BaseX-Talk August 2011

basex-talk@mailman.uni-konstanz.de

18 participants
22 discussions

Out of memory bug
by Ivan Lagunov 31 Jul '13

31 Jul '13

Hello, I've got 'Out of memory' error and corrupted database again, this time it's for 6.3 version. Steps: 1. Started server, started terminal client, checked there are no text and attribute indexes. 2. Started my Java application that runs several tests on database: querying, adding, removing. 3. Then I forgot to reopen terminal client and used the one that I opened in Step 1. 4. Run optimize command for the collection and got error. 5. Cannot open the collection any more as I'm getting 'Out of memory'. It's clear that I shouldn't have used the terminal client that I opened before execution of my Java application. But sometimes it's hard to remember. And it's completely unacceptable that these actions result in the corrupted database. You really should catch ArrayIndexOutOfBoundsException everywhere in order to save database from being corrupted. Terminal client stacktrace: > optimize Possible bug? Feedback is welcome: basex-talk(a)mailman.uni-konstanz.de BaseX 6.3: java.lang.ArrayIndexOutOfBoundsException: -1 org.basex.data.PathSummary.add(PathSummary.java:68) org.basex.core.cmd.Optimize.stats(Optimize.java:68) org.basex.core.cmd.Optimize.run(Optimize.java:34) org.basex.core.Command.run(Command.java:236) org.basex.core.Command.exec(Command.java:218) org.basex.core.Command.execute(Command.java:66) org.basex.server.ServerProcess.run(ServerProcess.java:161) > open products Out of Main Memory. Best regards, Ivan

4 8

deadlock in BaseXServer 6.2.7
by Godmar Back 23 Jun '12

23 Jun '12

Hi, we're observing that our BaseXServer 6.2.7 deadlocks. The stack traces are here: http://top.cs.vt.edu/~gback/bx/deadlock-6.2.7/basex-deadlock.txt Could you take a look to see if these ring any bells? Has this problem been addressed in a more recent version? - Godmar

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BaseX server deadlock
by Laurent Chevalier 03 Nov '11

03 Nov '11

Hi, A deadlock occurs in the following situation: a first client program opens an iterative query. For each iteration, this program does some processing and sends another reading request to BaseX (using another BaseX session). All works fine until a second client program (or another thread) sends an updating command to BaseX (like optimize for instance). This locks BaseX server. To unlock it, you have to kill the first program. I have read BaseX server code and found the reason for this behavior in the class org.basex.core.Lock: - with the iterative query, there is always at least one reader alive (readers=1). - when the updating query is received, it is put in the queue (index 0) and remains in it as long as there is a reading query running (that is to say, as long as the iterative reading query is running). - then a second reading request is received, it is put in the queue (index 1 as there is already the updating query in the queue). As it is only the second item of the queue, it remains in the queue as long as the first item in the queue (the updating query) has not been processed (BaseX processes the requests in the order of arrival, FIFO queue). But this first item can not be processed because there is the iterative reading query running. All queries are thus locked. Some may say that we should not send another query while we are in the loop of an iterative query but in our context of many sites being developed by several developers, it is possible that a developer codes this and we do not want BaseX to be locked in this case (whatever it is a mistake of the developer or not). I have found a solution to this problem by modifying the org.basex.core.Lock class. You will find my code hereafter. I do not use a queue anymore and i use a static mutex (called queueMutex) to synchronize all pending queries (threads). The "drawback" of this solution is that the queries are not processed anymore in the order of arrival but randomly. What do you think of this solution ? Do you plan to update BaseX locking mechanism ? I'm using BaseX 6.7.1 but I have seen that Lock.java has not been changed in BaseX 6.7.2. Here is my code : package org.basex.core; import java.util.Date; //import java.util.LinkedList; import java.util.Random; import org.basex.util.Util; /** * Management of executing read/write processes. * Supports multiple readers, limited by {@link MainProp#PARALLEL}, * and single writers (readers/writer lock). * * @author BaseX Team 2005-11, BSD License * @author Christian Gruen */ final class Lock { /** Queue for all waiting processes. */ // private final LinkedList<Object> queue = new LinkedList<Object>(); /** Mutex object. */ private final Object mutex = new Object(); /** Database context. */ private final Context ctx; /** Static mutex used to synchronize all pending queries. **/ private final static Object queueMutex = new Object(); /** Number of active readers. */ private int readers; /** Writer flag. */ private boolean writer; /** * Default constructor. * @param c context */ Lock(final Context c) { ctx = c; } /** * Modifications before executing a command. * @param w writing flag */ void lock(final boolean w) { synchronized(mutex) { int code = new Random(new Date().getTime()).nextInt(); // final Object o = new Object(); // queue.add(o); try { while(true) { synchronized(queueMutex) { // if(o == queue.get(0) && !writer) { if(!writer) { if(w) { if(readers == 0) { writer = true; break; } } else if(readers < Math.max(ctx.mprop.num(MainProp.PARALLEL), 1)) { ++readers; break; } } } mutex.wait(); } } catch(final InterruptedException ex) { Util.stack(ex); } // queue.remove(0); } } /** * Modifications after executing a command. * @param w writing flag */ synchronized void unlock(final boolean w) { synchronized(mutex) { if(w) { writer = false; } else { --readers; } mutex.notifyAll(); } } }

3 21

Problems in using BaseX REST server - IncompatibleClassChangeError javax.ws.rs.core.Response$Status does not implement the requested interface
by Pushkaraj Thorat 21 Oct '11

21 Oct '11

Hello, I am doing setup for REST enabled basex database with procedure mentioned in http://docs.basex.org/wiki/JAX-RX_API URL. Configuring & starting server and running failed due to class not found, but later I've modified the ./basexrest script as: (Included all the jars in lib folder) ######START #!/bin/bash # Path to this script PWD=`dirname $0` # Paths to distributed files or source directories BASEX=$PWD/BaseX.jar BASEXAPI=$PWD/../lib/basex-api.jar # Classpath LIB=$PWD/../lib LIB_CP="" for JAR_FILE in $LIB/*.jar do LIB_CP="$LIB/$JAR_FILE:$LIB_CP" done CP=$BASEX:$BASEXAPI:$LIB_CP # Options for virtual machine VM=-Xmx1g # Run REST server java -cp "$CP" $VM org.basex.api.jaxrx.JaxRxServer "$@" ######END after this, server started successfully, hit the URL - http://localhost:8984/basex/jax-rx I am getting following exception: java.lang.IncompatibleClassChangeError: Class javax.ws.rs.core.Response$Status does not implement the requested interface javax.ws.rs.core.Response$StatusType at com.sun.jersey.spi.container.ContainerResponse.getStatus(ContainerResponse.java:548) at com.sun.jersey.spi.container.ContainerResponse$CommittingOutputStream.commitWrite(ContainerResponse.java:156) at com.sun.jersey.spi.container.ContainerResponse$CommittingOutputStream.write(ContainerResponse.java:133) at org.basex.io.BufferedOutput.flush(BufferedOutput.java:50) at org.basex.io.PrintOutput.flush(PrintOutput.java:126) at org.basex.data.XMLSerializer.cls(XMLSerializer.java:206) at org.basex.data.Serializer.close(Serializer.java:219) at org.basex.api.jaxrx.BXJaxRx$1.code(BXJaxRx.java:96) at org.basex.api.jaxrx.BXCode.run(BXCode.java:53) at org.basex.api.jaxrx.BXOutput.write(BXOutput.java:53) at com.sun.jersey.core.impl.provider.entity.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:71) at com.sun.jersey.core.impl.provider.entity.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:57) at com.sun.jersey.spi.container.ContainerResponse.write(ContainerResponse.java:299) Your help is appreciated. Thanks, Pushkaraj

3 6

BaseX steps for Calabash?
by Florent Georges 05 Sep '11

05 Sep '11

Hi, Has anyone ever thought about writing extension steps for Calabash, in order to evaluate queries using BaseX? Using either the standalone processor, or to send queries to the server. Regards, -- Florent Georges http://fgeorges.org/ http://h2oconsulting.be/

2 6

SET textindex / attrindex switched around
by Daniël Knippers 29 Aug '11

29 Aug '11

@version 6.7.1 Good evening, Small bug-report: I noticed something odd with the SET command when connected as a client: > set attrindex Full-Text Index: OFF > set textindex Attribute Index: OFF In other words; when I want to change the value of 'attrindex' the reponse mentions the Full-Text Index, whereas trying to change 'textindex' seems to actually change the Attribute Index. -- Daniël

2 1

XML name characters and regexes with multi-character escapes?
by C. M. Sperberg-McQueen 25 Aug '11

25 Aug '11

Recently I had occasion to test a string to see whether it is an NCName. I typed something like: matches("foo","\i\c*") But instead of the value 'true', I got an error message saying that '\i\c*' is an invalid regular expression. I believe it is a valid regular expression and that \i and \c are defined as multi-character escapes in XSD. Other multi-character escapes (., \s, ...) seem to be supported. Am I missing something? Since \i and \c vary for different versions of XML, perhaps BaseX is expecting me to tell it which version of XML I want to be using for them? I'm currently using 6.5.1 and have not checked against the current version of BaseX, but I don't see anything about regular expressions in the change logs. -- **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

2 2

XQuery / BaseX: distinct after sort
by Mainberger, Christof 24 Aug '11

24 Aug '11

Hi, I got some performance problems with basex: My query is distinct-values(for $item in doc('gemaelde')/items/item order by $item/kuenstler/@order return $item/kuenstler). It takes about 26 s for 1.500 items. Is there any possibility to formulate the query in other ways to make this faster? Or indexes/materialized views to support such kind of queries? This problem occurs only on our Debian (virtual) server, not on my PC. Are there any configuration parameters for basex-server (ram etc.), which might help? Thanks! Christof Mainberger Leitung Museen, Archive und Repositorien Bibliotheksservice-Zentrum Baden-Wuerttemberg 78457 Konstanz / Germany Phone: +49 7531-884468 E-Mail: christof.mainberger(a)bsz-bw.de

2 2

Embedded BaseX server restart
by Igor Farinic 23 Aug '11

23 Aug '11

Hi, we have problem with restart (stop and immediate start) of embedded BaseX server. The root cause is that when you close server socket it remains in a timeout state for a period of time and restart fails, because it is not possible to bind to a socket in timeout state. Enabling SO_REUSEADDR prior to binding the socket using bind allows the socket to be bound even though a previous connection is in a timeout state. Following fix in BaseXServer class should help (lines 94 and 95): socket = new ServerSocket(); socket.setReuseAddress(true); SocketAddress endpoint = new InetSocketAddress(port); socket.bind(endpoint); esocket = new ServerSocket(); esocket.setReuseAddress(true); endpoint = new InetSocketAddress(context.mprop.num(MainProp.EVENTPORT)); esocket.bind(endpoint); regards, Igor Farinic

2 1

vanishing namespace declaration
by Igor Farinic 16 Aug '11

16 Aug '11

Hi, in BaseX 6.7.2 beta we are hitting new issue, that we haven't observed in 6.7.1. I store following xml: <task oid="91919191-76e0-59e2-86d6-998877665544" xmlns="http://midpoint.evolveum.com/xml/ns/public/common/common-1.xsd" xmlns:c="http://midpoint.evolveum.com/xml/ns/public/common/common-1.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:my="http://myself.me/schemas/whatever"> <extension> <my:shipState>capsized</my:shipState> <my:dead xsi:type="xsd:integer">42</my:dead> </extension> </task> ... and when I retrieve it, the xsd namespace declaration is missing. However the xsd namespace is used in value of xsi:type attribute. regards, Igor Farinic

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BaseX-Talk August 2011