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5268 discussions

Re: [basex-talk] Query exception
by Leonard Wörteler 11 Mar '11

11 Mar '11

Hi Gary, Am 11.03.2011 14:54, schrieb Gary Larsen: > I thought that this might have something > to do with distinct-values, but using group by syntax produced the same > error. I’ve included a few queries with these errors. could you provide us with an SSCCE [1] or the actual XML files of your database? I wasn't able to reproduce the reported bug(s) yet. > I ran into exception loading data last night but that was on a different > database so I don’t think it’s related. No, that shouldn't affect other databases at all. Cheers, Leo __________ [1] http://sscce.org/

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Query exception
by Gary Larsen 11 Mar '11

11 Mar '11

I'm testing out BaseX and getting remarkable query performance, first on a collection of ~3k documents, and then on ~27k docs (61m nodes). But there were some queries which ran on the small set but had exceptions on the large set. I thought that this might have something to do with distinct-values, but using group by syntax produced the same error. I've included a few queries with these errors. I ran into exception loading data last night but that was on a different database so I don't think it's related. Thanks, Gary Query: declare default element namespace 'http://developer.envisn.com/xmlns/envisn/netvisn/'; for $allInfo in distinct-values(collection('content2')//DbRefImpl/database) order by $allInfo return $allInfo Error: Possible bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 6.5.1 Java: Sun Microsystems Inc., 1.6.0_20 OS: Windows XP, x86 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 28194 org.basex.util.TokenSet.key(TokenSet.java:126) org.basex.data.Data.name(Data.java:386) org.basex.query.item.DBNode.nname(DBNode.java:117) org.basex.query.item.DBNode.qname(DBNode.java:130) org.basex.query.path.NameTest.eval(NameTest.java:107) org.basex.query.path.IterStep$1.next(IterStep.java:48) org.basex.query.path.AxisPath.iter(AxisPath.java:437) org.basex.query.path.AxisPath.iter(AxisPath.java:406) org.basex.query.func.FNSeq$3.<init>(FNSeq.java:146) org.basex.query.func.FNSeq.distinctValues(FNSeq.java:144) org.basex.query.func.FNSeq.iter(FNSeq.java:47) org.basex.query.QueryContext.iter(QueryContext.java:301) org.basex.query.expr.For$1.init(For.java:127) org.basex.query.expr.For$1.next(For.java:92) org.basex.query.expr.GFLWOR.iter(GFLWOR.java:289) org.basex.query.expr.GFLWOR.iter(GFLWOR.java:266) org.basex.query.QueryContext.iter(QueryContext.java:301) org.basex.query.QueryContext.iter(QueryContext.java:265) org.basex.query.QueryContext.eval(QueryContext.java:223) org.basex.query.QueryProcessor.execute(QueryProcessor.java:111) org.basex.core.cmd.AQuery.query(AQuery.java:83) org.basex.core.cmd.XQuery.run(XQuery.java:22) org.basex.core.Command.run(Command.java:292) org.basex.core.Command.exec(Command.java:274) org.basex.core.Command.execute(Command.java:67) org.basex.gui.GUI.exec(GUI.java:390) org.basex.gui.GUI$5.run(GUI.java:351) Query: declare default element namespace 'http://developer.envisn.com/xmlns/envisn/netvisn/'; for $allInfo in collection('content2')//DbRefImpl let $db := $allInfo/database group by $db order by $db return $db/text() Error: Possible bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 6.5.1 Java: Sun Microsystems Inc., 1.6.0_20 OS: Windows XP, x86 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 28194 org.basex.util.TokenSet.key(TokenSet.java:126) org.basex.data.Data.name(Data.java:386) org.basex.query.item.DBNode.nname(DBNode.java:117) org.basex.query.item.DBNode.qname(DBNode.java:130) org.basex.query.path.NameTest.eval(NameTest.java:107) org.basex.query.path.IterStep$1.next(IterStep.java:48) org.basex.query.path.AxisPath.iter(AxisPath.java:437) org.basex.query.path.AxisPath.iter(AxisPath.java:406) org.basex.query.QueryContext.iter(QueryContext.java:301) org.basex.query.expr.For$1.init(For.java:127) org.basex.query.expr.For$1.next(For.java:92) org.basex.query.expr.GFLWOR.iter(GFLWOR.java:289) org.basex.query.expr.GFLWOR.iter(GFLWOR.java:266) org.basex.query.QueryContext.iter(QueryContext.java:301) org.basex.query.QueryContext.iter(QueryContext.java:265) org.basex.query.QueryContext.eval(QueryContext.java:223) org.basex.query.QueryProcessor.execute(QueryProcessor.java:111) org.basex.core.cmd.AQuery.query(AQuery.java:83) org.basex.core.cmd.XQuery.run(XQuery.java:22) org.basex.core.Command.run(Command.java:292) org.basex.core.Command.exec(Command.java:274) org.basex.core.Command.execute(Command.java:67) org.basex.gui.GUI.exec(GUI.java:390) org.basex.gui.GUI$5.run(GUI.java:351) Query: declare default element namespace 'http://developer.envisn.com/xmlns/envisn/netvisn/'; for $allInfo in distinct-values(collection('content')//DbRefImpl[database='BOEING'][table='D _PROJ']/column) order by $allInfo return $allInfo Error: Possible bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 6.5.1 Java: Sun Microsystems Inc., 1.6.0_20 OS: Windows XP, x86 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 7176 org.basex.io.TableDiskAccess.read4(TableDiskAccess.java:123) org.basex.data.Data.size(Data.java:349) org.basex.data.DataPaths.doc(DataPaths.java:40) org.basex.data.DataPaths.doc(DataPaths.java:57) org.basex.data.Data.doc(Data.java:213) org.basex.query.QueryResources.addCollection(QueryResources.java:243) org.basex.query.QueryResources.collection(QueryResources.java:175) org.basex.query.func.FNGen.collection(FNGen.java:111) org.basex.query.func.FNGen.iter(FNGen.java:55) org.basex.query.QueryContext.iter(QueryContext.java:301) org.basex.query.expr.ParseExpr.value(ParseExpr.java:73) org.basex.query.func.Fun.comp(Fun.java:47) org.basex.query.path.Path.comp(Path.java:40) org.basex.query.expr.Arr.comp(Arr.java:35) org.basex.query.func.Fun.comp(Fun.java:43) org.basex.query.expr.For.comp(For.java:58) org.basex.query.expr.For.comp(For.java:1) org.basex.query.expr.GFLWOR.comp(GFLWOR.java:86) org.basex.query.QueryContext.compile(QueryContext.java:203) org.basex.query.QueryProcessor.compile(QueryProcessor.java:89) org.basex.core.cmd.AQuery.query(AQuery.java:75) org.basex.core.cmd.XQuery.run(XQuery.java:22) org.basex.core.Command.run(Command.java:292) org.basex.core.Command.exec(Command.java:274) org.basex.core.Command.execute(Command.java:67) org.basex.gui.GUI.exec(GUI.java:390) org.basex.gui.GUI$5.run(GUI.java:351)

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limit on number of attributes
by C. M. Sperberg-McQueen 09 Mar '11

09 Mar '11

Trying to use BaseX to index the XML version of the Unicode Database, I got a message saying an element had been encountered with too many attributes (more than 32). Is there a way to lift this limit for a particular database? If one wants to work with the Unicode database in XML (and let's face it, it will be a lot nicer in XML than in the semicolon-delimited form of the early Unicode releases), then one is going to have to work with elements which have a lot of attributes (haven't counted, probably fewer than a hundred). -- C. M. Sperberg-McQueen **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

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renaming a database
by Godmar Back 09 Mar '11

09 Mar '11

Last year [1], the functionality to rename a database was requested. We need this functionality as well. The option to rename the folder would require shutting down, and restarting, the BaseX server, which is not a good idea. The other alternative would be to retrieve the entire XML content of the source db, then create the target db with that content; this is wasteful and inefficient for large db. Please add a db rename functionality to the Java client binding. - Godmar [1] https://mailman.uni-konstanz.de/pipermail/basex-talk/2010-May/000298.html

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Re: [basex-talk] How to delete a node with PHP?
by Christian Grün 07 Mar '11

07 Mar '11

Dear Yoann Maingon, your code snippet looks fine to me. I would assume that a third command won't return any results, as they should have been deleted from your database: print $session->execute(“XQUERY //definition/item[@type=’test’]”); If that's not the case, or if I didn't answer your question, feel free to give us more details on your problem. Christian On Tue, Mar 8, 2011 at 12:46 AM, Yoann Maingon <yoann.maingon(a)prodeos.com> wrote: > > Hi, > > I’ve started using BaseX as a database for a PHP project. I can open the database and add nodes but I can’t delete nodes. > I’ve tested the XQUERY on the GUI and it works just fine. Any clue? > > Here is the xquery: > > Here is the php code: > […] > $session->execute(“OPEN data”); > $session->execute(“XQUERY delete nodes (//definition/item[@type=’test’])”); > > I’ve tried without “XQUERY” but gives the same result. > > Would be nice to have a working example of such use. > > Best Regards, > Yoann Maingon > > --------------------------------------- > Yoann Maingon > Prodeos > +33 6.64.32.49.66 > yoann.maingon(a)prodeos.com > www.prodeos.com

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How to delete a node with PHP?
by Yoann Maingon 07 Mar '11

07 Mar '11

Hi, I've started using BaseX as a database for a PHP project. I can open the database and add nodes but I can't delete nodes. I've tested the XQUERY on the GUI and it works just fine. Any clue? Here is the xquery: Here is the php code: [.] $session->execute("OPEN data"); $session->execute("XQUERY delete nodes (//definition/item[@type='test'])"); I've tried without "XQUERY" but gives the same result. Would be nice to have a working example of such use. Best Regards, Yoann Maingon --------------------------------------- Yoann Maingon Prodeos +33 6.64.32.49.66 <mailto:yoann.maingon@prodeos.com> yoann.maingon(a)prodeos.com LOGO_14032009_OnWhite_Signature www.prodeos.com

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Problem with Wikipedia database (or a more general namespace efficiency problem?)
by NewIntellectual 01 Mar '11

01 Mar '11

As both a stress test and to experiment, I created a database using a recent complete (current page) dump of English Wikipedia, a hefty file of 30.5 GB. I don't have enough memory apparently to create a full-text index of all of that text, so I created the DB without one. My first testing came up empty until I realized that I needed to deal with the namespace (ugh). Then I tried: declare default element namespace "http://www.mediawiki.org/xml/export-0.4/ "; //siteinfo This contains a small amount of data and occurs only once in the document (at /mediawiki/siteinfo). However, it's extremely slow (~33 seconds on my system). The query plan is: <IterPath> <Root/> <IterStep axis="child" test="*:mediawiki"/> <IterStep axis="child" test="*:siteinfo"/> </IterPath> Timing: - Parsing: 0.35 ms - Compiling: 0.22 ms - Evaluating: 33316.32 ms - Printing: 0.3 ms - Total Time: 33317.19 ms My surmise is that millions of node names are being checked rather than a path index being used to rapidly access the appropriate node(s). I don't think such a simple query should fail to be properly optimized. Another surmise is that it's related to namespaces not being indexed (?). While personally I very much dislike namespaces, they are common, and they have to be efficiently handled. To see if it made a difference, I also tried an explicitly named namespace test: declare namespace w="http://www.mediawiki.org/xml/export-0.4/"; //w:siteinfo This results in: <IterPath> <Root/> <IterStep axis="descendant" test="w:siteinfo"/> </IterPath> Timing: - Parsing: 0.33 ms - Compiling: 0.07 ms - Evaluating: 54288.51 ms - Printing: 0.3 ms - Total Time: 54289.23 ms So performance is even worse.

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EXPath ZIP Module
by Christian Grün 28 Feb '11

28 Feb '11

Dear all, BaseX now offers (slightly modified) support for the EXPath ZIP Module. This module allows everyone to extract files from ZIP archives, list its contents, create new archives, and update existing archives. As far as we know, our implementation is the first one which is simply usable out of the box, and may be the first complete implementation as well. The ZIP Module is included in our latest build, available at: http://files.basex.org/releases/latest/ Please have a look at our documentation to find more details and examples: http://docs.basex.org/wiki/ZIP_Functions All the best, Christian ___________________________ BaseX Christian Grün Uni KN, Box 188 78457 Konstanz, Germany http://www.inf.uni-konstanz.de/~gruen

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FindBugs for BaseX
by Godmar Back 26 Feb '11

26 Feb '11

2011/2/26 Leonard Wörteler <leonard.woerteler(a)uni-konstanz.de>: > Hi Godmar, > > that bug was pretty easy to fix, and I have no idea how the superfluous > downcast passed all our tests. It was introduced in version 6.2.8. Generally, downcasts are bad software engineering practice and can and should be avoided or minimized by proper design. Either change the method signature to let the compiler flag attends at passing incompatible types, or add virtual methods to a superclass/interface, or (last resort) use instanceof. Findbugs is a tool that flags errors such as these; you may have heard of it. Running Findbugs over the current codebase yields 563 warnings, some of which are clear bugs. I recommend you do that. For example: void delete(final int pre, final int size) { NSNode nd = root.find(pre); if(nd.pre == pre) nd = nd.par; if(nd == null) root = rootDummy; while(!nd.equals(rootDummy)) { nd.delete(pre, size); nd = nd.par; } } if 'nd == null', 'nd.equals()' crashes. If it can't be null, then 'root = rootDummy' is bogus. Or: case GRANT: final CmdPerm perm = consume(CmdPerm.class, cmd); if(perm == null) help(null, cmd); final String db = key(ON, null) ? name(cmd) : null; key(TO, cmd); return db == null ? new Grant(perm, name(cmd)) : new Grant(perm, name(cmd), db); if 'perm' is null, you crash in the 'Grant' constructor when calling perm.toString(). If it can't be null, the check is bogus. Or: @Override public boolean uses(final Use u) { return u == Use.CTX && (def == FunDef.MB || def == FunDef.MB || def == FunDef.EVAL || def == FunDef.RUN) || super.uses(u); } Did you mean to check for two different values instead of FunDef.MB twice. Or: // [CG] XQuery/Formatter: calendars and places are ignored if(cal != null || plc != null); Did you mean to return if cal != null || plc != null rather than doing nothing? Or in FTWrods.java if(iat == null) { final FTLexer lex = new FTLexer(ftt.opt); /* elided */ if(iat == null) { iat = ia; tl = t; } else if(mode == FTMode.M_ALL || mode == FTMode.M_ALLWORDS) { iat = FTIndexIterator.intersect(ia, iat, 0); tl += t; } else { iat = FTIndexIterator.union(ia, iat); tl = Math.max(t, tl); } iat.tokenNum(++ctx.ftoknum); } return iat.more() ? new FTNode(iat.matches(), data, iat.next(), tl, iat.indexSize(), iat.score()) : null; } The code in the else branch is dead - iat is always null where you test it due to the dominating test on entry. The 'intersect' and 'union' call is never made. Etc. well worth the time fixing. - Godmar

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Options to generate JSON file
by Jan Vlčinský (CAD) 26 Feb '11

26 Feb '11

Hi I shall export JSON file based on XML structures I have in my XQuery. Here I found http://demo.exist-db.org/xquery/json-test.xql/source sample, how eXistDB can produce JSON data. It is like import module namespace json="http://www.json.org"; 04. 05.declare option exist:serialize "method=xhtml media-type=text/html"; let $xml1 := 08.<root> 09.<h1>H</h1> 10.<p/> 11.<p>some text</p> 12.<h2>HH</h2> 13.</root> <script type="text/javascript"> 43.var data1 = {json:xml-to-json($xml1)}; BaseX does not provide this and I wonder, what options I have and what would anyone recommend 1. building up plain text piece by piece by XQuery 2. using some Java lib for this (there are more, any practical experience welcome) 3. Some other trick, which lives hidden to me (I already queried BaseX wiki and no hit) Jan -- *Ing. Jan Vlčinský* CAD programy Slunečnicová 338/3, 734 01 Karviná Ráj, Czech Republic tel: +420-597 602 024; mob: +420-608 979 040 skype: janvlcinsky; GoogleTalk: jan.vlcinsky(a)gmail.com http://cz.linkedin.com/in/vlcinsky

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