Search .. but no results

[jumpfunky]

That certainly looks like much more was indexed. But search is still not working?

Unfortunately no.
What's about the many errors:

ERROR ome.services.util.ServiceHandler - Method interface ome.services.util.Executor$Work.doWork invocation took 100399

[jmoore]

Those just point to very large transactions, which are to be expected with a full re-indexing. At this point, I'm afraid I don't know what's happening. It might be worth restarting your server after the previous re-indexing to see if it will pick up the newly created files. (I'm guessing the directory you listed earlier (Output of /home/omero/OMERO.data/FullText...) is much larger. If that doesn't work, the next thing I would suggest is to shutoff the server, delete the OMERO.data/FullText directory and then reset indexing in the configuration table.

Sorry for the hassle,
~Josh

[jumpfunky]

Hi josh,

thanks for your help!

and then reset indexing in the configuration table.

For this step I need some advice! How do i reset indexing in the configuration table?

Thanks
Thorsten

[jmoore]

Hi Thorsten,

apologies, I should have included this doc link:

If you need to re-index your database, stop your server, and:

• (Optionally) Delete the /OMERO/FullText directory
• Delete or set to 0 the entry from the configuration table: update configuration set value = 0 where name like 'PersistentEventLogLoader%';

I'll keep my fingers crossed.
~Josh.

[jumpfunky]

Hm, i've got an exception:

Code: Select all

omero@omerovm:~/OMERO.server$ java -Dlog4j.configuration=log4j-cli.properties -Xmx512M ome.services.fulltext.Main full
Exception in thread "main" java.lang.NoClassDefFoundError: ome/services/fulltext/Main
Caused by: java.lang.ClassNotFoundException: ome.services.fulltext.Main
   at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
   at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
   at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
   at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: ome.services.fulltext.Main.  Program will exit.


Maybe that's the big problem?

[jmoore]

That likely just means that your CLASSPATH variable is not properly set. However, if you've changed the configuration table, then the indexer process (var/log/Indexer-0.log) should already be re-indexing your data, and it shouldn't be necessary to force a re-indexing.

Cheers,
~Josh

[jumpfunky]

When I now try to use the OMERO.web search i get a very big exception:

Code: Select all

Traceback (most recent call last):

  File "/home/omero/OMERO.server/lib/python/django/core/handlers/base.py", line 111, in get_response
    response = callback(request, *callback_args, **callback_kwargs)

  File "/home/omero/OMERO.server/lib/python/omeroweb/decorators.py", line 376, in wrapped
    retval = f(request, *args, **kwargs)

  File "/home/omero/OMERO.server/lib/python/omeroweb/decorators.py", line 413, in wrapper
    context = f(request, *args, **kwargs)

  File "/home/omero/OMERO.server/lib/python/omeroweb/webclient/views.py", line 510, in load_searching
    manager.search(query_search, onlyTypes, date)

  File "/home/omero/OMERO.server/lib/python/omeroweb/webclient/controller/search.py", line 92, in search
    im_list = list(self.conn.searchObjects(["image"], query, created))

  File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3215, in searchObjects
    if search.hasNext(self.SERVICE_OPTS):

  File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3271, in __call__
    return self.handle_exception(e, *args, **kwargs)

  File "/home/omero/OMERO.server/lib/python/omeroweb/webclient/webclient_gateway.py", line 1875, in handle_exception
    e, *args, **kwargs)

  File "/home/omero/OMERO.server/lib/python/omero/gateway/__init__.py", line 3268, in __call__
    return self.f(*args, **kwargs)

  File "/home/omero/OMERO.server/lib/python/omero_api_Search_ice.py", line 378, in hasNext
    return _M_omero.api.Search._op_hasNext.invoke(self, ((), _ctx))

InternalException: exception ::omero::InternalException
{
    serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (org.hibernate.search.SearchException):
Unable to reopen IndexReader
   at org.hibernate.search.reader.SharingBufferReaderProvider$PerDirectoryLatestReader.refreshAndGet(SharingBufferReaderProvider.java:245)
   at org.hibernate.search.reader.SharingBufferReaderProvider.openReader(SharingBufferReaderProvider.java:123)
   at org.hibernate.search.query.FullTextQueryImpl.buildSearcher(FullTextQueryImpl.java:718)
   at org.hibernate.search.query.FullTextQueryImpl.list(FullTextQueryImpl.java:288)
   at ome.services.search.FullText.doWork(FullText.java:202)
   at sun.reflect.GeneratedMethodAccessor255.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
   at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:508)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
   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 $Proxy65.doWork(Unknown Source)
   at ome.services.util.Executor$Impl.execute(Executor.java:406)
   at ome.services.util.Executor$Impl.execute(Executor.java:350)
   at ome.services.SearchBean.hasNext(SearchBean.java:262)
   at sun.reflect.GeneratedMethodAccessor599.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   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.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 $Proxy89.hasNext(Unknown Source)
   at sun.reflect.GeneratedMethodAccessor599.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   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.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at $Proxy89.hasNext(Unknown Source)
   at sun.reflect.GeneratedMethodAccessor816.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
   at ome.services.throttling.Callback.run(Callback.java:56)
   at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
   at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:137)
   at ome.services.blitz.impl.SearchI.hasNext_async(SearchI.java:196)
   at sun.reflect.GeneratedMethodAccessor815.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   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 omero.cmd.CallContext.invoke(CallContext.java:59)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at $Proxy90.hasNext_async(Unknown Source)
   at omero.api._SearchTie.hasNext_async(_SearchTie.java:190)
   at omero.api._SearchDisp.___hasNext(_SearchDisp.java:1292)
   at omero.api._SearchDisp.__dispatch(_SearchDisp.java:1543)
   at IceInternal.Incoming.invoke(Incoming.java:159)
   at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
   at Ice.ConnectionI.message(ConnectionI.java:972)
   at IceInternal.ThreadPool.run(ThreadPool.java:577)
   at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
   at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)

    serverExceptionClass = ome.conditions.InternalException
    message =  Wrapped Exception: (org.hibernate.search.SearchException):
Unable to reopen IndexReader
}


<WSGIRequest
GET:<QueryDict: {u'images': [u'on'], u'query': [u'NSc']}>,
POST:<QueryDict: {}>,
COOKIES:{'sessionid': '5016fbc99cc31eacb8df27693b60af5b'},
META:{'CONTENT_LENGTH': '',
'CONTENT_TYPE': '',
'HTTP_ACCEPT': 'text/html, */*; q=0.01',
'HTTP_ACCEPT_CHARSET': 'ISO-8859-1,utf-8;q=0.7,*;q=0.3',
'HTTP_ACCEPT_ENCODING': 'gzip,deflate,sdch',
'HTTP_ACCEPT_LANGUAGE': 'de-DE,de;q=0.8,en-US;q=0.6,en;q=0.4',
'HTTP_CONNECTION': 'keep-alive',
'HTTP_COOKIE': 'sessionid=5016fbc99cc31eacb8df27693b60af5b',
'HTTP_HOST': '193.25.22.130:8080',
'HTTP_REFERER': 'http://193.25.22.130:8080/webclient/search/',
'HTTP_USER_AGENT': 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4',
'HTTP_X_REQUESTED_WITH': 'XMLHttpRequest',
'PATH_INFO': u'/webclient/load_searching/form/',
'QUERY_STRING': 'query=NSc&images=on',
'REQUEST_METHOD': 'GET',
'SCRIPT_NAME': u'',
'SERVER_NAME': '_',
'SERVER_PORT': '8080',
'SERVER_PROTOCOL': 'HTTP/1.1',
'wsgi.errors': <flup.server.fcgi_base.TeeOutputStream object at 0xaf1c70c>,
'wsgi.input': <flup.server.fcgi_base.InputStream object at 0xaf0a72c>,
'wsgi.multiprocess': True,
'wsgi.multithread': False,
'wsgi.run_once': False,
'wsgi.url_scheme': 'http',
'wsgi.version': (1, 0)}>

[jmoore]

Still looks like your /FullText directory is very unhappy. Can you walk me through the steps you took? Something like:

• Stopped server
• rm -rf /OMERO/FullText/*
• psql omero -c ...
• Started server

right?

What are the current contents of FullText? What's in Indexer-0.log?

Thanks,
~Josh

[jumpfunky]

Oh, i didnt stop and restart the server! I've done it now and additionaly done a full reindexing via...

Code: Select all

bin/omero admin reindex --full


the time on the server is not correct... so, dont be confused:
13:21-13:24: Time where I've forgot to stop / start the server
15:11: Server stopped and restarted!
15:14: Full reindexing


Thats the log:

Code: Select all

2012-10-10 13:21:40,018 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-4) Currently running; skipping
2012-10-10 13:21:44,020 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-5) Currently running; skipping
2012-10-10 13:21:48,017 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-3) Currently running; skipping
2012-10-10 13:21:52,017 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-2) Currently running; skipping
2012-10-10 13:21:56,016 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-5) Currently running; skipping
2012-10-10 13:21:59,567 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.screen.Screen:Id_2 for ome.model.meta.EventLog:Id_69
2012-10-10 13:22:00,023 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-3) Currently running; skipping
2012-10-10 13:22:00,568 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.screen.Screen:Id_2
2012-10-10 13:22:04,021 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-2) Currently running; skipping
2012-10-10 13:22:06,714 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.containers.Dataset:Id_3 for ome.model.meta.EventLog:Id_97
2012-10-10 13:22:07,714 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.containers.Dataset:Id_3
2012-10-10 13:22:07,732 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_98
2012-10-10 13:22:08,013 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-4) Currently running; skipping
2012-10-10 13:22:08,732 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:22:08,750 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Pixels:Id_3 for ome.model.meta.EventLog:Id_100
2012-10-10 13:22:09,751 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Pixels:Id_3
2012-10-10 13:22:09,766 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.LogicalChannel:Id_3 for ome.model.meta.EventLog:Id_101
2012-10-10 13:22:10,766 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.LogicalChannel:Id_3
2012-10-10 13:22:10,794 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Pixels:Id_3 for ome.model.meta.EventLog:Id_103
2012-10-10 13:22:11,794 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Pixels:Id_3
2012-10-10 13:22:11,813 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Pixels:Id_3 for ome.model.meta.EventLog:Id_104
2012-10-10 13:22:12,015 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-5) Currently running; skipping
2012-10-10 13:22:12,814 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Pixels:Id_3
2012-10-10 13:22:12,830 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_3 for ome.model.meta.EventLog:Id_108
2012-10-10 13:22:13,830 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.display.RenderingDef:Id_3
2012-10-10 13:22:14,875 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_3 for ome.model.meta.EventLog:Id_113
2012-10-10 13:22:15,875 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.display.RenderingDef:Id_3
2012-10-10 13:22:16,018 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-3) Currently running; skipping
2012-10-10 13:22:16,919 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_2 for ome.model.meta.EventLog:Id_116
2012-10-10 13:22:17,919 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.annotations.ImageAnnotationLink:Id_2
2012-10-10 13:22:17,936 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_3 for ome.model.meta.EventLog:Id_117
2012-10-10 13:22:18,936 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.display.RenderingDef:Id_3
2012-10-10 13:22:18,962 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_119
2012-10-10 13:22:19,963 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:22:19,991 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_120
2012-10-10 13:22:20,014 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-2) Currently running; skipping
2012-10-10 13:22:20,991 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:22:24,015 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-4) Currently running; skipping
2012-10-10 13:22:27,121 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) INDEXED 50 objects in 1 batch(es) [51100 ms.]
2012-10-10 13:22:27,123 ERROR [        ome.services.util.ServiceHandler] (2-thread-1) Method interface ome.services.util.Executor$Work.doWork invocation took 51102
2012-10-10 13:22:32,016 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-3) Currently running; skipping
2012-10-10 13:22:36,014 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-2) Currently running; skipping
2012-10-10 13:22:37,205 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.meta.Experimenter:Id_2
2012-10-10 13:22:40,014 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-4) Currently running; skipping
2012-10-10 13:22:40,271 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.meta.Experimenter:Id_2
2012-10-10 13:22:44,014 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-1) Currently running; skipping
2012-10-10 13:22:48,019 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-3) Currently running; skipping
2012-10-10 13:22:50,472 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_4
2012-10-10 13:22:50,503 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.containers.Dataset:Id_6 for ome.model.meta.EventLog:Id_242
2012-10-10 13:22:50,503 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.containers.Dataset:Id_6
2012-10-10 13:22:50,519 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.containers.Dataset:Id_7 for ome.model.meta.EventLog:Id_247
2012-10-10 13:22:50,519 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.containers.Dataset:Id_7
2012-10-10 13:22:50,545 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.containers.Project:Id_3 for ome.model.meta.EventLog:Id_248
2012-10-10 13:22:50,545 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.containers.Project:Id_3
2012-10-10 13:22:50,579 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_251
2012-10-10 13:22:50,579 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:22:50,853 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_6
2012-10-10 13:22:51,315 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_6
2012-10-10 13:22:51,345 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_6
2012-10-10 13:22:51,362 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_285
2012-10-10 13:22:51,362 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:22:51,397 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.OriginalFile:Id_70 for ome.model.meta.EventLog:Id_286
2012-10-10 13:22:51,397 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.OriginalFile:Id_70
2012-10-10 13:22:51,414 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.annotations.FileAnnotation:Id_8 for ome.model.meta.EventLog:Id_287
2012-10-10 13:22:51,415 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.annotations.FileAnnotation:Id_8
2012-10-10 13:22:51,435 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) INDEXED 50 objects in 1 batch(es) [23422 ms.]
2012-10-10 13:22:51,437 ERROR [        ome.services.util.ServiceHandler] (2-thread-5) Method interface ome.services.util.Executor$Work.doWork invocation took 23425
2012-10-10 13:22:52,046 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) INDEXED 3 objects in 1 batch(es) [29 ms.]
2012-10-10 13:22:56,034 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_7 for ome.model.meta.EventLog:Id_288
2012-10-10 13:22:56,034 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.annotations.ImageAnnotationLink:Id_7
2012-10-10 13:22:56,051 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Pixels:Id_7 for ome.model.meta.EventLog:Id_290
2012-10-10 13:22:56,051 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Pixels:Id_7
2012-10-10 13:22:56,066 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.LogicalChannel:Id_13 for ome.model.meta.EventLog:Id_291
2012-10-10 13:22:56,066 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.LogicalChannel:Id_13
2012-10-10 13:22:56,082 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Pixels:Id_7 for ome.model.meta.EventLog:Id_293
2012-10-10 13:22:56,083 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Pixels:Id_7
2012-10-10 13:22:56,099 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Pixels:Id_7 for ome.model.meta.EventLog:Id_294
2012-10-10 13:22:56,100 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Pixels:Id_7
2012-10-10 13:22:56,114 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_9 for ome.model.meta.EventLog:Id_298
2012-10-10 13:22:56,114 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.display.RenderingDef:Id_9
2012-10-10 13:22:56,131 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.OriginalFile:Id_70 for ome.model.meta.EventLog:Id_301
2012-10-10 13:22:56,131 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.OriginalFile:Id_70
2012-10-10 13:22:56,152 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_8 for ome.model.meta.EventLog:Id_302
2012-10-10 13:22:56,152 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.annotations.ImageAnnotationLink:Id_8
2012-10-10 13:22:56,166 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_9 for ome.model.meta.EventLog:Id_303
2012-10-10 13:22:56,167 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.annotations.ImageAnnotationLink:Id_9
2012-10-10 13:22:56,237 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Added to backlog:ome.model.core.Image:Id_8
2012-10-10 13:22:56,388 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Already in backlog:ome.model.core.Image:Id_8
2012-10-10 13:22:56,402 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Already in backlog:ome.model.core.Image:Id_8
2012-10-10 13:22:56,483 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Added to backlog:ome.model.core.Image:Id_9
2012-10-10 13:22:56,633 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Already in backlog:ome.model.core.Image:Id_9
2012-10-10 13:22:56,647 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Already in backlog:ome.model.core.Image:Id_9
2012-10-10 13:22:56,714 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Added to backlog:ome.model.core.Image:Id_10
2012-10-10 13:22:56,867 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Already in backlog:ome.model.core.Image:Id_10
2012-10-10 13:22:56,872 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) INDEXED 50 objects in 1 batch(es) [855 ms.]
2012-10-10 13:23:00,037 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) INDEXED 3 objects in 1 batch(es) [19 ms.]
2012-10-10 13:23:04,034 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Added to backlog:ome.model.core.Image:Id_10
2012-10-10 13:23:04,113 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Added to backlog:ome.model.core.Image:Id_11
2012-10-10 13:23:04,267 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Already in backlog:ome.model.core.Image:Id_11
2012-10-10 13:23:04,281 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Already in backlog:ome.model.core.Image:Id_11
2012-10-10 13:23:04,360 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Added to backlog:ome.model.core.Image:Id_12
2012-10-10 13:23:04,512 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Already in backlog:ome.model.core.Image:Id_12
2012-10-10 13:23:04,526 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Already in backlog:ome.model.core.Image:Id_12
2012-10-10 13:23:04,593 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Added to backlog:ome.model.core.Image:Id_13
2012-10-10 13:23:04,744 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Already in backlog:ome.model.core.Image:Id_13
2012-10-10 13:23:04,759 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Already in backlog:ome.model.core.Image:Id_13
2012-10-10 13:23:04,836 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-3) Added to backlog:ome.model.core.Image:Id_14
2012-10-10 13:23:04,898 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-3) INDEXED 50 objects in 1 batch(es) [879 ms.]
2012-10-10 13:23:08,046 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) INDEXED 5 objects in 1 batch(es) [30 ms.]
2012-10-10 13:23:12,134 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Added to backlog:ome.model.core.Image:Id_14
2012-10-10 13:23:12,149 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.core.Image:Id_14
2012-10-10 13:23:12,217 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Added to backlog:ome.model.core.Image:Id_15
2012-10-10 13:23:12,374 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.core.Image:Id_15
2012-10-10 13:23:12,397 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.core.Image:Id_15
2012-10-10 13:23:12,710 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_540
2012-10-10 13:23:12,710 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:23:12,727 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_541
2012-10-10 13:23:12,727 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:23:12,743 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_542
2012-10-10 13:23:12,744 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:23:12,824 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Added to backlog:ome.model.meta.Share:Id_915
2012-10-10 13:23:12,856 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.meta.Share:Id_915
2012-10-10 13:23:12,904 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Null returned! Purging since cannot index ome.model.roi.Line:Id_2 for ome.model.meta.EventLog:Id_562
2012-10-10 13:23:12,905 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Purged: class ome.model.roi.Line:Id_2
2012-10-10 13:23:12,934 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Null returned! Purging since cannot index ome.model.roi.Line:Id_2 for ome.model.meta.EventLog:Id_569
2012-10-10 13:23:12,934 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) Purged: class ome.model.roi.Line:Id_2
2012-10-10 13:23:13,302 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Added to backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:23:13,398 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:23:13,447 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:23:13,479 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-2) Already in backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:23:13,500 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) INDEXED 50 objects in 1 batch(es) [1482 ms.]
2012-10-10 13:23:16,045 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) INDEXED 4 objects in 1 batch(es) [32 ms.]
2012-10-10 13:23:16,109 WARN  [         ome.services.fulltext.PdfThread] ( Thread-25) Error reading pdf file
java.io.IOException: Pipe closed
   at java.io.PipedReader.receive(PipedReader.java:156)
   at java.io.PipedReader.receive(PipedReader.java:190)
   at java.io.PipedWriter.write(PipedWriter.java:133)
   at java.io.Writer.write(Writer.java:175)
   at java.io.Writer.write(Writer.java:140)
   at org.pdfbox.util.PDFTextStripper.writeCharacters(PDFTextStripper.java:549)
   at org.pdfbox.util.PDFTextStripper.flushText(PDFTextStripper.java:521)
   at org.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:337)
   at org.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:259)
   at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
   at ome.services.fulltext.PdfThread.run(PdfParser.java:92)
2012-10-10 13:23:16,109 WARN  [         ome.services.fulltext.PdfThread] ( Thread-26) Error reading pdf file
java.io.IOException: Pipe closed
   at java.io.PipedReader.receive(PipedReader.java:156)
   at java.io.PipedReader.receive(PipedReader.java:190)
   at java.io.PipedWriter.write(PipedWriter.java:133)
   at java.io.Writer.write(Writer.java:175)
   at java.io.Writer.write(Writer.java:140)
   at org.pdfbox.util.PDFTextStripper.writeCharacters(PDFTextStripper.java:549)
   at org.pdfbox.util.PDFTextStripper.flushText(PDFTextStripper.java:521)
   at org.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:337)
   at org.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:259)
   at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
   at ome.services.fulltext.PdfThread.run(PdfParser.java:92)
2012-10-10 13:23:20,106 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_14
2012-10-10 13:23:20,209 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) INDEXED 23 objects in 1 batch(es) [188 ms.]
2012-10-10 13:23:24,023 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-3) INDEXED 1 objects in 1 batch(es) [6 ms.]
2012-10-10 13:23:36,168 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.screen.Screen:Id_2 for ome.model.meta.EventLog:Id_69
2012-10-10 13:23:36,169 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.screen.Screen:Id_2
2012-10-10 13:23:36,206 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.containers.Dataset:Id_3 for ome.model.meta.EventLog:Id_97
2012-10-10 13:23:36,206 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.containers.Dataset:Id_3
2012-10-10 13:23:36,211 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_98
2012-10-10 13:23:36,211 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:23:36,217 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Pixels:Id_3 for ome.model.meta.EventLog:Id_100
2012-10-10 13:23:36,218 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Pixels:Id_3
2012-10-10 13:23:36,221 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.LogicalChannel:Id_3 for ome.model.meta.EventLog:Id_101
2012-10-10 13:23:36,222 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.LogicalChannel:Id_3
2012-10-10 13:23:36,228 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Pixels:Id_3 for ome.model.meta.EventLog:Id_103
2012-10-10 13:23:36,228 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Pixels:Id_3
2012-10-10 13:23:36,234 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Pixels:Id_3 for ome.model.meta.EventLog:Id_104
2012-10-10 13:23:36,234 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Pixels:Id_3
2012-10-10 13:23:36,238 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_3 for ome.model.meta.EventLog:Id_108
2012-10-10 13:23:36,238 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.display.RenderingDef:Id_3
2012-10-10 13:23:36,247 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_3 for ome.model.meta.EventLog:Id_113
2012-10-10 13:23:36,248 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.display.RenderingDef:Id_3
2012-10-10 13:23:36,258 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_2 for ome.model.meta.EventLog:Id_116
2012-10-10 13:23:36,258 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.annotations.ImageAnnotationLink:Id_2
2012-10-10 13:23:36,262 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_3 for ome.model.meta.EventLog:Id_117
2012-10-10 13:23:36,262 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.display.RenderingDef:Id_3
2012-10-10 13:23:36,267 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_119
2012-10-10 13:23:36,268 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:23:36,273 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_120
2012-10-10 13:23:36,273 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:23:36,307 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) INDEXED 50 objects in 1 batch(es) [290 ms.]
2012-10-10 13:23:40,069 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.meta.Experimenter:Id_2
2012-10-10 13:23:40,085 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.meta.Experimenter:Id_2
2012-10-10 13:23:40,137 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_4
2012-10-10 13:23:40,147 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.containers.Dataset:Id_6 for ome.model.meta.EventLog:Id_242
2012-10-10 13:23:40,147 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.containers.Dataset:Id_6
2012-10-10 13:23:40,152 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.containers.Dataset:Id_7 for ome.model.meta.EventLog:Id_247
2012-10-10 13:23:40,152 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.containers.Dataset:Id_7
2012-10-10 13:23:40,158 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.containers.Project:Id_3 for ome.model.meta.EventLog:Id_248
2012-10-10 13:23:40,158 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.containers.Project:Id_3
2012-10-10 13:23:40,170 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Image:Id_3 for ome.model.meta.EventLog:Id_251
2012-10-10 13:23:40,171 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Image:Id_3
2012-10-10 13:23:40,272 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_6
2012-10-10 13:23:40,360 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_6
2012-10-10 13:23:40,364 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_6
2012-10-10 13:23:40,369 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_285
2012-10-10 13:23:40,370 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:23:40,375 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.core.OriginalFile:Id_70 for ome.model.meta.EventLog:Id_286
2012-10-10 13:23:40,376 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.core.OriginalFile:Id_70
2012-10-10 13:23:40,382 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Null returned! Purging since cannot index ome.model.annotations.FileAnnotation:Id_8 for ome.model.meta.EventLog:Id_287
2012-10-10 13:23:40,382 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) Purged: class ome.model.annotations.FileAnnotation:Id_8
2012-10-10 13:23:40,385 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) INDEXED 50 objects in 1 batch(es) [367 ms.]
2012-10-10 13:23:44,034 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-3) INDEXED 3 objects in 1 batch(es) [16 ms.]
2012-10-10 13:23:48,023 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_7 for ome.model.meta.EventLog:Id_288
2012-10-10 13:23:48,023 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.annotations.ImageAnnotationLink:Id_7
2012-10-10 13:23:48,029 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Pixels:Id_7 for ome.model.meta.EventLog:Id_290
2012-10-10 13:23:48,029 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Pixels:Id_7
2012-10-10 13:23:48,033 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.LogicalChannel:Id_13 for ome.model.meta.EventLog:Id_291
2012-10-10 13:23:48,033 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.LogicalChannel:Id_13
2012-10-10 13:23:48,040 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Pixels:Id_7 for ome.model.meta.EventLog:Id_293
2012-10-10 13:23:48,040 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Pixels:Id_7
2012-10-10 13:23:48,046 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Pixels:Id_7 for ome.model.meta.EventLog:Id_294
2012-10-10 13:23:48,046 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Pixels:Id_7
2012-10-10 13:23:48,050 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.display.RenderingDef:Id_9 for ome.model.meta.EventLog:Id_298
2012-10-10 13:23:48,050 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.display.RenderingDef:Id_9
2012-10-10 13:23:48,056 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.OriginalFile:Id_70 for ome.model.meta.EventLog:Id_301
2012-10-10 13:23:48,056 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.OriginalFile:Id_70
2012-10-10 13:23:48,060 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_8 for ome.model.meta.EventLog:Id_302
2012-10-10 13:23:48,060 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.annotations.ImageAnnotationLink:Id_8
2012-10-10 13:23:48,063 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.annotations.ImageAnnotationLink:Id_9 for ome.model.meta.EventLog:Id_303
2012-10-10 13:23:48,064 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.annotations.ImageAnnotationLink:Id_9
2012-10-10 13:23:48,088 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_8
2012-10-10 13:23:48,134 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_8
2012-10-10 13:23:48,138 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_8
2012-10-10 13:23:48,161 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_9
2012-10-10 13:23:48,209 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_9
2012-10-10 13:23:48,213 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_9
2012-10-10 13:23:48,236 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_10
2012-10-10 13:23:48,282 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_10
2012-10-10 13:23:48,285 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) INDEXED 50 objects in 1 batch(es) [266 ms.]
2012-10-10 13:23:52,032 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) INDEXED 3 objects in 1 batch(es) [18 ms.]
2012-10-10 13:23:56,023 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_10
2012-10-10 13:23:56,047 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_11
2012-10-10 13:23:56,093 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_11
2012-10-10 13:23:56,097 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_11
2012-10-10 13:23:56,125 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_12
2012-10-10 13:23:56,173 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_12
2012-10-10 13:23:56,177 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_12
2012-10-10 13:23:56,201 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_13
2012-10-10 13:23:56,249 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_13
2012-10-10 13:23:56,253 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Already in backlog:ome.model.core.Image:Id_13
2012-10-10 13:23:56,276 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-1) Added to backlog:ome.model.core.Image:Id_14
2012-10-10 13:23:56,296 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) INDEXED 50 objects in 1 batch(es) [277 ms.]
2012-10-10 13:24:00,047 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-3) INDEXED 5 objects in 1 batch(es) [24 ms.]
2012-10-10 13:24:04,055 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_14
2012-10-10 13:24:04,059 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_14
2012-10-10 13:24:04,083 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.core.Image:Id_15
2012-10-10 13:24:04,129 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_15
2012-10-10 13:24:04,133 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.core.Image:Id_15
2012-10-10 13:24:04,214 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_540
2012-10-10 13:24:04,214 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:24:04,241 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_541
2012-10-10 13:24:04,241 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:24:04,273 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.core.Image:Id_7 for ome.model.meta.EventLog:Id_542
2012-10-10 13:24:04,274 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.core.Image:Id_7
2012-10-10 13:24:04,353 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.meta.Share:Id_915
2012-10-10 13:24:04,403 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.meta.Share:Id_915
2012-10-10 13:24:04,420 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.roi.Line:Id_2 for ome.model.meta.EventLog:Id_562
2012-10-10 13:24:04,420 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.roi.Line:Id_2
2012-10-10 13:24:04,428 ERROR [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Null returned! Purging since cannot index ome.model.roi.Line:Id_2 for ome.model.meta.EventLog:Id_569
2012-10-10 13:24:04,428 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) Purged: class ome.model.roi.Line:Id_2
2012-10-10 13:24:04,519 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Added to backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:24:04,573 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:24:04,689 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:24:04,750 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-5) Already in backlog:ome.model.containers.Dataset:Id_8
2012-10-10 13:24:04,786 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) INDEXED 50 objects in 1 batch(es) [768 ms.]
2012-10-10 13:24:04,802 WARN  [         ome.services.fulltext.PdfThread] ( Thread-43) Error reading pdf file
java.io.IOException: Pipe closed
   at java.io.PipedReader.receive(PipedReader.java:156)
   at java.io.PipedReader.receive(PipedReader.java:190)
   at java.io.PipedWriter.write(PipedWriter.java:133)
   at java.io.Writer.write(Writer.java:175)
   at java.io.Writer.write(Writer.java:140)
   at org.pdfbox.util.PDFTextStripper.writeCharacters(PDFTextStripper.java:549)
   at org.pdfbox.util.PDFTextStripper.flushText(PDFTextStripper.java:521)
   at org.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:337)
   at org.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:259)
   at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
   at ome.services.fulltext.PdfThread.run(PdfParser.java:92)
2012-10-10 13:24:04,803 WARN  [         ome.services.fulltext.PdfThread] ( Thread-44) Error reading pdf file
java.io.IOException: Pipe closed
   at java.io.PipedReader.receive(PipedReader.java:156)
   at java.io.PipedReader.receive(PipedReader.java:190)
   at java.io.PipedWriter.write(PipedWriter.java:133)
   at java.io.Writer.write(Writer.java:175)
   at java.io.Writer.write(Writer.java:140)
   at org.pdfbox.util.PDFTextStripper.writeCharacters(PDFTextStripper.java:549)
   at org.pdfbox.util.PDFTextStripper.flushText(PDFTextStripper.java:521)
   at org.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:337)
   at org.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:259)
   at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
   at ome.services.fulltext.PdfThread.run(PdfParser.java:92)
2012-10-10 13:24:08,050 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) INDEXED 4 objects in 1 batch(es) [27 ms.]
2012-10-10 13:24:08,117 WARN  [         ome.services.fulltext.PdfThread] ( Thread-45) Error reading pdf file
java.io.IOException: Pipe closed
   at java.io.PipedReader.receive(PipedReader.java:156)
   at java.io.PipedReader.receive(PipedReader.java:190)
   at java.io.PipedWriter.write(PipedWriter.java:133)
   at java.io.Writer.write(Writer.java:175)
   at java.io.Writer.write(Writer.java:140)
   at org.pdfbox.util.PDFTextStripper.writeCharacters(PDFTextStripper.java:549)
   at org.pdfbox.util.PDFTextStripper.flushText(PDFTextStripper.java:521)
   at org.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:337)
   at org.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:259)
   at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
   at ome.services.fulltext.PdfThread.run(PdfParser.java:92)
2012-10-10 13:24:08,120 WARN  [         ome.services.fulltext.PdfThread] ( Thread-46) Error reading pdf file
java.io.IOException: Pipe closed
   at java.io.PipedReader.receive(PipedReader.java:156)
   at java.io.PipedReader.receive(PipedReader.java:190)
   at java.io.PipedWriter.write(PipedWriter.java:133)
   at java.io.Writer.write(Writer.java:175)
   at java.io.Writer.write(Writer.java:140)
   at org.pdfbox.util.PDFTextStripper.writeCharacters(PDFTextStripper.java:549)
   at org.pdfbox.util.PDFTextStripper.flushText(PDFTextStripper.java:521)
   at org.pdfbox.util.PDFTextStripper.processPage(PDFTextStripper.java:337)
   at org.pdfbox.util.PDFTextStripper.processPages(PDFTextStripper.java:259)
   at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
   at ome.services.fulltext.PdfThread.run(PdfParser.java:92)
2012-10-10 13:24:12,036 INFO  [     ome.services.eventlogs.EventBacklog] (2-thread-4) Added to backlog:ome.model.core.Image:Id_14
2012-10-10 13:24:12,136 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-4) INDEXED 23 objects in 1 batch(es) [120 ms.]
2012-10-10 13:24:16,022 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-1) INDEXED 1 objects in 1 batch(es) [6 ms.]
2012-10-10 15:11:00,523 INFO  [                ome.services.blitz.Entry] (      main) Calling close on context ome.fulltext
2012-10-10 15:11:00,527 INFO  [.services.scheduler.SchedulerFactoryBean] (      main) Shutting down Quartz Scheduler
2012-10-10 15:11:00,527 INFO  [    ome.services.fulltext.FullTextThread] (      main) Shutting down Full-Text Indexer
2012-10-10 15:11:00,566 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Shutting down EHCache CacheManager
2012-10-10 15:11:00,583 INFO  [                ome.services.blitz.Entry] (      main) Finished shutdown.
2012-10-10 15:11:19,751 INFO  [                ome.services.blitz.Entry] (      main) Waiting 10000 ms on startup
2012-10-10 15:11:29,763 INFO  [                ome.services.blitz.Entry] (      main) Creating ome.fulltext. Please wait...
2012-10-10 15:11:32,521 INFO  [ng.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing EHCache CacheManager
2012-10-10 15:11:36,202 INFO  [  ome.services.fulltext.FullTextAnalyzer] (      main) Initialized FullTextAnalyzer
2012-10-10 15:11:42,184 INFO  [    ome.services.fulltext.FullTextThread] (      main) Initializing Full-Text Indexer
2012-10-10 15:11:42,702 INFO  [        ome.services.db.DatabaseIdentity] (      main) Using LSID format: urn:lsid:export.openmicroscopy.org:%s:9a03effd-4173-4f1a-9d8a-1d007310bcf8_%s%s
2012-10-10 15:11:43,146 INFO  [    ome.tools.hibernate.ExtendedMetadata] (      main) Calculating ExtendedMetadata...
2012-10-10 15:11:43,344 INFO  [.services.scheduler.SchedulerFactoryBean] (      main) Starting Quartz Scheduler now
2012-10-10 15:11:43,751 INFO  [                ome.services.blitz.Entry] (      main) ome.fulltext now accepting connections.
2012-10-10 15:11:45,031 INFO  [       ome.security.basic.CurrentDetails] (2-thread-2) Adding log:INSERT,class ome.model.meta.Session,1564
2012-10-10 15:11:45,050 INFO  [       ome.security.basic.CurrentDetails] (2-thread-3) Adding log:INSERT,class ome.model.meta.Session,1565
2012-10-10 15:11:45,176 INFO  [    ome.services.fulltext.FullTextThread] (2-thread-2) Currently running; skipping
2012-10-10 15:14:48,166 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-5) INDEXED 1 objects in 1 batch(es) [145 ms.]


Thats the contents of FullText:

Code: Select all

omero@omerovm:~/OMERO.data/FullText$ ls -al
total 604
drwxr-xr-x 2 omero omero   4096 Oct 10 15:16 .
drwxr-xr-x 8 omero omero   4096 Oct 10 13:23 ..
-rw-r--r-- 1 omero omero 553151 Oct 10 15:16 _299.cfs
-rw-r--r-- 1 omero omero    574 Oct 10 15:16 _29a.cfs
-rw-r--r-- 1 omero omero    562 Oct 10 15:16 _29b.cfs
-rw-r--r-- 1 omero omero    558 Oct 10 15:16 _29c.cfs
-rw-r--r-- 1 omero omero    586 Oct 10 15:16 _29d.cfs
-rw-r--r-- 1 omero omero    589 Oct 10 15:16 _29e.cfs
-rw-r--r-- 1 omero omero    580 Oct 10 15:16 _29f.cfs
-rw-r--r-- 1 omero omero    570 Oct 10 15:16 _29g.cfs
-rw-r--r-- 1 omero omero    576 Oct 10 15:16 _29h.cfs
-rw-r--r-- 1 omero omero    561 Oct 10 15:16 _29i.cfs
-rw-r--r-- 1 omero omero    569 Oct 10 15:16 _29j.cfs
-rw-r--r-- 1 omero omero    380 Oct 10 15:16 segments_29l
-rw-r--r-- 1 omero omero     20 Oct 10 15:16 segments.gen


Thats my data: https://dl.dropbox.com/u/560426/omerodata.png

When I search for a image name (e.g. NSc-bin01-16) by OMERO.web: No Results
When I search for a dataset (Sep): Found it!

So, why does OMERO.web finds the Dataset but not the images inside??

With OMERO.insight i dont find anything... no dataset, no image :-/

Edit: Because of the PDF exception, i removed all attachments and redone indexing... no further results :-/

[jumpfunky]

That's funny! I've change the name of one of my images... to myimage.bmp... and: Found it via Web an Insight!! Now I'am confused...

when I seach for "*.bmp" i get no results. if i search for "myimage" I found myimage.bmp. if i search for "*bmp" (without the dot!) I found myimage.bmp.
if i search for "my*" i found myimage.bmp

Now i've change the name of my image to "Nsc-im-50.bmp". Same results.

Maybe a bug of the importer? I going to try to import other images and search for it.