket.java:366)
   at java.net.Socket.<init>(Socket.java:180)
   at org.postgresql.core.PGStream.<init>(PGStream.java:62)
   at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:77)
   ... 97 more
2011-01-18 11:54:00,447 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2011-01-18 11:54:00,448 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:/Users/afraser/Desktop/omero/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:/Users/afraser/Desktop/omero/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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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:/Users/afraser/Desktop/omero/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:/Users/afraser/Desktop/omero/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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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:/Users/afraser/Desktop/omero/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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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(NativeConstructorAccessorImpl.java:39)
   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
   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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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 ome.conditions.DatabaseBusyException: Cannot acquire connection
   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$1.getObject(AbstractBeanFactory.java:290)
   at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
   at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:287)
   at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:189)
   at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
   ... 59 more
Caused by: ome.conditions.DatabaseBusyException: Cannot acquire connection
   at ome.services.db.SelfCorrectingDataSource.callWithRetries(SelfCorrectingDataSource.java:91)
   at ome.services.db.SelfCorrectingDataSource.getConnection(SelfCorrectingDataSource.java:59)
   at org.springframework.jdbc.datasource.DataSourceUtils.doGetConnection(DataSourceUtils.java:113)
   at org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy$TransactionAwareInvocationHandler.invoke(TransactionAwareDataSourceProxy.java:214)
   at $Proxy46.getMetaData(Unknown Source)
   at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:116)
   at org.hibernate.cfg.Configuration.buildSettingsInternal(Configuration.java:2163)
   at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2159)
   at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1383)
   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


Hopefully this makes the problem a little clearer.

Thanks,
-Adam

Hi Adam,

Speaking of which, are there any example datasets that I could play with?

You should be able to import any of these datasets into OMERO:

http://loci.wisc.edu/software/sample-data

The "Mouse kidney" dataset in particular might be a good one to try, as it has more acquisition metadata than the others.

Regards,
-Melissa

Ah ha! Thanks so much Melissa! This should make life much easier once I resolve these server issues. ^_^

Y'know, I completely forgot that Curtis mentioned having this data back in November.

Hey Adam. Another thing I forgot to mention during our call is that I can get you sample SPW data, in various proprietary formats, if you wish. Just let me know.

...do you know what SPW stands for?

Hi Adam,

Hey Adam. Another thing I forgot to mention during our call is that I can get you sample SPW data, in various proprietary formats, if you wish. Just let me know.

...do you know what SPW stands for?

"Screen-Plate-Well", which is just OME terminology for high-content screening (HCS) data.

-Melissa

afraser wrote:Anyway, here's Blitz-0.log:

Code: Select all

2011-01-14 13:56:26,491 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
Caused by: java.sql.SQLException: unable to connect to non-XA resource org.postgresql.Driver
   at bitronix.tm.resource.jdbc.lrc.LrcXADataSource.getXAConnection(LrcXADataSource.java:82)
   at bitronix.tm.resource.jdbc.PoolingDataSource.createPooledConnection(PoolingDataSource.java:167)
   at bitronix.tm.resource.common.XAPool.createPooledObject(XAPool.java:200)
   at bitronix.tm.resource.common.XAPool.grow(XAPool.java:310)
   at bitronix.tm.resource.common.XAPool.getInPool(XAPool.java:289)
   at bitronix.tm.resource.common.XAPool.getConnectionHandle(XAPool.java:72)
   at bitronix.tm.resource.common.XAPool.getConnectionHandle(XAPool.java:58)
   at bitronix.tm.resource.jdbc.PoolingDataSource.getConnection(PoolingDataSource.java:105)
   ... 83 more
Caused by: org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections.
   at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123)
   at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
   at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:124)
   at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
   at org.postgresql.jdbc3.Jdbc3Connection.<init>(Jdbc3Connection.java:24)
   at org.postgresql.Driver.makeConnection(Driver.java:386)
   at org.postgresql.Driver.connect(Driver.java:260)
   at bitronix.tm.resource.jdbc.lrc.LrcXADataSource.getXAConnection(LrcXADataSource.java:79)
   ... 90 more
Caused by: java.net.ConnectException: Connection refused
   at java.net.PlainSocketImpl.socketConnect(Native Method)
   at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
   at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
   at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
   at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
   at java.net.Socket.connect(Socket.java:519)
   at java.net.Socket.connect(Socket.java:469)
   at java.net.Socket.<init>(Socket.java:366)
   at java.net.Socket.<init>(Socket.java:180)
   at org.postgresql.core.PGStream.<init>(PGStream.java:62)
   at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:77)
   ... 97 more


Hopefully this makes the problem a little clearer.

Thanks,
-Adam

Definitely. Looks like your PostgreSQL configuration is not working correctly. Can you use the values from

Code: Select all

bin/omero config get | grep omero.db

to connect? Something like

Code: Select all

psql -h somehost -U someuser somedb -l

? If not, you'll probably need to either configure PostgreSQL for TCP connections or for your preferred authentication. See https://www.openmicroscopy.org/site/support/omero4/server/postgresql for more information.

Cheers,
~Josh