BaseX-Talk

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8 participants
5255 discussions

erreur librairies Saxon 11 avac BaseX 10.4
by Maud Ingarao (IHRIM - ENS de Lyon) 20 Mar '23

20 Mar '23

Bonjour à tous et toutes, En passant de BaseX 10.3 à BaseX 10.4, nous avons l'erreur ci-dessous. Quelque chose ne va pas avec les librairies XSLT Saxon.... Si nous mettons les anciennes librairies Saxon 9 à la place des librairies Saxon 11, l'erreur disparaît. Nous aimerions pouvoir utiliser les librairies les plus récentes. Merci de vos conseils :-) Amitiés, Maud HTTP ERROR 500 javax.xml.transform.TransformerFactoryConfigurationError: Provider net.sf.saxon.TransformerFactoryImpl could not be instantiated: java.lang.reflect.InvocationTargetException URI: /accueil STATUS: 500 MESSAGE: javax.xml.transform.TransformerFactoryConfigurationError: Provider net.sf.saxon.TransformerFactoryImpl could not be instantiated: java.lang.reflect.InvocationTargetException SERVLET: RESTXQ CAUSED BY: javax.xml.transform.TransformerFactoryConfigurationError: Provider net.sf.saxon.TransformerFactoryImpl could not be instantiated: java.lang.reflect.InvocationTargetException CAUSED BY: java.lang.reflect.InvocationTargetException CAUSED BY: java.lang.NoClassDefFoundError: org/xmlresolver/Resolver Caused by: javax.xml.transform.TransformerFactoryConfigurationError: Provider net.sf.saxon.TransformerFactoryImpl could not be instantiated: java.lang.reflect.InvocationTargetException at java.xml/javax.xml.transform.FactoryFinder.newInstance(FactoryFinder.java:181) at java.xml/javax.xml.transform.FactoryFinder.find(FactoryFinder.java:212) at java.xml/javax.xml.transform.TransformerFactory.newInstance(TransformerFactory.java:126) at org.basex.query.func.xslt.XsltTransform.transform(XsltTransform.java:70) at org.basex.query.func.xslt.XsltTransform.item(XsltTransform.java:36) at org.basex.query.expr.If.item(If.java:165) at org.basex.query.expr.DualMap.value(DualMap.java:82) at org.basex.query.expr.If.value(If.java:160) at org.basex.query.expr.If.value(If.java:160) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.func.StaticFunc.invokeInternal(StaticFunc.java:162) at org.basex.query.func.XQFunction.invoke(XQFunction.java:33) at org.basex.query.func.FuncCall.value(FuncCall.java:54) at org.basex.query.expr.ParseExpr.iter(ParseExpr.java:46) at org.basex.query.expr.constr.Constr.add(Constr.java:72) at org.basex.query.up.expr.Replace.item(Replace.java:49) at org.basex.query.expr.ParseExpr.value(ParseExpr.java:51) at org.basex.query.expr.If.value(If.java:160) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.expr.ParseExpr.item(ParseExpr.java:56) at org.basex.query.expr.If.item(If.java:165) at org.basex.query.expr.ItemMap.item(ItemMap.java:37) at org.basex.query.expr.ParseExpr.value(ParseExpr.java:51) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.expr.List.value(List.java:228) at org.basex.query.up.expr.TransformWith.value(TransformWith.java:74) at org.basex.query.expr.IterMap.value(IterMap.java:106) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.func.StaticFunc.invokeInternal(StaticFunc.java:162) at org.basex.query.func.XQFunction.invoke(XQFunction.java:33) at org.basex.query.func.FuncCall.value(FuncCall.java:54) at org.basex.query.expr.gflwor.Let$LetEval.next(Let.java:146) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.expr.List.value(List.java:228) at org.basex.query.up.expr.TransformWith.value(TransformWith.java:74) at org.basex.query.expr.IterMap.value(IterMap.java:106) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.func.StaticFunc.invokeInternal(StaticFunc.java:162) at org.basex.query.func.XQFunction.invoke(XQFunction.java:33) at org.basex.query.func.FuncCall.value(FuncCall.java:54) at org.basex.query.expr.gflwor.GFLWOR.value(GFLWOR.java:92) at org.basex.query.expr.Try.value(Try.java:93) at org.basex.query.expr.TypeCheck.value(TypeCheck.java:167) at org.basex.query.func.StaticFunc.invokeInternal(StaticFunc.java:162) at org.basex.query.func.XQFunction.invoke(XQFunction.java:33) at org.basex.query.func.FuncCall.value(FuncCall.java:54) at org.basex.query.expr.ParseExpr.iter(ParseExpr.java:46) at org.basex.query.scope.MainModule.iter(MainModule.java:48) at org.basex.query.QueryContext.lambda$4(QueryContext.java:354) at org.basex.query.QueryContext.run(QueryContext.java:763) at org.basex.query.QueryContext.iter(QueryContext.java:354) at org.basex.http.restxq.RestXqResponse.serialize(RestXqResponse.java:78) at org.basex.http.web.WebResponse.create(WebResponse.java:58) at org.basex.http.restxq.RestXqServlet.run(RestXqServlet.java:72) at org.basex.http.BaseXServlet.service(BaseXServlet.java:69) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1450) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:554) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624) at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1440) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:505) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594) at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1355) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) at org.eclipse.jetty.server.Server.handle(Server.java:516) at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:487) at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:732) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:479) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105) at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883) at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.xml/javax.xml.transform.FactoryFinder.newInstance(FactoryFinder.java:169) ... 88 more Caused by: java.lang.NoClassDefFoundError: org/xmlresolver/Resolver at net.sf.saxon.lib.CatalogResourceResolver.<init>(CatalogResourceResolver.java:46) at net.sf.saxon.Configuration.init(Configuration.java:366) at net.sf.saxon.Configuration.<init>(Configuration.java:229) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.lang.Class.newInstance(Class.java:584) at net.sf.saxon.Configuration.newConfiguration(Configuration.java:245) at net.sf.saxon.s9api.Processor.<init>(Processor.java:69) at net.sf.saxon.jaxp.SaxonTransformerFactory.<init>(SaxonTransformerFactory.java:59) at net.sf.saxon.TransformerFactoryImpl.<init>(TransformerFactoryImpl.java:42)

2 2

Progress bar (again)
by Zimmel, Daniel 16 Mar '23

16 Mar '23

Hey, I have a task that may take longer to execute (several minutes), so I felt I got to have a fancy progress bar on the command line to entertain me. No progress bar though, found this in the archives: https://mailman.uni-konstanz.de/pipermail/basex-talk/2020-November/015845.h… So this is the closest I got (running BaseX from an Ant task): xquery_update_db: [echo] XQuery Update (Database) wird ausgeführt: xquery/basex.reduce.xquery [apply] EXPORTER: omit-xml-declaration=no [apply] Database 'DEBUGX' was opened in 113.62 ms. [apply] "FORTSCHRITT: 0%" [apply] "FORTSCHRITT: *****5%" [apply] "FORTSCHRITT: **********10%" [apply] "FORTSCHRITT: ***************15%" [apply] "FORTSCHRITT: ********************20%" [apply] "FORTSCHRITT: *************************25%" While I am happy enough with this (it is quite accurate and I like the dramatically mounting effect), can anyone say what might be needed to implement this as a module? Daniel

2 4

"class file versions" discrepancy
by Murray, Gregory 15 Mar '23

15 Mar '23

Hello, I’m new to BaseX. I’m on a Mac with an Apple M1 chip, running macOS 12.6.3. I downloaded the ZIP distribution of BaseX. When I open BaseX.jar I get an error message saying to check the console. When I run basexgui at the command line, I get this error: Exception in thread "main" java.lang.UnsupportedClassVersionError: org/basex/BaseXGUI has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0 I updated Java to the latest version, according to the download page at java.com and according to the Update tab in the Java control panel in System Preferences. Running java -version returns this: java version "1.8.0_361" Java(TM) SE Runtime Environment (build 1.8.0_361-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.361-b09, mixed mode) However, I am still getting the same error when running basexgui. Is there a trick or workaround for this? Thanks, Greg

3 5

Formatting attributes as an indented list?
by Patrick Durusau 07 Mar '23

07 Mar '23

Greetings! I've been tasked with using BaseX to produce: ***** <wg class="cl" rule="S-IO" cltype="VerbElided"> <wg rule="NpaNp" role="s"> <wg type="group" appositioncontainer="true" rule="Np-Appos"> <w ref="PHM 1:1!1" after=" " class="noun" gbiType="proper" xml:id="n57001001001" lemma="Παῦλος" normalized="Παῦλος" strong="3972" number="singular" gender="masculine" case="nominative" gloss="Paul" domain="093001" ln="93.294a" morph="N-NSM" unicode="Παῦλος">Παῦλος</w> ***** The indenting is easy enough and I can even make it deeper if required but is there a command for serialization that will properly format the attributes? My personal suspicion is that inserting \n when each attribute is serialized (and not on the last one) is the easier route but I promised to investigate the command line. Have I overlooked something in the very fine manual? Hope everyone is having a great week! Patrick -- Patrick Durusau patrick(a)durusau.net Technical Advisory Board, OASIS (TAB) Editor, OpenDocument Format TC (OASIS), Project Editor ISO/IEC 26300 Co-Editor, ISO/IEC 13250-1, 13250-5 (Topic Maps) Another Word For It (blog): http://tm.durusau.net Homepage: http://www.durusau.net Twitter: patrickDurusau

4 10

Unable to set admin password
by Marco Lettere 20 Feb '23

20 Feb '23

Dear all, I'm trying to setup a new instance of BaseX 10 in order to start migrating some applications of ours. Anyway I'm unable to set the admin password. Followin https://docs.basex.org/wiki/BaseX_10#Migrating_Applications, I'm currently trying with [1] and [2] which both ask me to enter a new password. But afterwards I keep getting [3].... and I'm unable to access dba too. I cannot understand what I'm doing wrongly ... Any help? Thanks! [1] java -cp BaseX.jar org.basex.BaseX -c PASSWORD Password: newpassword [2] bin/basex -c PASSWORD Password: newpassword [3] bin/basexclient Username: admin Password: newpassword Access denied: admin

1 2

Examples and instructions
by kjkatinas＠gmail.com 19 Feb '23

19 Feb '23

Labas, Christian, Dar neturiu Lietuviska font tai rasisiu Angliskai. What I am looking for is documentation on how to perform simple UNION's and/or JOIN's. I have two DB's with data. DB1 has a small sample data set. DB2 is a master data repository. I need to find DB1 data that does not exist in the master repository. Sound simple enough, but I need examples with the proper syntax. Thanks in advance for your time and help. Linkejimai, KAS Kestutis J Katinas

2 1

reg: Stack Overflow: Try tail recursion?
by chandra sekhar n 17 Feb '23

17 Feb '23

Dear team, While using the below query on collection getting this try tail recursion issue. db:exists("3860_Master_Voice_JULY-21_Unbilled","SSBS_9038343_01131130904_02JUL21.xml") I am attaching a query plan and database info. Regards, Chandrasekhar

2 4

Help Diagnosing Memory Leak in SAXWrapper or Associated Code
by Eliot Kimber 13 Feb '23

13 Feb '23

I’ve worked out how to add a Xerces grammar cache to the XML parser. For current code from GitHub, I did this in SAXParser: public void parse() throws IOException { final InputSource is = inputSource(); final SAXSource saxs = new SAXSource(is); XMLReader reader = null; try { reader = saxs.getXMLReader(); if(reader == null) { reader = XmlParser.reader(options.get(MainOptions.DTD), options.get(MainOptions.XINCLUDE)); } final EntityResolver er = Resolver.entities(options); if(er != null) reader.setEntityResolver(er); saxh = new SAXHandler(builder, options.get(MainOptions.STRIPWS), options.get(MainOptions.STRIPNS)); reader.setDTDHandler(saxh); reader.setContentHandler(saxh); reader.setProperty(http://xml.org/sax/properties/lexical-handler, saxh); reader.setErrorHandler(saxh); if (true && options.get(MainOptions.DTD)) { XMLGrammarPool pool = getGrammarPool(); try { reader.setProperty(FEATURE_GRAMMAR_POOL, pool); } catch (final NoClassDefFoundError e) { } catch (final SAXNotRecognizedException | SAXNotSupportedException e) { } } reader.parse(is); ... Where getGrammarPool() is simply: static private XMLGrammarPool getGrammarPool() { XMLGrammarPool pool = grammarPool; if (pool == null) { pool = new XMLGrammarPoolImpl(); grammarPool = pool; //.set(pool); } return pool; } When I use the grammar cache to parse DITA docs (setting parse DTDs to true and specifying an XML catalog from DITA Open Toolkit) I see the expected speedup. For example, on a small set of about 2400 maps and topics, no-DTD parsing takes 7 seconds, grammar-cache parsing takes 20 seconds, and no-grammar-cache DTD parsing takes about 2.5 minutes. So roughly an 8x improvement (which is what I’ve measured using the same grammar cache with Saxon, for example). However, using the grammar cache causes some kind of extreme memory leak and I have no idea what it is. Without the grammar cache, parsing these topics requires only a few 100 metabytes of memory DTD or no, but with the grammar cache, memory usage starts at about 1GB and goes up from there. Parsing my full set of 40K maps and topics, memory grows by 1GB every 30 seconds or so until it eventually exceeds even the 14GB I allocated in my last test. The 1GB could be explained by the cache itself, which holds the parsed grammars. Using the debugger, I can see that the grammar cache itself is static once it’s populated with grammars (for my set it ends up loading 10 parsed grammars), so the grammar cache itself doesn’t seem to be the problem. I’m trying to use VisualVM to profile the memory but this is not something I have done before and I’m not sure what classes I should be focusing on. So my questions: 1. Any idea why the simple addition of the grammar cache would cause this kind of memory leak? 2. Any guidance on what classes I should focus on to find the culprit? My reason for using the grammar cache is to have all the default attributes populated in the database without requiring two hours to load my content (which is what I’ve measured in the past for DTD-aware parsing of my 40K content set). Another solution, specific to DITA, would be to use a custom SAX parser that injects the default attributes based on static configuration (for a given set of DITA grammars we know what the defaults will be for every element type and can easily generate the configuration a SAX parser would use). But the current code doesn’t seem to provide an easy way to swap in a custom SAX handler and I’m not really in a position to try to add that level of sophistication to the code. Modulo this memory issue, the grammar cache is a nice simple solution to the DTD parsing requirement that is general to any content set that has consistent DTD or XSDs across the set of documents to be parsed. Thanks, Eliot _____________________________________________ Eliot Kimber Sr Staff Content Engineer O: 512 554 9368 M: 512 554 9368 servicenow.com<https://www.servicenow.com> LinkedIn<https://www.linkedin.com/company/servicenow> | Twitter<https://twitter.com/servicenow> | YouTube<https://www.youtube.com/user/servicenowinc> | Facebook<https://www.facebook.com/servicenow>

2 2

XQuery Prolog with serialization settings - basex "Unknown option 'basex'?
by Patrick Durusau 13 Feb '23

13 Feb '23

Greetings! I have the following in the prolog of an XQuery: declare namespace output = 'http://www.w3.org/2010/xslt-xquery-serialization'; declare option output:method 'basex'; declare option output:basex 'indent=yes, newline=\n'; I'm following the example at: https://docs.basex.org/wiki/Serialization for CSV, reasoning the same form should work for basex. Sadly, BaseX 10.4 on Debian reports: [XQST0109] Unknown option 'basex Is it because basex isn't in the namespace of 'http://www.w3.org/2010/xslt-xquery-serialization'; ? OK so I change the namespace to http://tm.durusau.net and it runs! Sadly not applying the requested formatting. Some guidance on serialization please? Thanks! Patrick -- Patrick Durusau patrick(a)durusau.net Technical Advisory Board, OASIS (TAB) Editor, OpenDocument Format TC (OASIS), Project Editor ISO/IEC 26300 Co-Editor, ISO/IEC 13250-1, 13250-5 (Topic Maps) Another Word For It (blog): http://tm.durusau.net Homepage: http://www.durusau.net Twitter: patrickDurusau

2 2

basexhttp: default to index.html
by Christoph Gaukel 13 Feb '23

13 Feb '23

Hello, i successfully installed basex on my raspberry Pi. Now I want my jetty-server to answer with index.html. Currently it shows the subdirectories in directory .../webapp. cmd: curl https://personal-balance.com returns: <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <link href="jetty-dir.css" rel="stylesheet" /> <title>Directory: /</title> </head> <body> <h1 class="title">Directory: /</h1> <table class="listing"> <thead> <tr><th class="name"><a href="?C=N&O=D">Name  ⇧</a></th><th class="lastmodified"><a href="?C=M&O=A">Last Modified</a></th><th class="size"><a href="?C=S&O=A">Size</a></th></tr> </thead> <tbody> <tr><td class="name"><a href="/.logs/">.logs/ </a></td><td class="lastmodified">11.02.2023, 13:32:12 </td><td class="size">4.096 bytes </td></tr> <tr><td class="name"><a href="/chat/">chat/ </a></td><td class="lastmodified">01.12.2022, 11:06:52 </td><td class="size">4.096 bytes </td></tr> <tr><td class="name"><a href="/dba/">dba/ </a></td><td class="lastmodified">01.12.2022, 11:06:52 </td><td class="size">4.096 bytes </td></tr> <tr><td class="name"><a href="/restxq/">restxq/ </a></td><td class="lastmodified">10.02.2023, 12:35:22 </td><td class="size">4.096 bytes </td></tr> <tr><td class="name"><a href="/restxq.xqm">restxq.xqm </a></td><td class="lastmodified">29.07.2022, 13:41:16 </td><td class="size">2.492 bytes </td></tr> <tr><td class="name"><a href="/static/">static/ </a></td><td class="lastmodified">01.12.2022, 11:06:52 </td><td class="size">4.096 bytes </td></tr> <tr><td class="name"><a href="/WEB-INF/">WEB-INF/ </a></td><td class="lastmodified">10.02.2023, 16:19:26 </td><td class="size">4.096 bytes </td></tr> </tbody> </table> </body></html> web.xml and jetty.xml in .../webapp/WEB-INF/ are nearly in their original state. I only modified the location of restxq: <servlet-mapping> <servlet-name>RESTXQ</servlet-name> <url-pattern>*/restxq/**</url-pattern> </servlet-mapping> Kind regards, Christoph

2 1

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