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Upgrade from 4.2.2 to 4.3 did not work

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Upgrade from 4.2.2 to 4.3 did not work

Postby ScottG » Thu Jun 16, 2011 3:14 pm

Hi,

I went through the upgrade procedure outlined on the web site. Everything seemed to go well resulting in the final message "---------------------------------------------------------------------
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO4.3__0"

However 4.3 does not start. I get this message after it tries

"No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 5 minutes
Calling "stop" on remaining components
Waiting on shutdown. Use CTRL-C to exit"

The server is running on osx leopard, ice 3.3.1, postgres 8.3, python 2.5.1

Thanks for the help
ScottG
 
Posts: 17
Joined: Thu Jun 16, 2011 2:54 pm

Re: Upgrade from 4.2.2 to 4.3 did not work

Postby ScottG » Fri Jun 17, 2011 2:17 pm

Hi,

This is a compilation of the log files in the var directory. I hope this helps


Code: Select all
Processor-0.log
2011-06-16 15:48:39,240 ERROR [                       omero.util.Server] (MainThread) Failed initialization
Traceback (most recent call last):
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/util/__init__.py", line 422, in run
    self.impl = self.impl_class(ctx)
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/processor.py", line 658, in __init__
    omero.util.Servant.__init__(self, ctx, needs_session = needs_session)
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/util/__init__.py", line 499, in __init__
    self.ctx.newSession()
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/util/__init__.py", line 290, in newSession
    self.session = internal_service_factory(self.communicator, stop_event = self.stop_event)
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/util/__init__.py", line 193, in internal_service_factory
    raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2011-06-16 15:48:39,241 INFO  [                       omero.util.Server] (MainThread) Cleanup
2011-06-16 15:48:39,241 INFO  [                       omero.util.Server] (MainThread) Stopped
2011-06-16 15:48:39,241 INFO  [                       omero.util.Server] (MainThread) ********************************************************************************
2011-06-16 15:48:39,242 INFO  [              omero.processor.ProcessorI] (MainThread) Cleaning up
2011-06-16 15:48:39,242 INFO  [              omero.processor.ProcessorI] (MainThread) Done
2011-06-16 15:48:39,242 WARNI [                                  stderr] (MainThread) Traceback (most recent call last):
2011-06-16 15:48:39,242 WARNI [                                  stderr] (MainThread) File "/opt/Ice-3.3/python/Ice.py", line 766, in main
2011-06-16 15:48:39,242 INFO  [                    omero.util.Resources] (Thread-2  ) Halted
2011-06-16 15:48:39,243 WARNI [                                  stderr] (MainThread) status = self.run(args)
2011-06-16 15:48:39,243 WARNI [                                  stderr] (MainThread) File "/Users/omero/Desktop/omero_dist/lib/python/omero/util/__init__.py", line 426, in run
2011-06-16 15:48:39,243 WARNI [                                  stderr] (MainThread) sys.exit(100)
2011-06-16 15:48:39,243 WARNI [                                  stderr] (MainThread) SystemExit: 100

DropBox.log
2011-06-16 15:43:34,774 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 1
2011-06-16 15:43:37,776 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 2
2011-06-16 15:43:40,777 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 3
2011-06-16 15:43:43,779 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 4
2011-06-16 15:43:46,780 INFO  [                             omero.utils] (MainThread) Failed to get session on attempt 5
2011-06-16 15:43:49,781 WARNI [                             omero.utils] (MainThread) Reason: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2011-06-16 15:43:49,781 ERROR [                        fsclient.DropBox] (MainThread) Failed to get Session:
Traceback (most recent call last):
  File "lib/python/fsDropBox.py", line 87, in run
    retries=self.maxRetries, interval=self.retryInterval)
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/util/__init__.py", line 193, in internal_service_factory
    raise excpt
NoEndpointException: exception ::Ice::NoEndpointException
{
    proxy = BlitzManager -t @ BlitzAdapters
}
2011-06-16 15:43:49,782 ERROR [                        fsclient.DropBox] (MainThread) Quitting
2011-06-16 15:43:49,784 INFO  [                        fsclient.DropBox] (MainThread) Exiting with exit code: -1

Blitz-0.log
2011-06-16 10:23:49,194 INFO  [                ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please wait...
2011-06-16 10:23:51,295 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2011-06-16 10:23:55,020 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2011-06-16 10:24:00,641 INFO  [        ome.services.db.DatabaseIdentity] (      main) Using LSID format: urn:lsid:export.openmicroscopy.org:%s:4ad7f192-021f-4e5a-a626-d62d24b59be3_%s%s
2011-06-16 10:24:00,669 INFO  [                ome.io.nio.PixelsService] (      main) Constructed pixel buffer with path: /Volumes/dozer/OMERO402/ resolver: ome.services.OmeroFilePathResolver@e9212a
2011-06-16 10:24:00,888 INFO  [    ome.services.fulltext.FullTextThread] (      main) Initializing Full-Text Indexer
2011-06-16 10:24:00,896 INFO  [  ome.services.pixeldata.PixelDataThread] (      main) Initializing PixelDataThread (create events only)
2011-06-16 10:24:00,905 INFO  [          ome.services.util.DBPatchCheck] (      main) Verified database patch: OMERO4.3__0
2011-06-16 10:24:01,759 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: InCell3000
2011-06-16 10:24:01,761 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: Spider
2011-06-16 10:24:01,761 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: Volocity
2011-06-16 10:24:01,762 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: Imagic
2011-06-16 10:24:01,764 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: HamamatsuVMS
2011-06-16 10:24:01,765 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: CellSens
2011-06-16 10:24:01,780 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: NDPI
2011-06-16 10:24:01,790 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: Trestle
2011-06-16 10:24:01,791 INFO  [           ome.services.util.DBEnumCheck] (      main) Added format: SIS
2011-06-16 10:24:01,803 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2011-06-16 10:24:01,803 INFO  [    ome.services.util.ServerVersionCheck] (      main) OMERO Version: 4.3.0-77345008 Ready.
2011-06-16 10:24:01,803 INFO  [    ome.services.util.ServerVersionCheck] (      main) -------------------------------------------------
2011-06-16 10:24:02,931 INFO  [                 ome.system.UpgradeCheck] (      main) no update needed
2011-06-16 10:24:02,934 INFO  [    ome.tools.hibernate.ExtendedMetadata] (      main) Calculating ExtendedMetadata...
2011-06-16 10:24:03,017 INFO  [.services.scheduler.SchedulerFactoryBean] (      main) Starting Quartz Scheduler now
2011-06-16 10:24:03,024 INFO  [        ome.services.util.ServiceHandler] (      main)  Executor.doWork -- ome.services.util.NamespaceCheck.namespaceCheck
2011-06-16 10:24:03,024 INFO  [        ome.services.util.ServiceHandler] (      main)  Args:   [null, InternalSF@11317837]
2011-06-16 10:24:03,203 WARN  [k.jdbc.core.metadata.CallMetaDataContext] (      main) Unable to locate the corresponding parameter value for '$1' within the parameter values provided: [_event_id, _group_id, _user_id]
2011-06-16 10:24:03,203 WARN  [k.jdbc.core.metadata.CallMetaDataContext] (      main) Unable to locate the corresponding parameter value for '$2' within the parameter values provided: [_event_id, _group_id, _user_id]
2011-06-16 10:24:03,203 WARN  [k.jdbc.core.metadata.CallMetaDataContext] (      main) Unable to locate the corresponding parameter value for '$3' within the parameter values provided: [_event_id, _group_id, _user_id]
2011-06-16 10:24:03,224 INFO  [                 org.perf4j.TimingLogger] (      main) start[1308234243024] time[200] tag[omero.call.exception]
2011-06-16 10:24:03,226 WARN  [        ome.services.util.ServiceHandler] (      main) Unknown exception thrown.

org.springframework.dao.InvalidDataAccessApiUsageException: Required input parameter '$1' is missing
   at org.springframework.jdbc.core.CallableStatementCreatorFactory$CallableStatementCreatorImpl.createCallableStatement(CallableStatementCreatorFactory.java:209)
   at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:947)
   at org.springframework.jdbc.core.JdbcTemplate.call(JdbcTemplate.java:1003)
   at org.springframework.jdbc.core.simple.AbstractJdbcCall.executeCallInternal(AbstractJdbcCall.java:378)
   at org.springframework.jdbc.core.simple.AbstractJdbcCall.doExecute(AbstractJdbcCall.java:341)
   at org.springframework.jdbc.core.simple.SimpleJdbcCall.executeFunction(SimpleJdbcCall.java:146)
   at ome.util.actions.PostgresSqlAction.prepareSession(PostgresSqlAction.java:67)
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:592)
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
   at ome.util.SqlAction$LoggingSqlAction.invoke(SqlAction.java:65)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at $Proxy50.prepareSession(Unknown Source)
   at ome.security.basic.EventHandler.invoke(EventHandler.java:121)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at $Proxy64.doWork(Unknown Source)
   at ome.services.util.Executor$Impl.execute(Executor.java:371)
   at ome.services.util.NamespaceCheck.handleContextRefreshedEvent(NamespaceCheck.java:55)
   at ome.tools.spring.OnContextRefreshedEventListener.onApplicationEvent(OnContextRefreshedEventListener.java:67)
   at ome.tools.spring.OnContextRefreshedEventListener.onApplicationEvent(OnContextRefreshedEventListener.java:25)
   at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:97)
   at ome.services.messages.GlobalMulticaster.multicastEvent(GlobalMulticaster.java:55)
   at ome.system.OmeroContext.publishEvent(OmeroContext.java:327)
   at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:887)
   at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:426)
   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:501)
   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:196)
   at ome.services.blitz.Entry.main(Entry.java:114)
   
master.err
Traceback (most recent call last):
  File "lib/python/runTables.py", line 15, in <module>
    import omero.tables
  File "/Users/omero/Desktop/omero_dist/lib/python/omero/tables.py", line 35, in <module>
    tables = __import__("tables") # Pytables
ImportError: No module named tables
06/16/11 10:24:03.292 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t @ BlitzAdapters'
06/16/11 10:24:03.293 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1546: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t @ BlitzAdapters'



Scott G
ScottG
 
Posts: 17
Joined: Thu Jun 16, 2011 2:54 pm

Re: Upgrade from 4.2.2 to 4.3 did not work

Postby jmoore » Mon Jun 20, 2011 6:59 am

The critical errors which cause all the rest look like:
Code: Select all
2011-06-16 10:24:03,203 WARN  [k.jdbc.core.metadata.CallMetaDataContext] (      main) Unable to locate the corresponding parameter value for '$2' within the parameter values provided: [_event_id, _group_id, _user_id]


which most likely points to a version mismatch between various components. Could you paste the output of:
Code: Select all
bin/omero admin diagnostics


here?

Cheers,
~Josh
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany

Re: Upgrade from 4.2.2 to 4.3 did not work

Postby ScottG » Mon Jun 20, 2011 1:06 pm

Will do.
Code: Select all
================================================================================
OMERO Diagnostics 4.3.0-77345008
================================================================================
       
Commands:   java -version                  1.5.0     (/usr/bin/java)
Commands:   python -V                      2.5.1     (/usr/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                 8.3.5     (/sw/bin/psql)

Server:     icegridnode                    not started

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

Log files:  Blitz-0.log                    199.0 KB      errors=9    warnings=36 
Log files:  DropBox.log                    13.0 KB       errors=18   warnings=9   
Log files:  FileServer.log                 3.0 KB       
Log files:  Indexer-0.log                  16.0 KB     
Log files:  MonitorServer.log              3.0 KB       
Log files:  OMEROweb.log                   0.0 KB       
Log files:  PixelData-0.log                19.0 KB     
Log files:  Processor-0.log                163.0 KB      errors=45   warnings=315
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  master.err                     6.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     0.42 MB

Parsing Blitz-0.log:[line:19] => Server restarted <=
Parsing Blitz-0.log:[line:210] => Server restarted <=
Parsing Blitz-0.log:[line:401] => Server restarted <=
Parsing Blitz-0.log:[line:592] => Server restarted <=
Parsing Blitz-0.log:[line:783] => Server restarted <=
Parsing Blitz-0.log:[line:974] => Server restarted <=
Parsing Blitz-0.log:[line:1165] => Server restarted <=
Parsing Blitz-0.log:[line:1356] => Server restarted <=
Parsing Blitz-0.log:[line:1547] => Server restarted <=

Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:PATH=/opt/ice-3.3/bin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)       
Environment:DYLD_LIBRARY_PATH=/opt/ice-3.3/lib:

OMERO data dir: '/Volumes/dozer/OMERO402/'   Exists? True   Is writable? True
OMERO.web status... [NOT STARTED]


I hope this helps

Scott
ScottG
 
Posts: 17
Joined: Thu Jun 16, 2011 2:54 pm

Re: Upgrade from 4.2.2 to 4.3 did not work

Postby jmoore » Mon Jun 20, 2011 7:38 pm

Hi Scott,

sorry, the output of diagnostics didn't show anything particularly obvious. At the moment, I'm a bit at a loss to know what to try next, since I've never seen anything like this. Can you trace back over for me as many of the steps you took as you can? Has the machine been restarted? Has OMERO been restarted? Have you tried re-unzipping the file in a fresh directory?

Again, sorry for all the trouble.
Cheers,
~Josh.
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Re: Upgrade from 4.2.2 to 4.3 did not work

Postby ScottG » Mon Jun 20, 2011 9:59 pm

Hi Josh,

Well I followed the upgrade instructions and everything seemed go according to plan until the restart of the server. After it did not start I tried the error fix thing "psql -h localhost -U omero omero < sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql" even though i didn't get any errors and tried to restart again. Again in failed. I rebooted everything and again it failed. I downloaded the server again and tried again and still no luck. If i were to reinstall everything from scratch what do i need to save and do to bring it all back to life?

Scott
ScottG
 
Posts: 17
Joined: Thu Jun 16, 2011 2:54 pm

Re: Upgrade from 4.2.2 to 4.3 did not work

Postby jmoore » Tue Jun 21, 2011 8:12 am

Hi Scott,

the steps I would probably take at this point are:

  • 1. Restore the database from your backup to a second location, e.g. "omero43" below
  • 2. Re-run the upgrade
  • 3. Configure your server to use the new db
  • 4. Restart OMERO

If you could capture all of that from the console and paste it to us, that'd be very helpful. If that doesn't work, the next step may be to try to determine if this is related to your PostgreSQL version (8.3.5), though that seems unlikely.

Cheers,
~Josh.


Code: Select all
### [1] Restore DB example
createdb -O omero omero43
createlang plpgsql omero43
psql -h localhost -U omero omero43 < before_upgrade.db.dump

### [2] Re-run upgrade script
psql -h localhost -U omero omero43 < sql/psql/OMERO4.3__0/OMERO4.2__0.sql

### [3] Re-configure your server
bin/omero config set omero.db.name omero43

### [4] Re-start OMERO
bin/omero admin restart

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jmoore
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Re: Upgrade from 4.2.2 to 4.3 did not work

Postby ScottG » Tue Jun 28, 2011 6:02 pm

Hi Josh,

I had a bit of a give a mouse a muffin moment and ended up reinstalling the operating system, and all the components of omero though macports. Previously I had hand installed the various pieces. Now I have the system running at 4.3 what is the best way to reinstall the database from the backups. I have backups for before the 4.2.2 to 4.3 update and I have a backup of the 4.3 database after the conversion. The conversion if you remember did not end with any errors so it may be fine. If you wouldn't mind a detailed walk through of getting the database back up would be helpful.

Thanks in advance and all the best,
Scott
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Re: Upgrade from 4.2.2 to 4.3 did not work

Postby jmoore » Tue Jun 28, 2011 7:11 pm

Hi Scott.

I've added a section, "Restoring a database backup if something goes wrong", which seems to be made just for you.

Assuming you mean that you have the server running with a fresh database, you don't need to rename your database so you'll most likely want to do the following:
  • Turn off OMERO: bin/omero admin stop
  • Drop the fresh DB: dropdb omero
  • Re-create the DB as you did previously: createdb ... omero
  • Restore per the instructions: pg_restore ... -Fc -f before_upgrade.db.dump omero
  • Restart OMERO: bin/omero admin start

Hope that helps!
~Josh.
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Re: Upgrade from 4.2.2 to 4.3 did not work

Postby ScottG » Thu Jun 30, 2011 6:33 pm

Hi Josh,

Not quite there yet. When I try to import the old database with psql -h localhost -U omero omero < /Volumes/TestDisk/OMERO_backup/Backup/database/omero.2011-06-16.pg_dump. i get "ERROR: invalid byte sequence for encoding "UTF8": 0x82
HINT: This error can also happen if the byte sequence does not match the encoding expected by the server, which is controlled by "client_encoding". And a long list of other errors i could send if need be.

Any ideas on fixing this?



Scott
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