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Installation on Ubuntu 10.04

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The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.
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Installation on Ubuntu 10.04

Postby Ivo » Thu Jun 10, 2010 11:08 am

I have some Problems to start the Omero-Server.
It gives me a message like that:

~/Desktop/omero$ bin/omero admin start

No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................Failed to startup after 5 minutes

And here is the result of the diagnostic file:

~/Desktop/omero$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (/usr/bin/java)
Commands: python -V 2.6.5 (/usr/bin/python)
Commands: icegridnode --version 3.3.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.3.1 (/usr/bin/icegridadmin)
Commands: psql --version 8.4.4 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 inactive (disabled)
Server: DropBox inactive (disabled)
Server: FSServer active (pid = 11207, enabled)
Server: Indexer-0 inactive (disabled)
Server: OMERO.Glacier2 active (pid = 11211, enabled)
Server: OMERO.IceStorm active (pid = 11213, enabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Server: Web inactive (enabled)

Log dir: /home/~/Desktop/omero/var/log exists

Log files: Blitz-0.log 174.0 KB errors=8 warnings=16
Log files: DropBox.log 5.0 KB errors=8 warnings=4
Log files: FSServer.log 1.0 KB
Log files: Indexer-0.log 149.0 KB errors=8 warnings=16
Log files: OMEROweb.log 0.0 KB
Log files: OMEROweb.log.2010-06-10 0.0 KB
Log files: Processor-0.log 532.0 KB errors=143 warnings=1001
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 10.0 KB errors=0 warnings=8
Log files: master.out 0.0 KB
Log files: Total size 0.87 MB

I can't find a solution .

Best regard
Ivo
Ivo
 
Posts: 8
Joined: Wed Jun 02, 2010 3:04 pm
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Re: Installation on Ubuntu 10.04

Postby jmoore » Thu Jun 10, 2010 11:47 am

Hi Ivo,

my guess would be that something went awry during the configuration step or that your postgres is not reachable by the OMERO server.

What configuration values did you enter? If none, can you reach your database with:

Code: Select all
psql -h localhost -U omero omero -c "select * from dbpatch"


Does the /OMERO/ directory exist (or whatever value you configured for omero.data.dir)? Is it writeable by the user who started the server?

Could you attach your log files here to help us pinpoint the problem? Most important is var/log/Blitz-0.log, but feel free to zip them all up.

Cheers,
~Josh.
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Location: Germany
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Re: Installation on Ubuntu 10.04

Postby Ivo » Mon Jun 14, 2010 8:24 am

Hi jmoore,

Yes i can reach the database wit:
Code: Select all
psql -h localhost -U omero omero -c "select * from dbpatch"


It gives me a message like that:

    id | currentpatch | currentversion | permissions | finished | message | previouspatch | previousversion | external_id
    ----+--------------+----------------+-------------+----------------------------+-----------------+---------------+-----------------+-------------
    1 | 0 | OMERO4.1 | -35 | 2010-06-10 09:56:36.540968 | Database ready. | 0 | OMERO4.1 |
    (1 row)


      There exist some directory for omero. I have the whole omero folder which I downloaded on the Desktop and the installation created me a folder in the /OMERO directory.

      Here the var/log/Blitz-0.log File:

        2010-06-10 09:57:13,709 INFO [ ome.services.blitz.Entry] ( main) Creating OMERO.blitz. Please wait...
        2010-06-10 09:57:17,202 WARN [ java.util.prefs] ( main) Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
        2010-06-10 09:57:17,293 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Initializing EHCache CacheManager
        2010-06-10 09:57:17,521 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Found location in errorTimes: -1
        2010-06-10 09:57:17,521 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Removing 0 from errorTimes
        2010-06-10 09:57:17,522 WARN [ome.services.db.SelfCorrectingDataSource] ( main) Registering error with list: Current size: 0
        2010-06-10 09:57:17,522 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Sleeping for 0 then retry: 1
        2010-06-10 09:57:17,524 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Found location in errorTimes: -1
        2010-06-10 09:57:17,524 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Removing 0 from errorTimes
        2010-06-10 09:57:17,524 WARN [ome.services.db.SelfCorrectingDataSource] ( main) Registering error with list: Current size: 1
        2010-06-10 09:57:17,524 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Sleeping for 1000 then retry: 2
        2010-06-10 09:57:18,529 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Found location in errorTimes: -1
        2010-06-10 09:57:18,529 INFO [ome.services.db.SelfCorrectingDataSource] ( main) Removing 0 from errorTimes
        2010-06-10 09:57:18,529 WARN [ome.services.db.SelfCorrectingDataSource] ( main) Registering error with list: Current size: 2
        2010-06-10 09:57:18,533 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 64b8a5cb-7cfe-430e-8fc9-e4e10a70a9d7 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:84)
        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.LazyConnectionDataSourceProxy.afterPropertiesSet(LazyConnectionDataSourceProxy.java:163)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1368)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1334)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:473)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1245)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1010)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:472)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1245)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1010)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:472)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:495)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:162)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1245)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1010)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:472)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:308)
        at org.springframework.context.support.AbstractApplicationContext.getBeansOfType(AbstractApplicationContext.java:948)
        at org.springframework.context.support.AbstractApplicationContext.registerListeners(AbstractApplicationContext.java:702)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:378)
        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:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
        at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:100)
        at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:87)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:248)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:164)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:269)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:479)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:162)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:168)
        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:885)
        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)
        ... 115 more
        Caused by: org.postgresql.util.PSQLException: FATAL: password authentication failed for user "me"
        at org.postgresql.core.v3.ConnectionFactoryImpl.doAuthentication(ConnectionFactoryImpl.java:276)
        at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:95)
        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)
        ... 122 more
        2010-06-10 09:57:18,545 INFO [ng.ShutdownSafeEhcacheManagerFactoryBean] ( main) Shutting down EHCache CacheManager
        2010-06-10 09:57:18,547 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:/home/admin10/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:/home/admin10/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]: Cannot resolve reference to bean 'dataSource' while setting bean property 'dataSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAwareDataSource' defined in class path resource [ome/services/datalayer.xml]: Cannot resolve reference to bean 'lazyDataSource' while setting bean property 'targetDataSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'lazyDataSource' defined in class path resource [ome/services/datalayer.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:410)
        at ome.system.OmeroContext.getInstance(OmeroContext.java:203)
        at ome.services.blitz.Entry.start(Entry.java:203)
        at ome.services.blitz.Entry.main(Entry.java:121)
        Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/home/admin10/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:/home/admin10/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]: Cannot resolve reference to bean 'dataSource' while setting bean property 'dataSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'txAwareDataSource' defined in class path resource [ome/services/datalayer.xml]: Cannot resolve reference to bean 'lazyDataSource' while setting bean property 'targetDataSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'lazyDataSource' defined in class path resource [ome/services/datalayer.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:275)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:104)
        at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:479)
        at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:162)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:925)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:835)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:440)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory$1.run(AbstractAutowireCapableBeanFactory.java:409)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:380)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:264)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:221)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:261)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:185)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:168)
        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:885)
        at org.springframework.beans.factory.access.SingletonBeanFactoryLocator.useBeanFactory(SingletonBeanFactoryLocator.java:397)
        ... 3 more


Thanks,
Ivo
Ivo
 
Posts: 8
Joined: Wed Jun 02, 2010 3:04 pm
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Re: Installation on Ubuntu 10.04

Postby Ivo » Mon Jun 14, 2010 8:25 am

And here the master.err File:

    Traceback (most recent call last):
    File "lib/python/runTables.py", line 13, in <module>
    __import__("tables")
    ImportError: No module named tables
    Jun 10, 2010 9:57:16 AM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    Jun 10, 2010 9:57:17 AM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    06/10/10 09:57:18.625 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
    06/10/10 09:57:18.628 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
    06/10/10 10:09:45.828 icegridnode: error: an IceGrid registry is already running and listening on the client endpoints `tcp -h 127.0.0.1 -p 4061'
    Traceback (most recent call last):
    File "lib/python/runTables.py", line 13, in <module>
    __import__("tables")
    ImportError: No module named tables
    Jun 10, 2010 10:20:48 AM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    Jun 10, 2010 10:20:49 AM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    06/10/10 10:20:51.137 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
    06/10/10 10:20:51.141 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
    06/10/10 10:32:34.356 icegridnode: error: an IceGrid registry is already running and listening on the client endpoints `tcp -h 127.0.0.1 -p 4061'
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.py'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:33:13.894696 Web: warning: Restart 1
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:33:14.900038 Web: warning: Restart 2
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:33:15.905759 Web: warning: Restart 3
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:33:16.912395 Web: warning: Restart 4
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:33:17.917990 Web: warning: Restart 5
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    Traceback (most recent call last):
    File "/usr/lib/pymodules/python2.6/Ice.py", line 766, in main
    status = self.run(args)
    File "lib/python/shellserver.py", line 87, in run
    self.stop()
    File "lib/python/shellserver.py", line 65, in stop
    sys.exit(0)
    SystemExit: 0
    06/10/10 10:34:07.997 icegridnode: error: an IceGrid registry is already running and listening on the client endpoints `tcp -h 127.0.0.1 -p 4061'
    Traceback (most recent call last):
    File "lib/python/runTables.py", line 13, in <module>
    __import__("tables")
    ImportError: No module named tables
    Jun 10, 2010 10:38:30 AM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    Jun 10, 2010 10:38:31 AM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    06/10/10 10:38:32.645 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
    06/10/10 10:38:32.650 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:44:20.011518 Web: warning: Restart 1
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:44:21.017791 Web: warning: Restart 2
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:44:22.023123 Web: warning: Restart 3
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:44:23.028489 Web: warning: Restart 4
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    2010-06-10 10:44:24.034397 Web: warning: Restart 5
    Starting django...
    Error: Can't find the file 'custom_settings.py' in the directory containing '/home/admin10/Desktop/omero/lib/python/omeroweb/settings.pyc'.It appears you've customized things.
    You'll have to run 'bin/omero web [settings|superuser|syncdb]', passing it your settings module.
    (If the file custom_settings.py does indeed exist, it's causing an ImportError somehow.)
    Traceback (most recent call last):
    File "/usr/lib/pymodules/python2.6/Ice.py", line 766, in main
    status = self.run(args)
    File "lib/python/shellserver.py", line 87, in run
    self.stop()
    File "lib/python/shellserver.py", line 65, in stop
    sys.exit(0)
    SystemExit: 0
    06/10/10 12:20:22.942 icegridnode: error: an IceGrid registry is already running and listening on the client endpoints `tcp -h 127.0.0.1 -p 4061'
    06/10/10 12:20:40.862 icegridnode: error: an IceGrid registry is already running and listening on the client endpoints `tcp -h 127.0.0.1 -p 4061'
    06/10/10 12:21:01.262 icegridnode: error: an IceGrid registry is already running and listening on the client endpoints `tcp -h 127.0.0.1 -p 4061'
    Traceback (most recent call last):
    File "lib/python/runTables.py", line 13, in <module>
    __import__("tables")
    ImportError: No module named tables
    Jun 10, 2010 12:26:37 PM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    Jun 10, 2010 12:26:37 PM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    06/10/10 12:26:38.958 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
    06/10/10 12:26:38.961 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
    06/10/10 13:55:32.358 icegridnode: warning: exception occurred while deactivating `OMERO.Glacier2' using process proxy:
    Network.cpp:1220: Ice::ConnectionRefusedException:
    connection refused: Connection refused
    06/10/10 13:55:32.359 icegridnode: warning: exception occurred while deactivating `OMERO.IceStorm' using process proxy:
    Network.cpp:1220: Ice::ConnectionRefusedException:
    connection refused: Connection refused
    Traceback (most recent call last):
    File "lib/python/runTables.py", line 13, in <module>
    __import__("tables")
    ImportError: No module named tables
    Jun 10, 2010 2:34:52 PM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    Jun 10, 2010 2:34:52 PM java.util.prefs.FileSystemPreferences$7 run
    WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
    06/10/10 14:34:54.786 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
    06/10/10 14:34:54.789 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
    Reference.cpp:1546: Ice::NoEndpointException:
    no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'
    Starting django...
    2010-06-10 14:45:39.608906 Web: warning: Sent 3116 SIGTERM. Sleeping...
    2010-06-10 14:45:40.610220 Web: warning: tick
    2010-06-10 14:45:40.610480 Web: warning: Stopped.
    Traceback (most recent call last):
    File "/usr/lib/pymodules/python2.6/Ice.py", line 766, in main
    status = self.run(args)
    File "lib/python/shellserver.py", line 87, in run
    self.stop()
    File "lib/python/shellserver.py", line 65, in stop
    sys.exit(0)
    SystemExit: 0
    Starting django...
    /home/admin10/Desktop/omero/lib/python/omeroweb/webadmin/views.py:831: SyntaxWarning: import * only allowed at module level
    @isUserConnected
    [10/Jun/2010 13:47:21] "GET /webadmin HTTP/1.1" 301 0
    [10/Jun/2010 13:47:22] "GET /webadmin/ HTTP/1.1" 302 0
    [10/Jun/2010 13:47:22] "GET /webadmin/login/?url=/webadmin/ HTTP/1.1" 200 1764
    [10/Jun/2010 13:47:22] "GET /webadmin/static/css/layout.css HTTP/1.1" 200 3738
    [10/Jun/2010 13:47:22] "GET /webadmin/static/css/login.css HTTP/1.1" 200 435
    [10/Jun/2010 13:47:22] "GET /webadmin/static/images/logo.png HTTP/1.1" 200 28009
    [10/Jun/2010 13:47:22] "GET /webclient/static/images/ome.ico HTTP/1.1" 200 1406
    [10/Jun/2010 13:47:37] "POST /webadmin/login/ HTTP/1.1" 200 1951
    [10/Jun/2010 13:48:13] "POST /webadmin/login/ HTTP/1.1" 200 1953
    [10/Jun/2010 13:48:16] "POST /webadmin/login/ HTTP/1.1" 200 1951
    [10/Jun/2010 13:50:42] "POST /webadmin/login/ HTTP/1.1" 200 1955
    [10/Jun/2010 13:50:44] "POST /webadmin/login/ HTTP/1.1" 200 1955
    [10/Jun/2010 13:50:45] "POST /webadmin/login/ HTTP/1.1" 200 1955
    [10/Jun/2010 14:07:36] "POST /webadmin/login/ HTTP/1.1" 200 1955
    [10/Jun/2010 14:07:42] "POST /webadmin/login/ HTTP/1.1" 200 1952
    [10/Jun/2010 14:07:46] "POST /webadmin/login/ HTTP/1.1" 200 1950
    [10/Jun/2010 14:07:50] "POST /webadmin/login/ HTTP/1.1" 200 1951
    [10/Jun/2010 14:07:53] "POST /webadmin/login/ HTTP/1.1" 200 1953
    06/10/10 17:21:49.262 icegridnode: warning: exception occurred while deactivating `OMERO.IceStorm' using process proxy:
    Network.cpp:1220: Ice::ConnectionRefusedException:
    connection refused: Connection refused
    06/10/10 17:21:49.262 icegridnode: warning: exception occurred while deactivating `OMERO.Glacier2' using process proxy:
    Network.cpp:1220: Ice::ConnectionRefusedException:
    connection refused: Connection refused
    06/10/10 17:21:49.262 icegridnode: warning: exception occurred while deactivating `Processor-0' using process proxy:
    Network.cpp:1220: Ice::ConnectionRefusedException:
    connection refused: Connection refused
    Traceback (most recent call last):
    File "/usr/lib/pymodules/python2.6/Ice.py", line 766, in main
    status = self.run(args)
    File "lib/python/shellserver.py", line 87, in run
    self.stop()
    File "lib/python/shellserver.py", line 65, in stop
    sys.exit(0)
    SystemExit: 0


Thanks,
Ivo
Ivo
 
Posts: 8
Joined: Wed Jun 02, 2010 3:04 pm
Top

Re: Installation on Ubuntu 10.04

Postby cxallan » Mon Jun 14, 2010 8:29 am

Code: Select all
...
Caused by: org.postgresql.util.PSQLException: FATAL: password authentication failed for user "me"
...


If you succeeded with a PostgreSQL user "omero" and that user's password then your database properties are incorrect as you can see from the log line I just pasted above. Can you give me the output of the following please?

Code: Select all
bin/omero config get
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am
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Re: Installation on Ubuntu 10.04

Postby Ivo » Mon Jun 14, 2010 8:43 am

Code: Select all
admin10@admin10-desktop:~/Desktop/omero$ bin/omero config get
omero.db.name=myDatabase
omero.db.pass=TopSecret
omero.db.user=me
Ivo
 
Posts: 8
Joined: Wed Jun 02, 2010 3:04 pm
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Re: Installation on Ubuntu 10.04

Postby cxallan » Mon Jun 14, 2010 8:51 am

You need to set those values correctly and not just copy them from the example in the documentation. Assuming database "omero" username "omero" and password "omero":

Code: Select all
bin/omero config set omero.db.name omero
bin/omero config set omero.db.pass omero
bin/omero config set omero.db.name omero


These are the defaults, so if you have used "omero" for all of these options you can also:

Code: Select all
bin/omero config drop


This will reset all of those settings to the defaults, which you need not modify unless you are using a different PostgreSQL database name, username or password.
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am
Top

Re: Installation on Ubuntu 10.04

Postby Ivo » Mon Jun 14, 2010 9:17 am

Now it gives me a massage like that:

Code: Select all
admin10@admin10-desktop:~/Desktop/omero$ bin/omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit


It doesn't say: "failed to startup after 5 minutes"

Is it already running?
Ivo
 
Posts: 8
Joined: Wed Jun 02, 2010 3:04 pm
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Re: Installation on Ubuntu 10.04

Postby cxallan » Mon Jun 14, 2010 9:25 am

Yes, it's running.
cxallan
Site Admin
 
Posts: 509
Joined: Fri May 01, 2009 8:07 am
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Re: Installation on Ubuntu 10.04

Postby Ivo » Mon Jun 14, 2010 9:29 am

O.K. than thanks a lot for the support !!

Thanks,
Ivo
Ivo
 
Posts: 8
Joined: Wed Jun 02, 2010 3:04 pm
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