Hi Todd,
OK, i'll tell the users about this. They arent going to be happy.
But at least i can pass the buck onto you now :)
No, seriously though, it probably was an unclean tomcat shutdown that
caused this.
thanks for all your help.
regards,
Rohit
Todd Byrne wrote:
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)
