February 2013 - BaseX-Talk - mailman.uni-konstanz.de

issuing XQuery via basex command line
by Silver, Jonathan 27 Feb '13

27 Feb '13

I've just downloaded 7.6 and am trying to perform a query using the command line basex utility, It does not seem to work. I can execute the following using the GUI, but not from the utility, 1. Any ideas? Is this a limitation or a bug? I have not looked through the source code yet. 2. Is there any way to insert comments in the command file that is passed on basex -c filename.xq ? 3. Am I supposed to be able to split the for loop onto multiple lines? It does not appear so. Thanks, Jonathan Open factbook for $x in /mondial/country where $x/languages="English" return $x/religions

2 1

Re: [basex-talk] Address already in use
by McDonald, Shaun 27 Feb '13

27 Feb '13

Thanks, Ludovic. And many thanks to all three, whose assistance has helped me get the REST working! Cheers, Shaun > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Feb 2013 08:57:25 -0500 > From: "McDonald, Shaun" <Shaun.McDonald(a)oup.com> > To: "basex-talk(a)mailman.uni-konstanz.de" > <basex-talk(a)mailman.uni-konstanz.de> > Subject: [basex-talk] Address already in use > Message-ID: > <072DBA0C025AE84D92C277D05803771023FEF5089E(a)usmb02.us.oup > .com> > Content-Type: text/plain; charset="us-ascii" > > Thank you, both. I've dealt with that error, and now the browser just loads > indefinitely. > > The http server's listening on 8984 and configured to stop on 8985. The db > server is on 1984. > > Forgive me, I'm a link architect doing a POC without system support. It's been > a while since I've had to configure an app server. Would someone by chance > have example config values of a successful basexhttp installation? > > Thanks, again for your help. > > Cheers, > > Shaun > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 26 Feb 2013 12:09:45 -0500 > > From: "McDonald, Shaun" <Shaun.McDonald(a)oup.com> > > To: "basex-talk(a)mailman.uni-konstanz.de" > > <basex-talk(a)mailman.uni-konstanz.de> > > Subject: [basex-talk] Address already in use > > Message-ID: > > <072DBA0C025AE84D92C277D05803771023FEF5065F(a)usmb02.us.oup > > .com> > > Content-Type: text/plain; charset="us-ascii" > > > > Hi, > > > > I'm trying to access a database locally via HTTP on port 8984, and I > > keep getting "Address already in use" 503 Error. > > > > I've attached the error's log entry. > > > > Nothing else appears to be using that port. > > > > Thanks, > > > > Shaun > > ------------------------------ > > > > Message: 2 > > Date: Tue, 26 Feb 2013 18:13:27 +0100 > > From: Ludovic Kuty <mailing(a)kuty.be> > > To: basex-talk(a)mailman.uni-konstanz.de > > Subject: Re: [basex-talk] Address already in use > > Message-ID: <7BCFE308-49B1-4BE4-ABD4-509F9BE54431(a)kuty.be> > > Content-Type: text/plain; charset="windows-1252" > > > > Did you try a "netstat -nltp" as root under Linux to see if something > > is listening on the port ? > > > > On 26 Feb 2013, at 18:09, McDonald, Shaun wrote: > > > > > Hi, > > > > > > I?m trying to access a database locally via HTTP on port 8984, and I > > > keep > > getting ?Address already in use? 503 Error. > > > > > > I?ve attached the error?s log entry. > > > > > > Nothing else appears to be using that port. > > > > > > Thanks, > > > > > > Shaun > > > <2013-02-26-Error- > > Entry.log>__________________________________________ > > > _____ > > > BaseX-Talk mailing list > > > BaseX-Talk(a)mailman.uni-konstanz.de > > > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > > ------------------------------ > > > > Message: 3 > > Date: Tue, 26 Feb 2013 12:21:51 -0500 > > From: Liam R E Quin <liam(a)w3.org> > > To: Ludovic Kuty <mailing(a)kuty.be> > > Cc: basex-talk(a)mailman.uni-konstanz.de > > Subject: Re: [basex-talk] Address already in use > > Message-ID: <1361899311.21728.48.camel(a)localhost.localdomain> > > Content-Type: text/plain; charset="ISO-8859-15" > > > > On Tue, 2013-02-26 at 18:13 +0100, Ludovic Kuty wrote: > > > Did you try a "netstat -nltp" as root under Linux to see if > > > something is listening on the port ? > > > > or (as root) lsof -i TCP:8984 > > which will list the process, if any. > > > > Also make sure that you're contacting the right host :) BaseX has a > > habit of moving the configuration files around between releases, so > > sometimes the client isn't using the same conf file as the server. > > > > Liam > > > > -- > > Liam Quin - XML Activity Lead, W3C, http://www.w3.org/People/Quin/ > > Pictures from old books: http://fromoldbooks.org/ > > Ankh: irc.sorcery.net irc.gnome.org freenode/#xml > > > > > > > > ------------------------------ > > > ------------------------------ > > Message: 2 > Date: Wed, 27 Feb 2013 15:09:14 +0100 > From: Ludovic Kuty <mailing(a)kuty.be> > To: basex-talk(a)mailman.uni-konstanz.de > Subject: Re: [basex-talk] Address already in use > Message-ID: <82F1F468-ED5E-4754-9108-1ABEA8B4EC93(a)kuty.be> > Content-Type: text/plain; charset=us-ascii > > Here it is. I've just customized the paths to where BaseX is installed. > > # BaseX Property File. > > # General Options > DBPATH = /Users/ludo/Applications/basex/data > REPOPATH = /Users/ludo/Applications/basex/repo > DEBUG = false > LANG = English > LANGKEYS = false > > # Client/Server Architecture > HOST = localhost > PORT = 1984 > SERVERPORT = 1984 > EVENTPORT = 1985 > USER = > PASSWORD = > SERVERHOST = > PROXYHOST = > PROXYPORT = 80 > NONPROXYHOSTS = > TIMEOUT = 0 > KEEPALIVE = 0 > PARALLEL = 8 > LOG = true > LOGMSGMAXLEN = 1000 > > # HTTP Services > WEBPATH = /Users/ludo/Applications/basex/webapp > RESTXQPATH = restxq > HTTPLOCAL = false > STOPPORT = 8985 > > # Experimental Options > DBLOCKING = false > > On 27 Feb 2013, at 14:57, McDonald, Shaun wrote: > > > Thank you, both. I've dealt with that error, and now the browser just loads > indefinitely. > > > > The http server's listening on 8984 and configured to stop on 8985. The db > server is on 1984. > > > > Forgive me, I'm a link architect doing a POC without system support. It's > been a while since I've had to configure an app server. Would someone by > chance have example config values of a successful basexhttp installation? > > > > Thanks, again for your help. > > > > Cheers, > > > > Shaun > >> --------------------------------------------------------------------- > >> - > >> > >> Message: 1 > >> Date: Tue, 26 Feb 2013 12:09:45 -0500 > >> From: "McDonald, Shaun" <Shaun.McDonald(a)oup.com> > >> To: "basex-talk(a)mailman.uni-konstanz.de" > >> <basex-talk(a)mailman.uni-konstanz.de> > >> Subject: [basex-talk] Address already in use > >> Message-ID: > >> <072DBA0C025AE84D92C277D05803771023FEF5065F(a)usmb02.us.oup > >> .com> > >> Content-Type: text/plain; charset="us-ascii" > >> > >> Hi, > >> > >> I'm trying to access a database locally via HTTP on port 8984, and I > >> keep getting "Address already in use" 503 Error. > >> > >> I've attached the error's log entry. > >> > >> Nothing else appears to be using that port. > >> > >> Thanks, > >> > >> Shaun > >> ------------------------------ > >> > >> Message: 2 > >> Date: Tue, 26 Feb 2013 18:13:27 +0100 > >> From: Ludovic Kuty <mailing(a)kuty.be> > >> To: basex-talk(a)mailman.uni-konstanz.de > >> Subject: Re: [basex-talk] Address already in use > >> Message-ID: <7BCFE308-49B1-4BE4-ABD4-509F9BE54431(a)kuty.be> > >> Content-Type: text/plain; charset="windows-1252" > >> > >> Did you try a "netstat -nltp" as root under Linux to see if something > >> is listening on the port ? > >> > >> On 26 Feb 2013, at 18:09, McDonald, Shaun wrote: > >> > >>> Hi, > >>> > >>> I?m trying to access a database locally via HTTP on port 8984, and I > >>> keep > >> getting ?Address already in use? 503 Error. > >>> > >>> I?ve attached the error?s log entry. > >>> > >>> Nothing else appears to be using that port. > >>> > >>> Thanks, > >>> > >>> Shaun > >>> <2013-02-26-Error- > >> Entry.log>__________________________________________ > >>> _____ > >>> BaseX-Talk mailing list > >>> BaseX-Talk(a)mailman.uni-konstanz.de > >>> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > >> ------------------------------ > >> > >> Message: 3 > >> Date: Tue, 26 Feb 2013 12:21:51 -0500 > >> From: Liam R E Quin <liam(a)w3.org> > >> To: Ludovic Kuty <mailing(a)kuty.be> > >> Cc: basex-talk(a)mailman.uni-konstanz.de > >> Subject: Re: [basex-talk] Address already in use > >> Message-ID: <1361899311.21728.48.camel(a)localhost.localdomain> > >> Content-Type: text/plain; charset="ISO-8859-15" > >> > >> On Tue, 2013-02-26 at 18:13 +0100, Ludovic Kuty wrote: > >>> Did you try a "netstat -nltp" as root under Linux to see if > >>> something is listening on the port ? > >> > >> or (as root) lsof -i TCP:8984 > >> which will list the process, if any. > >> > >> Also make sure that you're contacting the right host :) BaseX has a > >> habit of moving the configuration files around between releases, so > >> sometimes the client isn't using the same conf file as the server. > >> > >> Liam > >> > >> -- > >> Liam Quin - XML Activity Lead, W3C, http://www.w3.org/People/Quin/ > >> Pictures from old books: http://fromoldbooks.org/ > >> Ankh: irc.sorcery.net irc.gnome.org freenode/#xml > >> > >> > >> > >> ------------------------------ > > _______________________________________________ > > BaseX-Talk mailing list > > BaseX-Talk(a)mailman.uni-konstanz.de > > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk

1 0

Address already in use
by McDonald, Shaun 27 Feb '13

27 Feb '13

Thank you, both. I've dealt with that error, and now the browser just loads indefinitely. The http server's listening on 8984 and configured to stop on 8985. The db server is on 1984. Forgive me, I'm a link architect doing a POC without system support. It's been a while since I've had to configure an app server. Would someone by chance have example config values of a successful basexhttp installation? Thanks, again for your help. Cheers, Shaun > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 12:09:45 -0500 > From: "McDonald, Shaun" <Shaun.McDonald(a)oup.com> > To: "basex-talk(a)mailman.uni-konstanz.de" > <basex-talk(a)mailman.uni-konstanz.de> > Subject: [basex-talk] Address already in use > Message-ID: > <072DBA0C025AE84D92C277D05803771023FEF5065F(a)usmb02.us.oup > .com> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I'm trying to access a database locally via HTTP on port 8984, and I keep > getting "Address already in use" 503 Error. > > I've attached the error's log entry. > > Nothing else appears to be using that port. > > Thanks, > > Shaun > ------------------------------ > > Message: 2 > Date: Tue, 26 Feb 2013 18:13:27 +0100 > From: Ludovic Kuty <mailing(a)kuty.be> > To: basex-talk(a)mailman.uni-konstanz.de > Subject: Re: [basex-talk] Address already in use > Message-ID: <7BCFE308-49B1-4BE4-ABD4-509F9BE54431(a)kuty.be> > Content-Type: text/plain; charset="windows-1252" > > Did you try a "netstat -nltp" as root under Linux to see if something is > listening on the port ? > > On 26 Feb 2013, at 18:09, McDonald, Shaun wrote: > > > Hi, > > > > I?m trying to access a database locally via HTTP on port 8984, and I keep > getting ?Address already in use? 503 Error. > > > > I?ve attached the error?s log entry. > > > > Nothing else appears to be using that port. > > > > Thanks, > > > > Shaun > > <2013-02-26-Error- > Entry.log>__________________________________________ > > _____ > > BaseX-Talk mailing list > > BaseX-Talk(a)mailman.uni-konstanz.de > > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > ------------------------------ > > Message: 3 > Date: Tue, 26 Feb 2013 12:21:51 -0500 > From: Liam R E Quin <liam(a)w3.org> > To: Ludovic Kuty <mailing(a)kuty.be> > Cc: basex-talk(a)mailman.uni-konstanz.de > Subject: Re: [basex-talk] Address already in use > Message-ID: <1361899311.21728.48.camel(a)localhost.localdomain> > Content-Type: text/plain; charset="ISO-8859-15" > > On Tue, 2013-02-26 at 18:13 +0100, Ludovic Kuty wrote: > > Did you try a "netstat -nltp" as root under Linux to see if something > > is listening on the port ? > > or (as root) lsof -i TCP:8984 > which will list the process, if any. > > Also make sure that you're contacting the right host :) BaseX has a habit of > moving the configuration files around between releases, so sometimes the > client isn't using the same conf file as the server. > > Liam > > -- > Liam Quin - XML Activity Lead, W3C, http://www.w3.org/People/Quin/ > Pictures from old books: http://fromoldbooks.org/ > Ankh: irc.sorcery.net irc.gnome.org freenode/#xml > > > > ------------------------------

2 1

On the client protocol level: Can a query be executed multiple times?
by Hans Hübner 26 Feb '13

26 Feb '13

I have a question regarding the client protocol: Can a query that has been prepared using the "QUERY" protocol message be executed only once, or multiple times? If it can be executed multiple times, with different parameter sets, how is the previous execution ended? The documentation of the "CLOSE" message seems to indicate the the query is unregistered when it is closed. Is there some documentation or sample code that illustrates the expected sequence of client messages for query execution? Thanks, Hans

3 9

Address already in use
by McDonald, Shaun 26 Feb '13

26 Feb '13

Hi, I'm trying to access a database locally via HTTP on port 8984, and I keep getting "Address already in use" 503 Error. I've attached the error's log entry. Nothing else appears to be using that port. Thanks, Shaun

3 2

Re : Ugly exception "java.lang.ArrayIndexOutOfBoundsException"
by Vincent 26 Feb '13

26 Feb '13

Hi, For information : I experienced the same kind of exception ( ArrayIndexOutOfBoundsException in TableDiskAcces with database corruption) on a regular basis with Basex 7.6. Since Java update (from jdk7u9 to jdk7u15), I never saw this exception again. Unfortunately, I don't have any explanation. Hope it can help you anyway. Regards, Vincent ----- Reply message ----- De : "Marco Lettere" <marco.lettere(a)dedalus.eu> Pour : <basex-talk(a)mailman.uni-konstanz.de> Objet : [basex-talk] Ugly exception "java.lang.ArrayIndexOutOfBoundsException" Date : mar., févr. 26, 2013 09:58 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.h… has been faced and solved https://mailman.uni-konstanz.de/pipermail/basex-talk/2013-February/004734.h… 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>$input/cda:id/data(@extension)</hdataext:documentid> <hdataext:documentname>concat($input/cda:templateId/data(@extension),'_',$input/cda:id/data(@extension),'.cda')</hdataext:documentname> <hdataext:documentrecord>concat($input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@root),'_',$input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@extension))</hdataext:documentrecord> <hdataext:documentaddress>concat("http://localhost:8984/rest/",$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>$input/cda:id/data(@extension)</hdataext:documentid> <hdataext:documentname>concat($input/cda:templateId/data(@extension),'_',$input/cda:id/data(@extension),'.cda')</hdataext:documentname> <hdataext:documentrecord>concat($input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@root),'_',$input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@extension))</hdataext:documentrecord> <hdataext:documentaddress>concat("http://localhost:8984/rest/",$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(a)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. _______________________________________________ BaseX-Talk mailing list BaseX-Talk(a)mailman.uni-konstanz.de https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk

1 0

Ugly exception "java.lang.ArrayIndexOutOfBoundsException"
by Marco Lettere 26 Feb '13

26 Feb '13

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>$input/cda:id/data(@extension)</hdataext:documentid> <hdataext:documentname>concat($input/cda:templateId/data(@extension),'_',$input/cda:id/data(@extension),'.cda')</hdataext:documentname> <hdataext:documentrecord>concat($input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@root),'_',$input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@extension))</hdataext:documentrecord> <hdataext:documentaddress>concat("http://localhost:8984/rest/",$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>$input/cda:id/data(@extension)</hdataext:documentid> <hdataext:documentname>concat($input/cda:templateId/data(@extension),'_',$input/cda:id/data(@extension),'.cda')</hdataext:documentname> <hdataext:documentrecord>concat($input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@root),'_',$input//cda:patientRole/cda:id[@root='2.16.840.1.113883.2.9.4.3.2']/data(@extension))</hdataext:documentrecord> <hdataext:documentaddress>concat("http://localhost:8984/rest/",$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(a)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.

3 4

Re: [basex-talk] Additional info on the invoke problem
by Christian Grün 26 Feb '13

26 Feb '13

Hi Arto, thanks for the test case. The bug has been fixed; please check out the latest stable snapshot [1]. Best, Christian [1] http://files.basex.org/releases/latest/

2 1

BaseX: moving to Java 7?
by Christian Grün 25 Feb '13

25 Feb '13

Dear subscribers, as you may know, the source code of BaseX is still based on Java 6. There following reasons would speak for a switch to Java 7: * as of Feb 15, Oracle will no longer post public updates for Java SE6 [1] * among various minor convenience features, Java 7 provides new I/O libraries to improve platform independence (e.g. support for symbolic links) Obviously, a switch would restrict those who are still bound to work with Java 6, so please speak out now if you still requires BaseX to be compatible with Java 6... Thanks all, Christian [1] http://www.oracle.com/technetwork/java/eol-135779.html

3 2

moving databases ... changing Input Path
by pw＠themail.co.uk 25 Feb '13

25 Feb '13

Hello List I have created a database using the GUI and loaded up a large number of files. I now want to move to a sever, so I naively just zipped up the database and moved it. I now find that some information is hard coded (and I think it is making operation on the server problematic). My question: Can properties such as the 'Input Path' be changed on the database that I uploaded [it is currently reporting the Input Path that was appropriate when the database was created]? If so, how? Cheers Peter

2 1