On 02/20/2013 03:42 PM, Leo Wörteler wrote:

Hi Marco,

Am 20.02.2013 13:20, schrieb Marco Lettere:

...

Hi all, yesterday I stumbled upon a strange bug which today showed up again in the exact same manner. I got this nasty exception:

Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 7.6 Java: Sun Microsystems Inc., 1.6.0_18 OS: Linux, i386 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 2 org.basex.io.random.TableDiskAccess.flush(TableDiskAccess.java:124) org.basex.data.DiskData.finishUpdate(DiskData.java:212) org.basex.core.cmd.Replace.run(Replace.java:78)

that actually sounds quite concerning. Do you have an example database

Yes. That was also my feeling ....

with which we can reproduce the failure? That would greatly help us find the bug you are experiencing.

Leo

I'll try to set it up.

Hi Marco,

thanks for trying. – It’s difficult to guess how the exception was caused in your scenario. The stack trace reported by Arto was caused by a bug in the implementation of xquery:eval() [1], while your stack trace seems to point to the replace command.

If you manage to reproduce the error, we’ll be glad to have a look at it, Christian

[1] https://github.com/BaseXdb/basex/commit/440f3c5499b6ec05806aabce55f285badfa1... ___________________________

On Tue, Feb 26, 2013 at 9:58 AM, Marco Lettere marco.lettere@dedalus.eu wrote:

Independently on how I hard I try, I'm not able to recreate the problem. It happened twice in two following days but now it's no t happening again ... I've seen that the mail reporting the same exception:

https://mailman.uni-konstanz.de/pipermail/basex-talk/2013-February/004690.ht...

has been faced and solved

https://mailman.uni-konstanz.de/pipermail/basex-talk/2013-February/004734.ht...

Can anyone tell on whether the problem, under the hood, was the same? Thank you. M.

On 02/20/2013 01:20 PM, Marco Lettere wrote:

Hi all, yesterday I stumbled upon a strange bug which today showed up again in the exact same manner.

I wanted to replace, by calling this REST uri (http://localhost:8984/rest/rlus/HCP/rules/CDAReports_rules.xml) from firefox's poster tool, the following resource

<hdataext:extension id="CDA2_REPORT" xmlns:hdataext="urn:dedalus:hdata:extensions" extensionId="CDA2_REPORT" contentType="application/xml"> <hdataext:namespace prefix="hl7v3" href="urn:hl7-org:v3" />

hdataext:documentid$input/cda:id/data(@extension)</hdataext:documentid>

hdataext:documentnameconcat($input/cda:templateId/data(@extension),'_',$input/cda:id/data(@extension),'.cda')</hdataext:documentname>

hdataext:documentrecordconcat($input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@root),'_',$input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@extension))</hdataext:documentrecord>

hdataext:documentaddressconcat("http://localhost:8984/rest/%22,$input)</hdataext:documentaddress> hdataext:documentmetadata()</hdataext:documentmetadata> </hdataext:extension>

with this one

<hdataext:extension id="CDA2_REPORT" xmlns:hdataext="urn:dedalus:hdata:extensions" extensionId="CDA2_REPORT" contentType="application/xml"> <hdataext:namespace prefix="hl7v3" href="urn:hl7-org:v3" /> <hdataext:namespace prefix="cda" href="urn:hl7-org:v3" />

hdataext:documentid$input/cda:id/data(@extension)</hdataext:documentid>

hdataext:documentnameconcat($input/cda:templateId/data(@extension),'_',$input/cda:id/data(@extension),'.cda')</hdataext:documentname>

hdataext:documentrecordconcat($input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@root),'_',$input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@extension))</hdataext:documentrecord>

hdataext:documentaddressconcat("http://localhost:8984/rest/%22,$input)</hdataext:documentaddress> hdataext:documentmetadata()</hdataext:documentmetadata> </hdataext:extension>

I got this nasty exception:

Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 7.6 Java: Sun Microsystems Inc., 1.6.0_18 OS: Linux, i386 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 2 org.basex.io.random.TableDiskAccess.flush(TableDiskAccess.java:124) org.basex.data.DiskData.finishUpdate(DiskData.java:212) org.basex.core.cmd.Replace.run(Replace.java:78) org.basex.core.Command.run(Command.java:342) org.basex.core.Command.exec(Command.java:321) org.basex.core.Command.execute(Command.java:78) org.basex.core.Command.execute(Command.java:90) org.basex.server.LocalSession.execute(LocalSession.java:97) org.basex.server.LocalSession.replace(LocalSession.java:81) org.basex.http.rest.RESTPut.run(RESTPut.java:59) org.basex.http.rest.RESTServlet.run(RESTServlet.java:14) org.basex.http.BaseXServlet.service(BaseXServlet.java:39) javax.servlet.http.HttpServlet.service(HttpServlet.java:848) org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:648) org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)

org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)

org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:559)

org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:232)

org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1072) org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:382)

org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:194)

org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1006)

org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)

org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116) org.eclipse.jetty.server.Server.handle(Server.java:365)

org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:485)

org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:937)

org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:998) org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:856) org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)

org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)

org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:627)

org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:51)

org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)

org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543) java.lang.Thread.run(Thread.java:619) 1 resource(s) replaced in 2.47 ms.

and as a MUCH WORSE side effect ... my database is completely messed up. It shows up in the basexgui but when I try to open it nothing happens and the basexgui yields the following exception:

Exception occurred during event dispatching: java.lang.RuntimeException: Data Access out of bounds:

• pre value: 0
• #used blocks: 0
• #total locks: 0
• access: -1 (0 > -1] at org.basex.util.Util.notexpected(Util.java:53) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:488) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:189) at org.basex.data.Data.kind(Data.java:283) at org.basex.query.value.node.DBNode.<init>(DBNode.java:49) at org.basex.query.value.node.FTPosNode.<init>(FTPosNode.java:22) at org.basex.data.Nodes.serialize(Nodes.java:227) at org.basex.data.Nodes.serialize(Nodes.java:222) at org.basex.gui.view.text.TextView.setText(TextView.java:142) at org.basex.gui.view.text.TextView.refreshContext(TextView.java:104) at org.basex.gui.view.text.TextView.refreshInit(TextView.java:90) at org.basex.gui.view.ViewNotifier.init(ViewNotifier.java:80) at org.basex.gui.dialog.DialogProgress.execute(DialogProgress.java:204) at org.basex.gui.dialog.DialogProgress.execute(DialogProgress.java:146) at org.basex.gui.dialog.DialogProgress.execute(DialogProgress.java:124) at org.basex.gui.dialog.DialogManage.close(DialogManage.java:249) at org.basex.gui.dialog.DialogManage.action(DialogManage.java:145) at

org.basex.gui.layout.BaseXButton$1.actionPerformed(BaseXButton.java:39) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6263) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6028) at java.awt.Container.processEvent(Container.java:2041) at java.awt.Component.dispatchEventImpl(Component.java:4630) at java.awt.Container.dispatchEventImpl(Container.java:2099) at java.awt.Component.dispatchEvent(Component.java:4460) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) at java.awt.Container.dispatchEventImpl(Container.java:2085) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4460) at java.awt.EventQueue.dispatchEvent(EventQueue.java:599) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:178) at java.awt.Dialog$1.run(Dialog.java:1046) at java.awt.Dialog$3.run(Dialog.java:1098) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Dialog.show(Dialog.java:1096) at java.awt.Component.show(Component.java:1563) at java.awt.Component.setVisible(Component.java:1515) at java.awt.Window.setVisible(Window.java:842) at java.awt.Dialog.setVisible(Dialog.java:986) at org.basex.gui.layout.BaseXDialog.finish(BaseXDialog.java:111) at org.basex.gui.dialog.DialogManage.<init>(DialogManage.java:119) at org.basex.gui.GUICommands$2.execute(GUICommands.java:52) at org.basex.gui.layout.BaseXButton$3.actionPerformed(BaseXButton.java:95) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6263) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6028) at java.awt.Container.processEvent(Container.java:2041) at java.awt.Component.dispatchEventImpl(Component.java:4630) at java.awt.Container.dispatchEventImpl(Container.java:2099) at java.awt.Component.dispatchEvent(Component.java:4460) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) at java.awt.Container.dispatchEventImpl(Container.java:2085) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4460) at java.awt.EventQueue.dispatchEvent(EventQueue.java:599) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

any hints? Thank you. M.

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