Thanks that helps allot but it appears you have truncated database files which isn't going to be recoverable. I am going to come up with a fix to better represent this to the user but the data in that collection is pretty much lost.
So the way I would try to recover the rest of the data is to 1) shutdown tomcat. 2) Go to /software/jakarta-tomcat-5.0.30/webapps/xindice/WEB-INF/ 3) remove "db/globalJobs1/globalJobs1.tbl" 4) startup tomcat 5)run $XINDICE_HOME/xindice.sh export -v -c xmldb:xindice://localhost:8080/db -n db -f backup If you get any more errors just find the collection name and delete corresponding ".tbl" file. Then just repeat the steps again until it runs cleanly. Take note of which files you delete or make a back up by copying the entire db directory somewhere else. This problem usually happens with a unclean shutdown of tomcat, power failure that time of thing. Hope this helps. If you have any questions let me know. Todd Rohit Mathur wrote: > Hi Todd > > Below is the exception i see in catalina.out . However, i get this > exception when i try to access the globalJobs1 through the db browser on > my internet browser. I have been executing the export command using the > core xindice install (i.e. not the webapp install) > I think its the same error though, occurs when parsing through the > colleciton. > > I tried to run xindice.sh in the webapps/xindice/WEB-INF dir for > exporting, but couldnt get it to work. > > after setting JAVA_HOME, > > export XINDICE_HOME=/software/jakarta-tomcat-5.0.30/webapps/xindice/WEB-INF/ > [EMAIL PROTECTED] WEB-INF]# ./xindice.sh export -v -c > xmldb:xindice://localhost:8080/db -n globalJobs1 -f globalJobs1 > bash: ./xindice.sh: Permission denied > > and after changing permissions > > [EMAIL PROTECTED] WEB-INF]# ./xindice.sh export -v -c > xmldb:xindice://localhost:8080/db -n globalJobs1 -f globalJobs1 > : bad interpreter: No such file or directory > > regards, > > Rohit > > hope this is good enough > > May 16, 2006 2:56:40 PM org.apache.xindice.core.filer.BTree getBTreeNode > WARNING: Ignored exception > java.io.EOFException > at java.io.DataInputStream.readShort(DataInputStream.java:377) > at > org.apache.xindice.core.filer.BTree$BTreeNode.read(BTree.java:495) > at org.apache.xindice.core.filer.BTree.getBTreeNode(BTree.java:372) > at org.apache.xindice.core.filer.BTree.access$800(BTree.java:71) > at > org.apache.xindice.core.filer.BTree$BTreeNode.getChildNode(BTree.java:536) > at > org.apache.xindice.core.filer.BTree$BTreeNode.query(BTree.java:937) > at > org.apache.xindice.core.filer.BTree$BTreeNode.query(BTree.java:937) > at org.apache.xindice.core.filer.BTree.query(BTree.java:221) > at > org.apache.xindice.core.filer.BTreeFiler$BTreeFilerRecordSet.<init>(BTreeFiler.java:191) > at > org.apache.xindice.core.filer.BTreeFiler.getRecordSet(BTreeFiler.java:174) > at > org.apache.xindice.core.Collection.listDocuments(Collection.java:1007) > at > org.apache.xindice.server.UglyBrowser.getHierarchy(UglyBrowser.java:157) > at org.apache.xindice.server.UglyBrowser.doGet(UglyBrowser.java:78) > at > org.apache.xindice.server.XindiceServlet.doGet(XindiceServlet.java:82) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:689) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252 > ) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:214) > at > org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104) > at > org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520) > at > org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:198) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:152) > at > org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104) > at > org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137) > at > org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:118) > at > org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:102) > at > org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) > at > org.apache.catalina.core.StandardValveContext.invokeNext(StandardValveContext.java:104) > at > org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:520) > at > org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:929) > at > org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:160) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:799) > at > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol > .java:705) > at > org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:577) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) > at java.lang.Thread.run(Thread.java:534) > > Todd Byrne wrote: > >>Hi Rohit, >> >>So I need you to run that export command again and send me the expection >>thats going to be printed in your catalina.log . It should look like : >> >>Ignored exception >>(stack trace) >> >>If I can get that stack trace maybe I can write up a patch and you can >>still recover your data. >> >>Todd >> >>Rohit Mathur wrote: >> >> >>>Hi Todd, >>> >>>sorry about that last message, since i saw the error i was expecting, i >>>didnt think to check the export command syntax. >>> >>> >>> >>>>xindice.sh export -v -c xmldb:xindice://localhost:8080/db -n >>>> >>>> >>>globalJobs1 -f globalJobs1 >>>trying to register database >>> >>>Creating directory globalJobs1/db >>>Extracting 0 files from xmldb:xindice://localhost:8080/db >>>Creating directory globalJobs1/db/products >>>Extracting 0 files from xmldb:xindice://localhost:8080/db/products >>>............... >>>Creating directory globalJobs1/db/site >>>Extracting 1 files from xmldb:xindice://localhost:8080/db/site >>>Creating directory globalJobs1/db/jobs >>>Extracting 0 files from xmldb:xindice://localhost:8080/db/jobs >>>Creating directory globalJobs1/db/jobs/globalJobs1 >>>XMLDB Exception 0: Failed to execute command 'ListDocuments' on server: >>>http://localhost:8080/xindice/,message: java.lang.Exception: >>>java.lang.NullPointerException >>>org.xmldb.api.base.XMLDBException: Failed to execute command >>>'ListDocuments' on server: http://localhost:8080/xindice/, message: >>>java.lang.Exception: java.lang.NullPointerException >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124) >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.listResources(CollectionImpl.java:488) >>> ..... >>>Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception: >>>java.lang.NullPointerException >>> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java) >>> ... 8 more >>>[EMAIL PROTECTED]: java.lang.Exception: >>>java.lang.NullPointerException >>> .... >>> at >>>org.apache.xindice.tools.command.ExportTree.process(ExportTree.java:148) >>> at >>>org.apache.xindice.tools.command.ExportTree.execute(ExportTree.java:71) >>> at org.apache.xindice.tools.XMLTools.execute(XMLTools.java:293) >>> at org.apache.xindice.tools.XMLTools.process(XMLTools.java:171) >>> at org.apache.xindice.tools.XMLTools.main(XMLTools.java:82) >>> >>>and listing the document is where i encountered the null pointer error >>>in the first place. >>>I am able to list other documents/collections in this db >>> >>> >>> >>>>xindice.sh ld -v -c xmldb:xindice://localhost:8080/db/jobs/globalJobs1 >>>> >>>> >>>trying to register database >>>XMLDB Exception 0: Failed to execute command 'ListDocuments' on server: >>>http://localhost:8080/xindice/,message: java.lang.Exception: >>>java.lang.NullPointerException >>>org.xmldb.api.base.XMLDBException: Failed to execute command >>>'ListDocuments' on server: http://localhost:8080/xindice/, message: >>>java.lang.Exception: java.lang.NullPointerException >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124) >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.listResources(CollectionImpl.java:488) >>> at >>>org.apache.xindice.tools.command.ListCollectionDocuments.execute(ListCollectionDocuments.java:55) >>> at org.apache.xindice.tools.XMLTools.execute(XMLTools.java:293) >>> at org.apache.xindice.tools.XMLTools.process(XMLTools.java:171) >>> at org.apache.xindice.tools.XMLTools.main(XMLTools.java:82) >>>Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception: >>>java.lang.NullPointerException >>> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java) >>> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java) >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112) >>> ... 5 more >>>[EMAIL PROTECTED]: java.lang.Exception: >>>java.lang.NullPointerException >>> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java) >>> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java) >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112) >>> at >>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.listResources(CollectionImpl.java:488) >>> at >>>org.apache.xindice.tools.command.ListCollectionDocuments.execute(ListCollectionDocuments.java:55) >>> at org.apache.xindice.tools.XMLTools.execute(XMLTools.java:293) >>> at org.apache.xindice.tools.XMLTools.process(XMLTools.java:171) >>> at org.apache.xindice.tools.XMLTools.main(XMLTools.java:82) >>> >>>hope this helps/is fixable >>> >>>thanks a lot for your quick responses. i'm new to this project, and i >>>havent worked with xindice before so i'm all at sea here. >>> >>>Rohit >>> >>>Todd Byrne wrote: >>> >>> >>> >>>>I wasn't quite clear but try this: >>>> >>>>xindice.sh export -v -c xmldb:xindice://localhost:8080/db -n >>>>globalJobs1 -f globalJobs1 >>>> >>>>Also try listing the documents from database and retriving them one by one. >>>> >>>>$XINDICE_HOME/bin/xindice ld -c >>>>xmldb:xindice://localhost:8080/db/globalJobs1 >>>> >>>>Todd >>>> >>>> >>>>Rohit Mathur wrote: >>>> >>>> >>>> >>>> >>>>>Hi Todd, >>>>> >>>>>So the original db was running off an application that was a wrapper >>>>>around xindice, which is why i didnt want to send details. >>>>>I have since copied the db over to another machine where I'm running the >>>>>xindice 1.1b4. >>>>> >>>>>I tried what you recommended on a subset of the db (i.e. db/jobs). >>>>>Here is the error i get >>>>> >>>>>$ xindice.sh export -v -c xmldb:xindice://localhost:8080/db/jobs -n >>>>>test -f test >>>>>trying to register database >>>>> >>>>>Creating directory test/jobs >>>>>Extracting 0 files from xmldb:xindice://localhost:8080/db/jobs >>>>>Creating directory test/jobs/globalJobs1 >>>>>XMLDB Exception 0: Failed to execute command 'ListDocuments' on server: >>>>>http://localhost:8080/xindice/,message: java.lang.Exception: >>>>>java.lang.NullPointerException >>>>>org.xmldb.api.base.XMLDBException: Failed to execute command >>>>>'ListDocuments' on server: http://localhost:8080/xindice/, message: >>>>>java.lang.Exception: java.lang.NullPointerException >>>>> at >>>>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:124) >>>>> at >>>>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.listResources(CollectionImpl.java:488) >>>>> at >>>>>org.apache.xindice.tools.command.ExportTree.process(ExportTree.java:111) >>>>> at >>>>>org.apache.xindice.tools.command.ExportTree.process(ExportTree.java:148) >>>>> at >>>>>org.apache.xindice.tools.command.ExportTree.execute(ExportTree.java:71) >>>>> at org.apache.xindice.tools.XMLTools.execute(XMLTools.java:293) >>>>> at org.apache.xindice.tools.XMLTools.process(XMLTools.java:171) >>>>> at org.apache.xindice.tools.XMLTools.main(XMLTools.java:82) >>>>>Caused by: org.apache.xmlrpc.XmlRpcException: java.lang.Exception: >>>>>java.lang.NullPointerException >>>>> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java) >>>>> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java) >>>>> at >>>>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112) >>>>> ... 7 more >>>>>[EMAIL PROTECTED]: java.lang.Exception: >>>>>java.lang.NullPointerException >>>>> at org.apache.xmlrpc.XmlRpcClient$Worker.execute(XmlRpcClient.java) >>>>> at org.apache.xmlrpc.XmlRpcClient.execute(XmlRpcClient.java) >>>>> at >>>>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.runRemoteCommand(CollectionImpl.java:112) >>>>> at >>>>>org.apache.xindice.client.xmldb.xmlrpc.CollectionImpl.listResources(CollectionImpl.java:488) >>>>> at >>>>>org.apache.xindice.tools.command.ExportTree.process(ExportTree.java:111) >>>>> at >>>>>org.apache.xindice.tools.command.ExportTree.process(ExportTree.java:148) >>>>> at >>>>>org.apache.xindice.tools.command.ExportTree.execute(ExportTree.java:71) >>>>> at org.apache.xindice.tools.XMLTools.execute(XMLTools.java:293) >>>>> at org.apache.xindice.tools.XMLTools.process(XMLTools.java:171) >>>>> at org.apache.xindice.tools.XMLTools.main(XMLTools.java:82) >>>>> >>>>>thanks, >>>>> >>>>>Rohit >>>>> >>>>>P.S. I am able to add/remove collections from db/jobs, but not from >>>>>db/globalJobs1 >>>>> >>>>>[EMAIL PROTECTED] wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>You could try running xindice command line tool like this to export the >>>>>>data and then reload it. >>>>>> >>>>>>$XINDICE_HOME/bin/xindice export -c xmldb:xindice://localhost:8080/db/ >>>>>>-n test -f test >>>>>> >>>>>>Maybe I can work with you to narrow down where this null pointer is >>>>>>coming >>>>>>from. Are you using the latest release? >>>>>> >>>>>>Todd >>>>>> >>>>>> >>>>>>On Fri, 12 May 2006, Rohit Mathur wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Hi, >>>>>>> >>>>>>>Is there any utility out there that can recover the data from a >>>>>>>collection. >>>>>>> >>>>>>>Is it at all possible to do this at all? >>>>>>> >>>>>>>One particular collection has "gone bad". The rest of the db is working >>>>>>>great. >>>>>>>I am unable to query it or create a collection within it. >>>>>>> >>>>>>>I get a null pointer exception from the data. >>>>>>> >>>>>>>thanks >>>>>>> >>>>>>>Rohit >>>>>>> >>>>>>>java.lang.NullPointerException at >>>>>>>org.apache.xindice.core.filer.BTree$BTreeNode.query(BTree.java:937) at >>>>>>>org.apache.xindice.core.filer.BTree$BTreeNode.query(BTree.java:937) at >>>>>>>org.apache.xindice.core.filer.BTree.query(BTree.java:221) at >>>>>>>org.apache.xindice.core.filer.BTreeFiler$BTreeFilerRecordSet.(BTreeFiler.java:191) >>>>>>> >>>>>>>at >>>>>>>org.apache.xindice.core.filer.BTreeFiler.getRecordSet(BTreeFiler.java:174) >>>>>>> >>>>>>>at >>>>>>>org.apache.xindice.core.Collection.listDocuments(Collection.java:1007) >>>>>>>at >>>>>>>org.apache.xindice.server.UglyBrowser.getHierarchy(UglyBrowser.java:157) >>>>>>>at org.apache.xindice.server.UglyBrowser.doGet(UglyBrowser.java:78) at >>>>>>>org.apache.xindice.server.XindiceServlet.doGet(XindiceServlet.java:82) >>>>>>>at javax.servlet.http.HttpServlet.service(HttpServlet.java:740) at >>>>>>>javax.servlet.http.HttpServlet.service(HttpServlet.java:853) at >>>>>>>org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:247) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:193) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:260) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480) >>>>>>> >>>>>>>at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995) >>>>>>>at >>>>>>>org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480) >>>>>>> >>>>>>>at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995) >>>>>>>at >>>>>>>org.apache.catalina.core.StandardContext.invoke(StandardContext.java:2415) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:180) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.valves.ErrorDispatcherValve.invoke(ErrorDispatcherValve.java:170) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:172) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:509) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:641) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480) >>>>>>> >>>>>>>at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995) >>>>>>>at >>>>>>>org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:174) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline$StandardPipelineValveContext.invokeNext(StandardPipeline.java:643) >>>>>>> >>>>>>>at >>>>>>>org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:480) >>>>>>> >>>>>>>at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:995) >>>>>>>at >>>>>>>org.apache.coyote.tomcat4.CoyoteAdapter.service(CoyoteAdapter.java:223) >>>>>>>at >>>>>>>org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:432) >>>>>>> >>>>>>>at >>>>>>>org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConnection(Http11Protocol.java:386) >>>>>>> >>>>>>>at >>>>>>>org.apache.tomcat.util.net.TcpWorkerThread.runIt(PoolTcpEndpoint.java:534) >>>>>>> >>>>>>>at >>>>>>>org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:530) >>>>>>> >>>>>>>at java.lang.Thread.run(Thread.java:534) >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >
