BaseX-Talk March 2011

basex-talk@mailman.uni-konstanz.de

30 participants
43 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

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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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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

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collections in 6.5.1
by C. M. Sperberg-McQueen 04 May '11

04 May '11

Thanks to Christian Grün's prompt response to my question about attributes, I upgraded to Basex 6.5.1 the other day. And I've run into an unexpected behavior. I have several versions of the Unicode database in XML (the Unicode consortium started shipping XML versions with 5.1.0, and I've created XML documents with the information I need for all the earlier versions); they are all in directory ~/2011/Unicode. But when I ask to create a new database in the GUI, giving that directory as the path and accepting the default pattern of *.xml, the only document in the resulting database appears to be the small schemas.xml file that nXML mode placed in one of the subdirectories of ~/2011/Unicode when I edited an XSLT stylesheet there. What I was expecting was that all the XML documents in that subtree of the file directory would be added -- I think that was the behavior in earlier versions. Has something changed? Or have I gotten out of practice and done something wrong? I hope this is clear; I can try to explain further if needed. Thanks! -- **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

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tf/idf
by Wiard Vasen 06 Apr '11

06 Apr '11

Dear sirs of Basex, I am doing my Master thesis on the letters of Vincent van Gogh at the University of Amsterdam. For that purpose I use BaseX to analyze the letters. I wonder, is there the possibility to generate a tf/idf score automatically? In your faq I noticed there needs to be a special term like 'SET SCORING 0' to be able to get a tf/idf score. This information I get from the following page: http://docs.basex.org/wiki/Full-Text Could you help me with this? I would be very grateful. Kind regards,

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BaseX 6.6.1
by Christian Grün 01 Apr '11

01 Apr '11

Dear all, thanks to everyone who gave us great feedback on BaseX 6.6, either by e-mail or directly at the XMLPrague conference! This way, we were able to finish Version 6.6.1 just one week later, which offers some exciting performance improvements and some more bug fixes: XQuery: [ADD] index rewritings added for .../text()[. = ..] syntax [ADD] optimizations of mixed axis path expressions, e.g.: //x/name() [MOD] index rewritings on collections fixed and generalized [MOD] faster evaluation of filters with pos. predicates, e.g.: $x[5] [FIX] fixed relocation of let clauses in GFLWOR expressions [FIX] trace function returned wrong original results [FIX] variables in catch clauses were discarded [FIX] HOF optimizations and fixes GUI: [FIX] language option (for Japanese, German, etc. interface) fixed To be continued, Christian BaseX Team, 2011

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BaseX Issue Tracker
by Christian Grün 31 Mar '11

31 Mar '11

Hi, once again I'd like to remind all of you of our GitHub Issue Tracker, which lists some of the features to come next: https://github.com/BaseXdb/basex/issues You're invited to give your votes on the given issues, or add new entries. The more feedback we get, the better we'll be able to decide which features will be implemented first. Christian ___________________________ Christian Grün Uni KN, Box 188 78457 Konstanz, Germany http://www.inf.uni-konstanz.de/~gruen

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abstract method error?
by Meredith Gregory 31 Mar '11

31 Mar '11

Dear BaseXes, i'm attempting to use the published API from Java (well Scala, really, but we're all JVM family, here...). i'm running into an abstract method error (see the trace below). Any clues would be gratefully appreciated. Best wishes, --greg scala> val db = Class.forName( "org.basex.api.xmldb.BXDatabase" ).newInstance().asInstanceOf[Database] val db = Class.forName( "org.basex.api.xmldb.BXDatabase" ).newInstance().asInstanceOf[Database] db: org.xmldb.api.base.Database = org.basex.api.xmldb.BXDatabase@69dbb4d1 scala> DatabaseManager.registerDatabase( db ) DatabaseManager.registerDatabase( db ) java.lang.AbstractMethodError: org.basex.api.xmldb.BXDatabase.getNames()[Ljava/lang/String; at org.xmldb.api.DatabaseManager.registerDatabase(Unknown Source) at .<init>(<console>:25) at .<clinit>(<console>) at RequestResult$.<init>(<console>:9) at RequestResult$.<clinit>(<console>) at RequestResult$scala_repl_result(<console>) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at scala.tools.nsc.Interpreter$Request$$anonfun$loadAndRun$1$$anonfun$apply$17.apply(Interpreter.scala:988) at scala.tools.nsc.Interpreter$Request$$anonfun$loadAndRun$1$$a... scala> -- L.G. Meredith Managing Partner Biosimilarity LLC 7329 39th Ave SW Seattle, WA 98136 +1 206.650.3740 http://biosimilarity.blogspot.com

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Re: [basex-talk] Xquery through the PERL (or Java) API
by Isidro Vila Verde 30 Mar '11

30 Mar '11

Sorry!!! I am been in a process of focus in little details that I missed the most obvious: reboot the server. I just did that and (this) the problem disappear. I am going now to check if the update problem stills or also go disappear. Sorry the noise on the channel. Just a question. The GUI doesn't use the server to access to the DB? Isidro Em 30-03-2011 15:54, Isidro Vila Verde escreveu: > Dear Andreas, > > Thank you for you quick answer~. I didn't know about logs. It is in > fact a great help, but for presente it seems the query is correctly > received. > This is what I got > > 07:50:25.999 [127.0.0.1:39722] LOGIN serprest OK > 07:50:26.193 [127.0.0.1:39722] QUERY(0) declare > namespace saf="urn:OECD:StandardAuditFile-Tax:PT_1.00_01"; > declare option output:method "xml"; let $col := > collection('invoiceDB') let $invoice := > $col/saf:Invoice[saf:InvoiceNo/text() = '279'] return > $invoice OK > 07:50:26.193 [127.0.0.1:39722] QUERY(0) OK > 07:50:26.307 [127.0.0.1:39722] INIT(0) OK > 07:50:26.319 [127.0.0.1:39722] EXEC(0) OK > 07:50:26.320 [127.0.0.1:39722] INFO(0) OK > 07:50:26.320 [127.0.0.1:39722] CLOSE(0) OK > 07:50:26.347 [127.0.0.1:39722] LOGOUT serprest OK > > Regards > > Isidro > > Em 30-03-2011 15:45, Andreas Weiler escreveu: >> Dear Isidro, >> >> as a quick help, you could have a look at the log files on the >> server, they are located >> in your BaseXData folder (.logs). >> >> Here you can check if the query did arrive correctly at the server. >> >> -- Andreas >> >> Am 30.03.2011 um 16:39 schrieb Isidro Vila Verde: >> >>> Dear all, >>> >>> I have a very strange situation when invoking this xquery >>> >>> declare namespace saf="urn:OECD:StandardAuditFile-Tax:PT_1.00_01"; >>> declare option output:method "xml"; >>> >>> let $col := collection('invoiceDB') >>> let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() = '279'] >>> return $invoice >>> >>> When invoked from GUI it returns the right XML element, but the same >>> query invoked through the perl (or java) API it returns a null result. >>> >>> Bellow is the perl (andf java version) code. What is more strange is >>> that it works for any other value of node saf:InvoiceNo/text(). It >>> just doesn't work for the value 279. >>> >>> In collection invoice DB each saf:Invoice is a single document and >>> the invoiceNo/text()='279' is the "last" document. The collection >>> was just created from a input directory and no other operations was >>> performed on it. >>> >>> Can you help please? >>> >>> I am using the last Basex 6.6 version on ubuntu with java-6-sun. >>> >>> I came to this error when I was in a process to identify why a >>> update operation through the perl API corrupted the database while >>> the same upadate query works fine when invoked from GUI. >>> So, my problem is not exactly this one but I can go any further >>> without resolving this. >>> >>> I notice, on page https://github.com/BaseXdb/BaseX, there is no API >>> version not the last basex 6.6. Should I go back to the version 6.5? >>> >>> >>> Thanks in advance for your help >>> >>> Isidro >>> >>> ------------------Perl Version----------------------------- >>> #!/usr/bin/perl >>> use strict; >>> use lib qw|/var/www/serprest/perl/3rd-party|; >>> use BaseXClient; >>> use warnings; >>> >>> eval { >>> my $session = Session->new("localhost", 1984, "serprest", >>> ".prest,ser"); >>> >>> my $q = q| >>> declare namespace >>> saf="urn:OECD:StandardAuditFile-Tax:PT_1.00_01"; >>> declare option output:method "xml"; >>> >>> let $col := collection('invoiceDB') >>> let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() = >>> '279'] >>> return $invoice >>> |; >>> my $query = $session->query($q); >>> $query->init(); >>> print $query->execute(); >>> print $query->info(); >>> $query->close(); >>> $session->close(); >>> }; >>> >>> # print exception >>> print qq|<error>$@</error>| if $@; >>> >>> >>> ------------------Java Version----------------------------- >>> import java.io.IOException; >>> >>> public final class QueryTeste { >>> public static void main(final String[] args) { >>> try { >>> BaseXClient session = >>> new BaseXClient("localhost", 1984, "serprest", ".prest,ser"); >>> >>> try { >>> String input = "declare namespace >>> saf=\"urn:OECD:StandardAuditFile-Tax:PT_1.00_01\";" >>> + "declare option output:method \"xml\";" >>> + "let $col := collection('invoiceDB')" >>> + "let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() >>> = '279']" >>> + "return $invoice"; >>> BaseXClient.Query query = session.query(input); >>> System.out.print(query.init()); >>> while(query.more()) { >>> System.out.println(query.next()); >>> } >>> System.out.print(query.close()); >>> } catch(IOException ex) { >>> ex.printStackTrace(); >>> } >>> session.close(); >>> } catch(IOException ex) { >>> ex.printStackTrace(); >>> } >>> } >>> } >>> ----------------------------------------------- >>> >>> >>> >>> >>> >>> >>> --- >>> avast! Antivirus: Outbound message clean. >>> Virus Database (VPS): 110330-0, 30-03-2011 >>> Tested on: 30-03-2011 15:39:30 >>> avast! - copyright (c) 1988-2011 AVAST Software. >>> http://www.avast.com >>> >>> >>> >>> _______________________________________________ >>> BaseX-Talk mailing list >>> BaseX-Talk(a)mailman.uni-konstanz.de >>> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk >> >> >> --- >> avast! Antivirus: Inbound message clean. >> Virus Database (VPS): 110330-0, 30-03-2011 >> Tested on: 30-03-2011 15:47:51 >> avast! - copyright (c) 1988-2011 AVAST Software. >> http://www.avast.com >> >> >> > > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 110330-0, 30-03-2011 > Tested on: 30-03-2011 15:54:40 > avast! - copyright (c) 1988-2011 AVAST Software. > http://www.avast.com > > > > > > --- > avast! Antivirus: Inbound message clean. > Virus Database (VPS): 110330-0, 30-03-2011 > Tested on: 30-03-2011 16:16:17 > avast! - copyright (c) 1988-2011 AVAST Software. > http://www.avast.com > > > --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 110330-0, 30-03-2011 Tested on: 30-03-2011 16:22:03 avast! - copyright (c) 1988-2011 AVAST Software. http://www.avast.com

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Fwd: Xquery through the PERL (or Java) API
by Andreas Weiler 30 Mar '11

30 Mar '11

Forwarding to mailing list. Anfang der weitergeleiteten E-Mail: > Von: Isidro Vila Verde <jvverde(a)gmail.com> > Datum: 30. März 2011 16:54:37 MESZ > An: Andreas Weiler <andreas.weiler(a)uni-konstanz.de> > Betreff: Re: [basex-talk] Xquery through the PERL (or Java) API > > Dear Andreas, > > Thank you for you quick answer~. I didn't know about logs. It is in fact a great help, but for presente it seems the query is correctly received. > This is what I got > > 07:50:25.999 [127.0.0.1:39722] LOGIN serprest OK > 07:50:26.193 [127.0.0.1:39722] QUERY(0) declare namespace saf="urn:OECD:StandardAuditFile-Tax:PT_1.00_01"; declare option output:method "xml"; let $col := collection('invoiceDB') let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() = '279'] return $invoice OK > 07:50:26.193 [127.0.0.1:39722] QUERY(0) OK > 07:50:26.307 [127.0.0.1:39722] INIT(0) OK > 07:50:26.319 [127.0.0.1:39722] EXEC(0) OK > 07:50:26.320 [127.0.0.1:39722] INFO(0) OK > 07:50:26.320 [127.0.0.1:39722] CLOSE(0) OK > 07:50:26.347 [127.0.0.1:39722] LOGOUT serprest OK > > Regards > > Isidro > > Em 30-03-2011 15:45, Andreas Weiler escreveu: >> Dear Isidro, >> >> as a quick help, you could have a look at the log files on the server, they are located >> in your BaseXData folder (.logs). >> >> Here you can check if the query did arrive correctly at the server. >> >> -- Andreas >> >> Am 30.03.2011 um 16:39 schrieb Isidro Vila Verde: >> >>> Dear all, >>> >>> I have a very strange situation when invoking this xquery >>> >>> declare namespace saf="urn:OECD:StandardAuditFile-Tax:PT_1.00_01"; >>> declare option output:method "xml"; >>> >>> let $col := collection('invoiceDB') >>> let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() = '279'] >>> return $invoice >>> >>> When invoked from GUI it returns the right XML element, but the same query invoked through the perl (or java) API it returns a null result. >>> >>> Bellow is the perl (andf java version) code. What is more strange is that it works for any other value of node saf:InvoiceNo/text(). It just doesn't work for the value 279. >>> >>> In collection invoice DB each saf:Invoice is a single document and the invoiceNo/text()='279' is the "last" document. The collection was just created from a input directory and no other operations was performed on it. >>> >>> Can you help please? >>> >>> I am using the last Basex 6.6 version on ubuntu with java-6-sun. >>> >>> I came to this error when I was in a process to identify why a update operation through the perl API corrupted the database while the same upadate query works fine when invoked from GUI. >>> So, my problem is not exactly this one but I can go any further without resolving this. >>> >>> I notice, on page https://github.com/BaseXdb/BaseX, there is no API version not the last basex 6.6. Should I go back to the version 6.5? >>> >>> >>> Thanks in advance for your help >>> >>> Isidro >>> >>> ------------------Perl Version----------------------------- >>> #!/usr/bin/perl >>> use strict; >>> use lib qw|/var/www/serprest/perl/3rd-party|; >>> use BaseXClient; >>> use warnings; >>> >>> eval { >>> my $session = Session->new("localhost", 1984, "serprest", ".prest,ser"); >>> >>> my $q = q| >>> declare namespace saf="urn:OECD:StandardAuditFile-Tax:PT_1.00_01"; >>> declare option output:method "xml"; >>> >>> let $col := collection('invoiceDB') >>> let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() = '279'] >>> return $invoice >>> |; >>> my $query = $session->query($q); >>> $query->init(); >>> print $query->execute(); >>> print $query->info(); >>> $query->close(); >>> $session->close(); >>> }; >>> >>> # print exception >>> print qq|<error>$@</error>| if $@; >>> >>> >>> ------------------Java Version----------------------------- >>> import java.io.IOException; >>> >>> public final class QueryTeste { >>> public static void main(final String[] args) { >>> try { >>> BaseXClient session = >>> new BaseXClient("localhost", 1984, "serprest", ".prest,ser"); >>> >>> try { >>> String input = "declare namespace saf=\"urn:OECD:StandardAuditFile-Tax:PT_1.00_01\";" >>> + "declare option output:method \"xml\";" >>> + "let $col := collection('invoiceDB')" >>> + "let $invoice := $col/saf:Invoice[saf:InvoiceNo/text() = '279']" >>> + "return $invoice"; >>> BaseXClient.Query query = session.query(input); >>> System.out.print(query.init()); >>> while(query.more()) { >>> System.out.println(query.next()); >>> } >>> System.out.print(query.close()); >>> } catch(IOException ex) { >>> ex.printStackTrace(); >>> } >>> session.close(); >>> } catch(IOException ex) { >>> ex.printStackTrace(); >>> } >>> } >>> } >>> ----------------------------------------------- >>> >>> >>> >>> >>> >>> >>> --- >>> avast! Antivirus: Outbound message clean. >>> Virus Database (VPS): 110330-0, 30-03-2011 >>> Tested on: 30-03-2011 15:39:30 >>> avast! - copyright (c) 1988-2011 AVAST Software. >>> http://www.avast.com >>> >>> >>> >>> _______________________________________________ >>> BaseX-Talk mailing list >>> BaseX-Talk(a)mailman.uni-konstanz.de >>> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk >> >> >> --- >> avast! Antivirus: Inbound message clean. >> Virus Database (VPS): 110330-0, 30-03-2011 >> Tested on: 30-03-2011 15:47:51 >> avast! - copyright (c) 1988-2011 AVAST Software. >> http://www.avast.com >> >> >> > > > > --- > avast! Antivirus: Outbound message clean. > Virus Database (VPS): 110330-0, 30-03-2011 > Tested on: 30-03-2011 15:54:40 > avast! - copyright (c) 1988-2011 AVAST Software. > http://www.avast.com > > >

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BaseX-Talk March 2011