On 15/09/15 17:39, Todd Detwiler wrote:
Let me start with what I'm trying to do. Basically, I'm writing a
script, that will run off of a cron job, that will rebuild my TDB store
(and Lucene indexes) on a regular basis. I looked into using the TDB
command line scripts, but they fail because another JVM (the tomcat app)
is already using the TDB store. I looked into using Sparql update
through Fuseki, but I like the idea of the store being read only (and
therefore update is not allowed). So, I am experimenting with having my
script interact with the Tomcat Manager, stopping the running Fuseki app
(but not all of tomcat), making changes, and then restarting. I am able
to stop it fine, using a url like:
(domain):(port)/manager/text/stop?path=/fuseki
However, the corresponding call to start fails:
(domain):(port)/manager/text/start?path=/fuseki
I am getting a stack trace in the tomcat log file that indicates an
issue with file locks related to Lucene indexing. Now, if I stop tomcat
entirely, and start it again, everything works fine. But I don't want to
shut down the other services. Do I need to add a listener that performs
some sort of operation when Tomcat stops? Have others encountered the
same issue. I've included the stack trace at the bottom of this message.
I'd appreciate any insight anyone could offer. Or let me know if you
think using Sparql update would be a preferred way of rebuilding the store?
Thanks,
Todd
Hi Todd,
Firstly, which version of jena are you using? There were some changes to
the Lucene indexing around updates that changed the way it works which
may play into this. I see "com.hp.hpl.jena" so it's not the latest.
Also, I don't know what stopping a webapp in Tomcat actually does. The
standard ServletContextListener only has an operation called
synchronously so it is tricky to clear up in-flight transactions (TDB
does not have forced system aborts by design). Fuseki2, and maybe wider,
needs a proper service lifecycle.
Restarting is clearly calling assembler processing.
Could you protect the update endpoints with the tomcat configuration to,
say, only respond to requests for localhost? While forcing listening
to a specific host isn't very safe, localhost is different because it
means the request was on the loop back interface so can't be done from
outside.
SPARQL Update (in the latest version where text changes and database
changes are coordinated) is
Andy
15-Sep-2015 09:02:55.968 SEVERE [http-nio-8080-exec-10]
org.apache.catalina.core.StandardContext.listenerStart Exception sending
context initialized event to listener instance of class
org.apache.jena.fuseki.server.FusekiServerListener
com.hp.hpl.jena.assembler.exceptions.AssemblerException: caught: null
doing:
root: http://localhost/jena_example/#indexLucene with type:
http://jena.apache.org/text#TextIndexLucene assembler class: class
org.apache.jena.query.text.assembler.TextIndexLuceneAssembler
root: http://localhost/jena_example/#text_dataset with type:
http://jena.apache.org/text#TextDataset assembler class: class
org.apache.jena.query.text.assembler.TextDatasetAssembler
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:138)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:117)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:81)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:52)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:48)
at
org.apache.jena.query.text.assembler.TextDatasetAssembler.open(TextDatasetAssembler.java:63)
at
org.apache.jena.query.text.assembler.TextDatasetAssembler.open(TextDatasetAssembler.java:41)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:130)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.open(AssemblerGroup.java:117)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$ExpandingAssemblerGroup.open(AssemblerGroup.java:81)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:52)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerBase.open(AssemblerBase.java:48)
at
org.apache.jena.fuseki.build.Builder.buildDataService(Builder.java:76)
at
org.apache.jena.fuseki.build.Builder.buildDataAccessPoint(Builder.java:61)
at
org.apache.jena.fuseki.build.FusekiConfig.servicesAndDatasets(FusekiConfig.java:133)
at
org.apache.jena.fuseki.build.FusekiConfig.readConfigFile(FusekiConfig.java:75)
at
org.apache.jena.fuseki.server.FusekiServer.initServerConfiguration(FusekiServer.java:248)
at
org.apache.jena.fuseki.server.FusekiServer.initializeDataAccessPoints(FusekiServer.java:216)
at
org.apache.jena.fuseki.server.FusekiServerListener.init(FusekiServerListener.java:70)
at
org.apache.jena.fuseki.server.FusekiServerListener.contextInitialized(FusekiServerListener.java:45)
at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4729)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5167)
at
org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at
org.apache.catalina.manager.ManagerServlet.start(ManagerServlet.java:1293)
at
org.apache.catalina.manager.HTMLManagerServlet.start(HTMLManagerServlet.java:673)
at
org.apache.catalina.manager.HTMLManagerServlet.doPost(HTMLManagerServlet.java:221)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.filters.CsrfPreventionFilter.doFilter(CsrfPreventionFilter.java:213)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:108)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:614)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:617)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:518)
at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091)
at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:668)
at
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1521)
at
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1478)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.nio.channels.OverlappingFileLockException
at sun.nio.ch.SharedFileLockTable.checkList(FileLockTable.java:255)
at sun.nio.ch.SharedFileLockTable.add(FileLockTable.java:152)
at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1075)
at java.nio.channels.FileChannel.tryLock(FileChannel.java:1155)
at
org.apache.lucene.store.NativeFSLock.obtain(NativeFSLockFactory.java:217)
at org.apache.lucene.store.Lock.obtain(Lock.java:72)
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:702)
at
org.apache.jena.query.text.TextIndexLucene.openIndexWriter(TextIndexLucene.java:121)
at
org.apache.jena.query.text.TextIndexLucene.<init>(TextIndexLucene.java:114)
at
org.apache.jena.query.text.TextDatasetFactory.createLuceneIndex(TextDatasetFactory.java:97)
at
org.apache.jena.query.text.assembler.TextIndexLuceneAssembler.open(TextIndexLuceneAssembler.java:96)
at
org.apache.jena.query.text.assembler.TextIndexLuceneAssembler.open(TextIndexLuceneAssembler.java:47)
at
com.hp.hpl.jena.assembler.assemblers.AssemblerGroup$PlainAssemblerGroup.openBySpecificType(AssemblerGroup.java:130)
... 54 more
