Re: [GeoNetwork-devel] [GeoNetwork-users] Can't create metadata and templates. Error: Timer already

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Hi all,

I have found mention of the "Timer already cancelled" error at URL: 

http://osdir.com/ml/users/2010-07/msg01393.html

which says to  

'Remove "timeBetweenEvictionRunsMillis" attribute, or set it to "-1".'

which I have done in
the /geonetwork/webapps/geonetwork/WEB-INF/config.xml file.  This didn't
fix the problem but I have noticed the following errors in the
catalina.out file:

...

2012-05-31 17:18:01,736 INFO  [jeeves.engine] -    Adding resource :
main-db
2012-05-31 17:18:01,740 WARN  [jeeves.dbmspool] - Using transaction
isolation setting SERIALIZABLE
31/05/2012 5:18:01 PM org.geotools.data.postgis.PostgisDBInfo <init>
SEVERE: ERROR: function postgis_version() does not exist
  Hint: No function matches the given name and argument types. You might
need to add explicit type casts.
  Position: 8
2012-05-31 17:18:02,114 INFO  [jeeves.engine] - Initializing
services...

...

2012-05-31 17:18:02,582 INFO  [jeeves.engine] -    Adding service : csw
2012-05-31 17:18:02,583 WARN  [jeeves.engine] - Raised exception while
registering service. Skipped.
2012-05-31 17:18:02,583 WARN  [jeeves.engine] -    Service   : csw
2012-05-31 17:18:02,583 WARN  [jeeves.engine] -    Package   :
org.fao.geonet
2012-05-31 17:18:02,583 WARN  [jeeves.engine] -    Exception :
java.lang.ClassNotFoundException:
org.fao.geonet.services.main.CswDispatcher
2012-05-31 17:18:02,583 WARN  [jeeves.engine] -    Message   :
org.fao.geonet.services.main.CswDispatcher
2012-05-31 17:18:02,584 WARN  [jeeves.engine] -    Stack     :
java.lang.ClassNotFoundException:
org.fao.geonet.services.main.CswDispatcher
        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1680)
        at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1526)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:169)
        at
jeeves.server.dispatchers.ServiceManager.buildService(ServiceManager.java:210)
        at
jeeves.server.dispatchers.ServiceManager.addService(ServiceManager.java:173)
        at
jeeves.server.JeevesEngine.initServices(JeevesEngine.java:582)
        at
jeeves.server.JeevesEngine.loadConfigFile(JeevesEngine.java:300)
        at
jeeves.server.JeevesEngine.loadConfigFile(JeevesEngine.java:317)
        at jeeves.server.JeevesEngine.init(JeevesEngine.java:152)
        at
jeeves.server.sources.http.JeevesServlet.init(JeevesServlet.java:76)
        at javax.servlet.GenericServlet.init(GenericServlet.java:212)
        at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1206)
        at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1026)
        at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)

...

2012-05-31 17:18:06,667 DEBUG [jeeves] - Adding xml to /summary/def
2012-05-31 17:18:08,321 WARN  [geonetwork.spatial] - Failure to make
_writer, maybe a problem but might also not be an issue:<error
id="error">
  <message />
  <class>NullPointerException</class>
  <stack>
    <at class="org.fao.geonet.kernel.search.spatial.SpatialIndexWriter"
file="SpatialIndexWriter.java" line="129" method="&lt;init&gt;" />
    <at class="org.fao.geonet.kernel.search.SearchManager$Spatial"
file="SearchManager.java" line="1412" method="createWriter" />
    <at class="org.fao.geonet.kernel.search.SearchManager$Spatial"
file="SearchManager.java" line="1390" method="&lt;init&gt;" />
    <at class="org.fao.geonet.kernel.search.SearchManager"
file="SearchManager.java" line="373" method="&lt;init&gt;" />
    <at class="org.fao.geonet.Geonetwork" file="Geonetwork.java"
line="339" method="start" />
    <at class="jeeves.server.JeevesEngine" file="JeevesEngine.java"
line="525" method="initAppHandler" />
    <at class="jeeves.server.JeevesEngine" file="JeevesEngine.java"
line="161" method="init" />
    <at class="jeeves.server.sources.http.JeevesServlet"
file="JeevesServlet.java" line="76" method="init" />
    <at class="javax.servlet.GenericServlet" file="GenericServlet.java"
line="212" method="init" />
    <at class="org.apache.catalina.core.StandardWrapper"
file="StandardWrapper.java" line="1206" method="loadServlet" />
    <skip>...</skip>
  </stack>
</error>
2012-05-31 17:18:08,321 ERROR [geonetwork.spatial] - Unable to call
reset on Spatial writer: null
java.lang.NullPointerException
        at org.fao.geonet.kernel.search.SearchManager
$Spatial.createWriter(SearchManager.java:1419)
        at org.fao.geonet.kernel.search.SearchManager
$Spatial.<init>(SearchManager.java:1390)
        at
org.fao.geonet.kernel.search.SearchManager.<init>(SearchManager.java:373)
        at org.fao.geonet.Geonetwork.start(Geonetwork.java:339)
        at
jeeves.server.JeevesEngine.initAppHandler(JeevesEngine.java:525)
        at jeeves.server.JeevesEngine.init(JeevesEngine.java:161)
        at
jeeves.server.sources.http.JeevesServlet.init(JeevesServlet.java:76)
        at javax.servlet.GenericServlet.init(GenericServlet.java:212)
        at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1206)
        at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1026)
        at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
        at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
        at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
        at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
        at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
        at
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1079)
        at
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1002)
        at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:506)
        at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)
        at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
        at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
        at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)
        at
org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
        at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)
        at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
        at
org.apache.catalina.core.StandardService.start(StandardService.java:525)

...

2012-05-31 17:18:08,324 ERROR [geonetwork.index] - Rebuilding lucene
index
2012-05-31 17:18:08,612 INFO  [jeeves.apphand] -   - Access manager...
2012-05-31 17:18:08,620 INFO  [jeeves.apphand] -   - Xml serializer and
Data manager...
2012-05-31 17:18:08,646 WARN  [geonetwork.settings] - Unable to find
Settings row for: system/site/svnUuid. Check settings table.
2012-05-31 17:18:09,308 WARN  [geonetwork.svnmanager] - Recreating
subversion repository
at /data/jakarta/geonetwork-asdd/webapps/geonetwork/WEB-INF/data/metadata_subversion as previous repository was empty
2012-05-31 17:18:09,505 INFO  [jeeves.apphand] -   - Harvest manager...
2012-05-31 17:18:10,217 INFO  [jeeves.apphand] -   - Catalogue services
for the web...
2012-05-31 17:18:10,250 INFO  [jeeves.apphand] -   - Open Archive
Initiative (OAI-PMH) server...
2012-05-31 17:18:10,273 INFO  [jeeves.apphand] -   - Metadata
notifier ...
2012-05-31 17:18:10,273 INFO  [jeeves.apphand] - Site ID is :
dd714eee-01f6-4d00-a84c-16a03a50a3f4
2012-05-31 17:18:10,277 INFO  [jeeves.engine] - --- Handler started
---------------------------------------
2012-05-31 17:18:10,277 INFO  [jeeves.engine] - Starting schedule
manager...
2012-05-31 17:18:10,278 INFO  [jeeves.engine] - Memory used is  :
-113902 Kb
2012-05-31 17:18:10,278 INFO  [jeeves.engine] - Total memory is :
3728320 Kb
2012-05-31 17:18:10,278 INFO  [jeeves.engine] - Startup time is : 8
(secs)
2012-05-31 17:18:10,278 INFO  [jeeves.engine] - === System working
=========================================
31/05/2012 5:18:10 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080

...

INFO: Server startup in 19261 ms
2012-05-31 17:18:19,551 ERROR [geonetwork.datamanager] - The metadata
document index with id=1 is corrupt/invalid - ignoring it. Error: null
java.lang.NullPointerException
        at
org.fao.geonet.kernel.search.spatial.SpatialIndexWriter.<init>(SpatialIndexWriter.java:129)
        at org.fao.geonet.kernel.search.SearchManager
$Spatial.writerNoLocking(SearchManager.java:1529)
        at org.fao.geonet.kernel.search.SearchManager
$Spatial.writer(SearchManager.java:1515)
        at
org.fao.geonet.kernel.search.SearchManager.delete(SearchManager.java:835)
        at
org.fao.geonet.kernel.search.SearchManager.buildIndexDocument(SearchManager.java:721)
        at
org.fao.geonet.kernel.search.SearchManager.index(SearchManager.java:639)
        at
org.fao.geonet.kernel.DataManager.indexMetadata(DataManager.java:524)
        at org.fao.geonet.kernel.DataManager
$IndexMetadataTask.run(DataManager.java:340)
        at java.util.concurrent.ThreadPoolExecutor
$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor
$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
Exception in thread "Timer-1" java.lang.NullPointerException
        at org.fao.geonet.kernel.search.SearchManager$Spatial
$Committer.run(SearchManager.java:1560)
        at java.util.TimerThread.mainLoop(Timer.java:512)
        at java.util.TimerThread.run(Timer.java:462)

...

Any hints on what to do to fix this would be greatly appreciated.

I'm running: 

psql (PostgreSQL) 8.4.11
contains support for command-line editing

 and it appears to have the 270 dagaa bs upgrades.

Thanks.

John H.

On Thu, 2012-05-31 at 14:30 +1000, john.hockaday wrote:
> Hi All,
> 
> Sorry for cross posting.
> 
> I have tried to fix the "corrupt/invalid ignoring it. Error: Timer
> already cancelled." error by doing the following:
> 
> sudo su - postgres
> psql -d gndb
> delete from metadatarating;
> delete from validation;
> delete from metadatacateg;
> delete from operationallowed;
> delete from metadata;
> 
> reindex database gndb force;
> 
> \q
> 
> 
> I had to delete from the metadarating, validation, metadatacateg and
> operationallowed because of links to the metadata table or each other.
> 
> I then start GN and tried to load just one services metadata record. The
> catalina.out file showed this:
> 
> ...
> 
>              &lt;/gmd:function&gt;&#xD;
>             &lt;/gmd:CI_OnlineResource&gt;&#xD;
>           &lt;/srv:connectPoint&gt;&#xD;
>         &lt;/srv:SV_OperationMetadata&gt;&#xD;
>       &lt;/srv:containsOperations&gt;&#xD;
>     &lt;/srv:SV_ServiceIdentification&gt;&#xD;
>   &lt;/gmd:identificationInfo&gt;&#xD;
> &lt;/gmd:MD_Metadata&gt;</data>
>   <group>11</group>
>   <uuidAction>overwrite</uuidAction>
>   <validate>on</validate>
>   <file_type>single</file_type>
> </request>
> 2012-05-31 14:13:41,911 ERROR [geonetwork.datamanager] - The metadata
> document index with id=1 is corrupt/invalid - ignoring it. Error: null
> java.lang.NullPointerException
>         at
> org.fao.geonet.kernel.search.spatial.SpatialIndexWriter.<init>(SpatialIndexWriter.java:129)
>         at org.fao.geonet.kernel.search.SearchManager
> $Spatial.writerNoLocking(SearchManager.java:1529)
>         at org.fao.geonet.kernel.search.SearchManager
> $Spatial.writer(SearchManager.java:1515)
>         at
> org.fao.geonet.kernel.search.SearchManager.delete(SearchManager.java:835)
>         at
> org.fao.geonet.kernel.search.SearchManager.buildIndexDocument(SearchManager.java:721)
>         at
> org.fao.geonet.kernel.search.SearchManager.index(SearchManager.java:639)
>         at
> org.fao.geonet.kernel.DataManager.indexMetadata(DataManager.java:524)
>         at org.fao.geonet.kernel.DataManager
> $IndexMetadataTask.run(DataManager.java:340)
>         at java.util.concurrent.ThreadPoolExecutor
> $Worker.runTask(ThreadPoolExecutor.java:886)
>         at java.util.concurrent.ThreadPoolExecutor
> $Worker.run(ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
> 2012-05-31 14:13:41,913 INFO  [jeeves.service] -    -> dispatching to
> output for : metadata.insert.paste
> 2012-05-31 14:13:41,929 INFO  [jeeves.service] -      -> transforming
> with
> stylesheet : /data/jakarta/geonetwork-asdd/webapps/geonetwork/xsl/metadata-insert-results.xsl
> 2012-05-31 14:13:41,957 ERROR [geonetwork.datamanager] - The metadata
> document index with id=1 is corrupt/invalid - ignoring it. Error: null
> java.lang.NullPointerException
>         at
> org.fao.geonet.kernel.search.spatial.SpatialIndexWriter.<init>(SpatialIndexWriter.java:129)
>         at org.fao.geonet.kernel.search.SearchManager
> $Spatial.writerNoLocking(SearchManager.java:1529)
>         at org.fao.geonet.kernel.search.SearchManager
> $Spatial.writer(SearchManager.java:1515)
>         at
> org.fao.geonet.kernel.search.SearchManager.delete(SearchManager.java:835)
>         at
> org.fao.geonet.kernel.search.SearchManager.buildIndexDocument(SearchManager.java:721)
>         at
> org.fao.geonet.kernel.search.SearchManager.index(SearchManager.java:639)
>         at
> org.fao.geonet.kernel.DataManager.indexMetadata(DataManager.java:524)
>         at org.fao.geonet.kernel.DataManager
> $IndexMetadataTask.run(DataManager.java:340)
>         at java.util.concurrent.ThreadPoolExecutor
> $Worker.runTask(ThreadPoolExecutor.java:886)
>         at java.util.concurrent.ThreadPoolExecutor
> $Worker.run(ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
> 2012-05-31 14:13:42,854 INFO  [jeeves.service] -      -> end
> transformation for : metadata.insert.paste
> 2012-05-31 14:13:42,854 INFO  [jeeves.service] -    -> output ended
> for : metadata.insert.paste
> 2012-05-31 14:13:42,855 INFO  [jeeves.service] -  -> dispatch ended
> for : metadata.insert.paste
> Exception in thread "Timer-1" java.lang.NullPointerException
>         at org.fao.geonet.kernel.search.SearchManager$Spatial
> $Committer.run(SearchManager.java:1560)
>         at java.util.TimerThread.mainLoop(Timer.java:512)
>         at java.util.TimerThread.run(Timer.java:462)
> 2012-05-31 14:14:03,028 INFO  [jeeves.request] -
> ==========================================================
> 2012-05-31 14:14:03,028 INFO  [jeeves.request] - HTML Request (from
> 175.107.172.1) : /geonetwork/srv/en/metadata.show
> 2012-05-31 14:14:03,028 DEBUG [jeeves.request] - Method       : GET
> 2012-05-31 14:14:03,028 DEBUG [jeeves.request] - Content type : null
> 2012-05-31 14:14:03,029 DEBUG [jeeves.request] - Accept       :
> text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
> 2012-05-31 14:14:03,029 DEBUG [jeeves.request] - Session id is
> C8678D2BE6E8F6FA3D2238FB96A32FAB
> 2012-05-31 14:14:03,029 INFO  [jeeves.service] - Dispatching :
> metadata.show
> 2012-05-31 14:14:03,029 DEBUG [jeeves.service] -  -> parameters are :
> <request>
>   <id>1</id>
> </request>
> 2012-05-31 14:14:03,118 INFO  [jeeves.service] -    -> dispatching to
> output for : metadata.show
> 2012-05-31 14:14:03,129 ERROR [geonetwork.datamanager] - The metadata
> document index with id=1 is corrupt/invalid - ignoring it. Error: Timer
> already cancelled.
> java.lang.IllegalStateException: Timer already cancelled.
>         at java.util.Timer.sched(Timer.java:354)
>         at java.util.Timer.schedule(Timer.java:170)
>         at org.fao.geonet.kernel.search.SearchManager
> $Spatial.writer(SearchManager.java:1514)
>         at
> org.fao.geonet.kernel.search.SearchManager.delete(SearchManager.java:835)
> 2012-05-31 14:14:03,129 INFO  [jeeves.webapp.metadata.show] - Creating
> default metadata tab
>         at
> org.fao.geonet.kernel.search.SearchManager.buildIndexDocument(SearchManager.java:721)
>         at
> org.fao.geonet.kernel.search.SearchManager.index(SearchManager.java:639)
>         at
> org.fao.geonet.kernel.DataManager.indexMetadata(DataManager.java:524)
> 2012-05-31 14:14:03,130 INFO  [jeeves.webapp.metadata.show] - Creating
> default metadata position
>         at org.fao.geonet.kernel.DataManager
> $IncreasePopularityTask.run(DataManager.java:3168)
>         at java.util.concurrent.ThreadPoolExecutor
> $Worker.runTask(ThreadPoolExecutor.java:886)
>         at java.util.concurrent.ThreadPoolExecutor
> $Worker.run(ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
> 2012-05-31 14:14:03,137 DEBUG [jeeves.service] - Log search in asynch
> mode - start.
> 2012-05-31 14:14:03,141 DEBUG [jeeves.service] - Log search in asynch
> mode - end.
> 2012-05-31 14:14:03,162 DEBUG [jeeves.service] - Log search in asynch
> mode - start.
> 2012-05-31 14:14:03,162 DEBUG [jeeves.service] - Log search in asynch
> mode - end.
> 2012-05-31 14:14:03,169 DEBUG [jeeves.service] - Log search in asynch
> mode - start.
> 2012-05-31 14:14:03,171 DEBUG [jeeves.service] - Log search in asynch
> mode - end.
> 2012-05-31 14:14:03,259 INFO  [jeeves.service] -      -> transforming
> with
> stylesheet : /data/jakarta/geonetwork-asdd/webapps/geonetwork/xsl/metadata-show.xsl
> 2012-05-31 14:14:06,893 INFO  [jeeves.service] -      -> end
> transformation for : metadata.show
> 2012-05-31 14:14:06,893 INFO  [jeeves.service] -    -> output ended
> for : metadata.show
> 2012-05-31 14:14:06,893 INFO  [jeeves.service] -  -> dispatch ended
> for : metadata.show
> 
> 
> Where should I look next to fix this problem? Why does the "Timer
> already cancelled" error keep on coming up when I have cleared all the
> metadata and relations from the postgis database?
> 
> Any help would be much appreciated.
> 
> Thanks.
> 
> 
> John H.
> 
> On Wed, 2012-05-30 at 17:19 +1000, john.hockaday wrote:
> > Hi All,
> > 
> > I have GN 2.7 snapshot. I have managed to get the system setup but when
> > I do a search for metadata I get zero results. This also applies when I
> > am logged in as 'admin'.
> > 
> > I tried to create "New metadata" but I am told "No templates available,
> > import templates first".  If I then go back and select a template in the
> > pick list eg. 'anzmeta' then select "Add templates" 
> > 
> > I saw Andrea Peri's post in the archives about copying
> > WEB-INF/data/config
> > 
> > into the
> > DATA_DIRECTORY/config
> > 
> > but I don't have those directories.
> > 
> > I get the following in the catalina.out file when I try to load the 
> > anzmeta template:
> > 
> > (See attached addAnzmetaTemplate.txt for output)
> > 
> > I still get the same error when I select "New metadata"
> > 
> > If I select 19139 metadata schema and then select "Add template" I get
> > the follow errors in the catalina.out file:
> > 
> > (See attached add19139Template.txt for output)
> > 
> > If I try to "Add sample metadata" for the 19139 schema I get the
> > following in the catalina.out file:
> > 
> > (See attached add19139SampleMetadata.txt for output)
> > 
> >  and the message:
> > 
> > (See attached Screenshot.png for Error Message Box)
> > 
> > Have I broken my Postgis database? Can I fix it somehow? I don't want to
> > lose all the services metadata and harvesting configuration that I have
> > in the database.
> > 
> > Thanks.
> > 
> > John Hockaday
> > 
> > ------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and 
> > threat landscape has changed and how IT managers can respond. Discussions 
> > will include endpoint security, mobile security and the latest in malware 
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> > _______________________________________________ GeoNetwork-users mailing list Geo...@li... https://lists.sourceforge.net/lists/listinfo/geonetwork-users GeoNetwork OpenSource is maintained at http://sourceforge.net/projects/geonetwork
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> GeoNetwork-users mailing list
> Geo...@li...
> https://lists.sourceforge.net/lists/listinfo/geonetwork-users
> GeoNetwork OpenSource is maintained at http://sourceforge.net/projects/geonetwork

Re: [GeoNetwork-devel] [GeoNetwork-users] Can't create metadata and templates. Error: Timer already

Re: [GeoNetwork-devel] [GeoNetwork-users] Can't create metadata and templates. Error: Timer already cancelled.