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Bugreport: org.basex.server.ClientQuery.cache(ClientQuery.java:81)
by Bodo Hüsemann 08 Mar '13

08 Mar '13

Moin zusammen, ich habe meine Base-X Applikation von Version 7.2 auf 7.6 und versuchsweise auf 7.6.1 (Beta) umgestellt (embedded Base-X Server). Hierbei wirft die BaseX Lib bei parallelen XQuery Anfragen bei gleichzeitigen Inserts (ich verwende einen Threadpool) reproduzierbar die unten angehängte Fehlermeldung (in Variationen auch mit anderen Fehlercodes, aber immer an der gleichen Stelle/Zeile und beim gleichen Aufruf). Der Fehler tritt nicht bei jeder Anfrage auf (es scheint also eine bestimmte Concurrency Situation vorzuliegen). Die betreffende Funktion im Applikationscode ist wie folgt: public ArrayList<String> query(String inQuery, String[][] inArgs){ ClientSession mySession = null; ClientQuery myQuery = null; ArrayList<String> tmpString = new ArrayList<String>(); try { mySession = getClientSession(); myQuery = mySession.query(inQuery); // bind variable if (inArgs != null){ for (int i=0; i < inArgs.length; i++){ myQuery.bind("$" + inArgs[i][0], inArgs[i][1]); } } while (myQuery.more()){ // ** hier wird die Exception geworfen ** tmpString.add(myQuery.next()); } } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } finally { if (myQuery != null){ try { myQuery.close(); } catch (BaseXException e) { // ignore } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } } return tmpString; } Hier noch getClientSession: private static ClientSession getClientSession() throws IOException { ClientSession mySession = new ClientSession("localhost", 1984, "admin", "admin"); return mySession; } In der Version 7.2 war noch alles ok. Wahlweise habe ich auch schon Java-Heap Space Fehler an gleicher Stelle bekommen. Und in einem Fall ist die Datenbank plötzlich auf über 1GB angewachsen (vielleicht ein anderes Problem). Bevor ich anfange hierzu einen Minimalcase zu produzieren (was vermutlich recht aufwändig werden wird, da der Fehler nur unter Lastbedingungen auftritt) liefere ich vorab schon mal diesen Fehlerbericht. Vielleicht fällt ja direkt ein Problem ins Auge.... Wie immer vielen Dank für diese Klasse XML-DB und viele Grüße, Bodo -- Anhang Fehlermeldungen mit Version 7.6.1 (in 7.6 war die Zeilennr: 79) org.basex.core.BaseXException: -146032 at org.basex.server.ClientQuery.cache(ClientQuery.java:81) at org.basex.server.Query.more(Query.java:74) at de.infabswissarmy.control.XMLDBManagerBaseX.query(XMLDBManagerBaseX.java:86) at de.infabswissarmy.control.XMLDBManagerBaseX.queryDoc(XMLDBManagerBaseX.java: 121) at de.infabswissarmy.control.QueryTask.httpQuery(QueryTask.java:180) at de.infabswissarmy.control.QueryTask.run(QueryTask.java:271) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) org.basex.core.BaseXException: 0 at org.basex.server.ClientQuery.cache(ClientQuery.java:81) at org.basex.server.Query.more(Query.java:74) at de.infabswissarmy.control.XMLDBManagerBaseX.query(XMLDBManagerBaseX.java:86) at de.infabswissarmy.control.XMLDBManagerBaseX.queryDoc(XMLDBManagerBaseX.java: 121) at de.infabswissarmy.control.QueryTask.httpQuery(QueryTask.java:180) at de.infabswissarmy.control.QueryTask.run(QueryTask.java:271) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) org.basex.core.BaseXException: java.lang.ArrayIndexOutOfBoundsException at org.basex.server.ClientQuery.cache(ClientQuery.java:81) at org.basex.server.Query.more(Query.java:74) at de.infabswissarmy.control.XMLDBManagerBaseX.query(XMLDBManagerBaseX.java:86) at de.infabswissarmy.control.XMLDBManagerBaseX.queryDoc(XMLDBManagerBaseX.java: 121) at de.infabswissarmy.control.QueryTask.httpQuery(QueryTask.java:180) at de.infabswissarmy.control.QueryTask.run(QueryTask.java:271) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

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Re: [basex-talk] Beginner Qs concerning scope and focus of BaseX
by Johannes.Lichtenberger 08 Mar '13

08 Mar '13

On 03/07/2013 11:04 PM, Silver, Jonathan wrote: > Thanks for the [long] reply. I really do appreciate the extra information. > It seems to me that what I am asking would be a common kind of thing. > > I think that you indicated that I could add a datetimestamp to a node and then have multiple copies. > At least that would get me to have multiple versions. Yes, for instance, but it adds extra information to each changed node and the identity is getting lost (for instance that's great and almost necessary to determine the differences between versions efficiently). It would be best if the storage system itself is capable of this for instance through extending the XDM and identifying a node through a simple tuple: unique ID (and never reuse IDs of deleted nodes) + version or an equivalent. But I suppose it's a great way to do versioning with BaseX. However, determining differences might become cumbersome. A versioning system usually adds references to new versions (as in persistent datastructures[1]). However that always implies some additional overhead through copying of leaf to root paths in tree-based index-structures (for instance the B+-tree shadowing) or at least some kind of overhead in a dictionary to reference the data-pages. I think BaseX is designed to provide the best possible query performance, such that providing snapshots of documents in a collection does not make much sense, but Christian might have additional information (also regarding your second paragraph which I didn't address as I don't know how documents are referenced). kind regards Johannes [1] http://en.wikipedia.org/wiki/Persistent_data_structure

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Beginner Qs concerning scope and focus of BaseX
by Silver, Jonathan 07 Mar '13

07 Mar '13

1. The YouTube intro video has no sound. [2] http:/ / www. youtube. com/ watch?v=xILHKGPGaJ4& hd=1 I've tried it with different browsers and different players. 2. Documents are added to a database using add, with a file pathname (or url..) is it the same pathname that is always Used to refer to that document? Or can I reference it another way? I created a database, added 3 documents using the Add command. In list, no input path is displayed, how would I request the second document? 3. If I had a different versions of the factbook xml file (maybe one each year) and so the contents like populations or even languages Change each year, can I and how would I use baseX to manage these? I'd want to do normal queries but I'd also want to do queries for specific years And do queries for what has changed - or changed the most? I'm reading up on XQuery, but some of this looks beond XQuery and required DB support. Thanks, jonathan

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Re: [basex-talk] Linking BaseX to Fuseki RDF triplestore over http
by pw＠themail.co.uk 07 Mar '13

07 Mar '13

Hi Pascal I have not exceeded the limit, but then I'm not working in the DDI arena or something similar where this is a certainty. I think that the database needs to move to a 64bit architecture to handle the large node numbers that are seen in data-centric (rather than document-centric) XML and clearly there is a similar need for those running data archives to have pratically limitless scope for namespaces Peter > > > >---- Original Message ---- >From: pascal.heus(a)gmail.com >To: basex-talk(a)mailman.uni-konstanz.de >Subject: Re: [basex-talk] Linking BaseX to Fuseki RDF triplestore >over http >Date: Thu, 07 Mar 2013 16:34:11 +0100 > >>Peter: >>Thanks for sharing this. One of the concern I have with using >RDF-XML >>and BaseX is the limit of 256 namespaces per database. >>Any thoughts of that topic? >>best >>*P >> >>On 3/7/13 10:43 AM, pw(a)themail.co.uk wrote: >>> Hi List >>> You might be interested in >>> >http://www.slideshare.net/PeterWinstanley1/open-data-edinburghnapier2 >0130305 >>> Peter >>> >>> _______________________________________________ >>> BaseX-Talk mailing list >>> BaseX-Talk(a)mailman.uni-konstanz.de >>> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk >>> >> >>_______________________________________________ >>BaseX-Talk mailing list >>BaseX-Talk(a)mailman.uni-konstanz.de >>https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk >>

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Linking BaseX to Fuseki RDF triplestore over http
by pw＠themail.co.uk 07 Mar '13

07 Mar '13

Hi List You might be interested in http://www.slideshare.net/PeterWinstanley1/open-data-edinburghnapier20 130305 Peter

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Using xquery in a xslt stylesheet
by Raymond Meester 07 Mar '13

07 Mar '13

I thought I share this one, just in case someone needs to call BaseX (xquery the database in this example) from xslt: Greets, Raymond Example: <?xml version="1.0" encoding="utf-8"?> <xsl:stylesheet version="2.0" exclude-result-prefixes="xsl basex" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:basex="java:org.basex.server.ClientSession">  <xsl:variable name="session" select="basex:new('localhost', 1984, 'admin','admin')"/> <xsl:template match="/">  <xsl:variable name="query"><xsl:text>XQUERY for $doc in db:open("SampleDB") return $doc</xsl:text></xsl:variable> <example>  <xsl:value-of select="basex:execute($session,string($query))"/> </example> </xsl:template> </xsl:stylesheet>

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Some general questions
by Kuranov, Anton 05 Mar '13

05 Mar '13

Hello, We are looking for fast and simple Java XML database engine for our integration solution. I've found BaseX that seems to be a good option but I have some questions about it: - Performance. How it feels on large databases, about 50-100 millions of nodes? Does performance degrades significally? What is the maximum number of nodes that BaseX have been tested with? - Streamable queries. We will need to send large datasets to client including the whole database. Does BaseX provides a streamable queries without caching whole resultset nowhere in memory (something like server cursors in RDBMS)? If we will use XQJ API and Java as middleware, is it will possible to create a fully streamable service to retrieve large amounts of data directly from database? - Failover. Our clients strongly require failover mode. I saw that at the moment BaseX does not support clustering and replication but it can be done at OS level using distributed file systems like Ceph or ClusterFS. Can we have two o more BaseX instances connected to the same shared storage? - What transaction isolation levels BaseX supports? Do BaseX transactions support JTA architecture? Regards, Antón ________________________________ Este correo electrónico y, en su caso, cualquier fichero anexo al mismo, contiene información de carácter confidencial exclusivamente dirigida a su destinatario o destinatarios. Si no es vd. el destinatario indicado, queda notificado que la lectura, utilización, divulgación y/o copia sin autorización está prohibida en virtud de la legislación vigente. En el caso de haber recibido este correo electrónico por error, se ruega notificar inmediatamente esta circunstancia mediante reenvío a la dirección electrónica del remitente. Evite imprimir este mensaje si no es estrictamente necesario. This email and any file attached to it (when applicable) contain(s) confidential information that is exclusively addressed to its recipient(s). If you are not the indicated recipient, you are informed that reading, using, disseminating and/or copying it without authorisation is forbidden in accordance with the legislation in effect. If you have received this email by mistake, please immediately notify the sender of the situation by resending it to their email address. Avoid printing this message if it is not absolutely necessary.

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Problem using xquery:eval using Basex 7.6
by Freihalter Thomas 04 Mar '13

04 Mar '13

Hi, I read in the Basex-Archive about a bug in xquery:eval, is this related to this bug? list() .... stockdevel_stock_work_COUTRY 122 34188 ... Here is my xquery, it is okay for a small selection size: XQUERY let $xquery := "db:open('stockdevel_stock_work_COUTRY')/*[@n='NZ']" for $i in xquery:eval($xquery) return $i <COUTRY n="NZ" s="valid" t="2013-03-04T22:10:29.308+0100" v="1"> <COUNTRY>Neuseeland</COUNTRY> <REGION>REGION EM</REGION> </COUTRY> if the selection size is greater then about 100: XQUERY let $xquery := "db:open('stockdevel_stock_work_COUTRY')/*" for $i in xquery:eval($xquery) return $i .... <COUTRY n="NZ" s="valid" t="2013-03-04T" v="1"> <COUNTRY>Neuseeland</COUNTRY> <REGION>REGION EM</REGION> </COUTRY> ..... Sometimes I get : 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_35 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 7 org.basex.util.Compress.pull(Compress.java:139) org.basex.util.Compress.unpack(Compress.java:121) org.basex.data.DiskData.txt(DiskData.java:268) org.basex.data.DiskData.text(DiskData.java:235) org.basex.io.serial.Serializer.node(Serializer.java:343) org.basex.io.serial.Serializer.serialize(Serializer.java:99) org.basex.io.serial.Serializer.serialize(Serializer.java:84) org.basex.core.cmd.AQuery.query(AQuery.java:90) org.basex.core.cmd.XQuery.run(XQuery.java:22) 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.server.ClientListener.run(ClientListener.java:145) Or using this xquery with restxq http://localhost:8984/restxq ... Unexpected error: 48 or Unexpected error: java.lang.ArrayIndexOutOfBoundsException Regards, Thomas Freihalter

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Setting up RESTXQ in more than one place
by Wendell Piez 02 Mar '13

02 Mar '13

Hi BaseX, Did I mention recently what a great product you have here? So I have found by tweaking webapp/WEB-INF/web.xml I can point BaseX to someplace other than its restxq directory to find its RESTXQ .xqm files. This is cool. (I am encapsulating code for maximum portability and this is a help.) But in this project we are also looking forward to when we'll be serving multiple different datasets with different document types and logic, and we wish to keep them separate. Will I be able to ask BaseX to look in more than one place for its RESTXQ? (For its databases?) Thanks -- Wendell -- Wendell Piez | http://www.wendellpiez.com XML | XSLT | electronic publishing Eat Your Vegetables _____oo_________o_o___ooooo____ooooooo_^

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Whitespace anomaly running XSLT from BaseX
by Wendell Piez 01 Mar '13

01 Mar '13

Friends, I am encountering an odd whitespace-handling anomaly in BaseX when invoking Saxon to transform files behind RESTXQ. Briefly, if I have this in my XSLT: <xsl:text> </xsl:text> (the common way to get a space character in my result) I get nothing, and this <xsl:text> Boo! </xsl:text> gets me "Boo!" (leading and trailing whitespace trimmed). But I can't duplicate this behavior running BaseX from the GUI. I am sure there is a 'trim' or 'chop' setting somewhere that is allowing this, but I don't know where to look. Any ideas? Thanks, Wendell -- Wendell Piez | http://www.wendellpiez.com XML | XSLT | electronic publishing Eat Your Vegetables _____oo_________o_o___ooooo____ooooooo_^

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