BaseX-Talk

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6 participants
5250 discussions

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

add a 'path' argument to the CREATE command
by Fabrice Etanchaud 25 Feb '13

25 Feb '13

Dear all @ BaseX, Db :create has now a path argument. Could the CREATE command get this argument too ? For the moment, one have to do the following set of commands to create a collection and put the documents in a specific path : - Create... - Rename... - Optimize... - Close So, optimization is done twice, with a real impact on creation's duration. Does somebody have comments on the possibility to directly move data from a collection to another without having to export and add files ? I'm writing Talend components for BaseX, is this interesting other people out there ? Best regards from the snowy French Riviera... Fabrice Etanchaud Questel-Orbit

1 0

On the client protocol level: Can a query be executed multiple times?
by Francis Avila 24 Feb '13

24 Feb '13

I have no official connection to basex, but I have played around with the server protocol with the idea of writing a Python driver for it that is more idiomatic Python and that better manages changes of state on the connection. What I have discovered, at least as of BaseX 7.3, is the following: A query can be executed multiple times, where "execute" means any of the result-producing commands: RESULTS, EXECUTE, FULL A query *cannot* have any parameters rebound. In other words it's not possible to prepare a query, bind an external variable, execute the query, then bind another variable, execute again, and get another answer. Although no error will be reported when a var is rebound the results act as if it were not rebound. So once a query is executed, you must treat the query as an immutable result. If you wish to issue the same query with a different bound value, you must create a new query with QUERY (producing a new query id). Also, since there is no iterative partial execution of queries (like an SQL cursor, for example) and all results are returned at once, your question "how is the previous execution ended?" is not meaningful. The previous execution is ended when you receive results. Closing a query deregisters it. It no longer has any existence, and any attempt to use it will return an error "Unknown Query ID". Also note that query text does not seem to be evaluated when the query ID is created, so any syntax errors will not be caught until you directly (RESULTS, EXECUTE, FULL commands) or indirectly (OPTIONS command, maybe UPDATING as well?) execute the query. I have written a very low level BaseX console in Python which I use to examine the exact semantics of the client-server protocol. Below is a log from one of those demonstrating many of the things I have said. Lines that start with "?" are user-entered commands. A bare integer produces a byte of that value, and a double-quoted string produces a null-terminated utf8 string. Lines starting with ">" are the bytes sent to the server, and "<" are the bytes received from the server. Note that I have no idea what the "INFO" command is supposed to indicate! ? 0 "declare variable external $x; $x to $x+10" > '\x00declare variable external $x; $x to $x+10\x00' < '0\x00\x00' ? 6 0 > '\x06\x00\x00' < '\x00\x01Unknown Query ID: \x00' ? 6 "0" > '\x060\x00' < '1\x00\x00' ? 3 "0" "x" "1" "xs:integer" > '\x030\x00x\x001\x00xs:integer\x00' < '\x00\x00' ? 6 "0" > '\x060\x00' < '\x00\x00' ? 7 "0" > '\x070\x00' < "\x00\x01Stopped at line 1, column 17:\n[XPST0003] Expecting '$', found 'e'.\x00" ? \2 "0" > '\x020\x00' < '\x00\x00' ? 0 "declare variable $x external'; $x to $x+10" > "\x00declare variable $x external'; $x to $x+10\x00" < '2\x00\x00' ? 2 "2" > '\x022\x00' < '\x00\x00' ? 0 "declare variable $x external; $x to $x+10" > '\x00declare variable $x external; $x to $x+10\x00' < '3\x00\x00' ? 6 "3" > '\x063\x00' < '\x00\x00' ? 7 "3" > '\x073\x00' < 'byte-order-mark=no,cdata-section-elements=,doctype-public=,doctype-system=,encoding=UTF-8,escape-uri-attributes=no,format=yes,include-content-type=no,indent=yes,indents=2,media-type=,method=xml,newline=\\n,normalization-form=NFC,omit-xml-declaration=yes,separator= ,standalone=omit,suppress-indentation=,tabulator=no,template=,undeclare-prefixes=no,use-character-maps=,version=,wrap-prefix=,wrap-uri=\x00\x00' ? 3 "3" "x" "0" "xs:integer" > '\x033\x00x\x000\x00xs:integer\x00' < '\x00\x00' ? 5 "3" > '\x053\x00' < '0 1 2 3 4 5 6 7 8 9 10\x00\x00' ? 4 "3" > '\x043\x00' < '40\x0041\x0042\x0043\x0044\x0045\x0046\x0047\x0048\x0049\x00410\x00\x00\x00' ? 31 "3" > '\x1f3\x00' < '40\x0041\x0042\x0043\x0044\x0045\x0046\x0047\x0048\x0049\x00410\x00\x00\x00' ? 3 "3" "x" "5" "xs:integer" > '\x033\x00x\x005\x00xs:integer\x00' < '\x00\x00' ? 4 "3" > '\x043\x00' < '40\x0041\x0042\x0043\x0044\x0045\x0046\x0047\x0048\x0049\x00410\x00\x00\x00' ? 5 "3" > '\x053\x00' < '0 1 2 3 4 5 6 7 8 9 10\x00\x00' ? 2 "3" > '\x023\x00' < '\x00\x00' ? 6 "3" > '\x063\x00' < '\x00\x01Unknown Query ID: 3\x00' ? > From: Hans Hübner <hans.huebner(a)gmail.com> > Subject: [basex-talk] On the client protocol level: Can a query be executed multiple times? > Date: February 23, 2013 2:41:30 PM CST > To: basex-talk(a)mailman.uni-konstanz.de > > > 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

1 0

Re: [basex-talk] Xquery over all collections
by pw＠themail.co.uk 24 Feb '13

24 Feb '13

Hi Lukas Sorry to be so long in actually picking this up... but I think that let $r := (collection('A'), collection('B'),collection('C'))//br is a lot faster than let $r := for $d in db:list() return collection($d)//br Any thoughts? Cheers Peter > > > >---- Original Message ---- >From: lukaskircher1(a)gmail.com >To: pw(a)themail.co.uk >Subject: Re: [basex-talk] Xquery over all collections >Date: Wed, 6 Feb 2013 08:40:07 +0100 > >>Hi Peter, >> >>for example, if I look for all *<br>* elements over all >>documents/collections: >> >>*for $d in db:list()* >>*return collection($d)//br* >>* >>* >>Is this what you were looking for? >> >>Cheers, >>Lukas >> >> >>On Wed, Feb 6, 2013 at 1:13 AM, <pw(a)themail.co.uk> wrote: >> >>> let $r := (collection('A'), collection('B'), >>> collection('C')) >>> >>

1 0

BaseX C# Client Slow Remote Performance
by Scott Graves 22 Feb '13

22 Feb '13

I'm testing inserts / updates / queries and ran into a puzzling issue. Testing for the existence of a node where the client and server are running on the same box executes in about 4-7ms; however, testing the same query on a remote server executes in a minimum of 1-1.5s. I've tested on both jre6 and jre7 as well as BaseX installations on 2 different servers. Same issue either way. Although the logs appear to be from 127.0.0.1, I'm actually using an SSH tunnel for testing remotely but there's no real difference. 13:40:51.212 127.0.0.1:32264 admin OK Database 'LibraryDatabase' was opened in 0.84 ms. 1.21 ms 13:40:51.222 127.0.0.1:32264 admin OK QUERY[0] for $d in /db/table[@name='Music Library']/Setting/DataList/Data where $d/@Key='Id' and $d/@Value='0F5349957FB73A4585FBC7A392D4DEBA20F41667869FE6A8EDB14332E80C255C' return $d 0.12 ms 13:40:51.232 127.0.0.1:32264 admin OK ITER[0] 1.56 ms 13:40:51.247 127.0.0.1:32264 admin REQUEST EXIT 13:40:51.247 127.0.0.1:32264 admin OK 0.32 ms 13:40:52.327 127.0.0.1:32265 admin REQUEST CHECK LibraryDatabase 13:40:52.327 127.0.0.1:32265 admin OK Database 'LibraryDatabase' was opened in 0.8 ms. 1.17 ms Any help would be appreciated. I've spent only 1 day experimenting so far. - Scott

2 4

BACKUP/RESTORE - 32 bits limitation / java 7
by Fabrice Etanchaud 22 Feb '13

22 Feb '13

Dear BaseX users, BACKUPing a big database (leading to a bigger than 2 Go archive) is ok, But RESTOREing it fails because archive is corrupted. It seems to be related to the 32 bit zip library limitation, that may be solved with java 7. Did someone already try BACKUP/RESTORing big databases with BaseX running on a java 7 jre ? Best regards, Fabrice Etanchaud Questel-Orbit

2 1

OPTIMIZE ALL : <DBNAME>_224548755 could not be renamed
by Fabrice Etanchaud 22 Feb '13

22 Feb '13

Dear BaseX Team, It seems to be a problem with the OPTIMIZE ALL command. When applied on a <DBNAME> collection, it ends up with the following message : "<DBNAME>_224548755 could not be renamed" I suppose a new optimized collection is being created aside the current one, and cannot be renamed as <DBNAME> at the end ? Best regards, Fabrice Etanchaud Questel-Orbit

2 1

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