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Re: [basex-talk] Query corrupts my database
by Christian Grün 21 Jan '11

21 Jan '11

Hi Mark, this is due to a missing namespace declaration. You can either explicitly specify your namespace... declare default element namespace "http://www.w3.org/2002/07/owl#"; doc('test')/Ontology ...or use a namespace wildcard to match the root element: doc('test')/*:Ontology Hope this helps, Christian On Thu, Jan 20, 2011 at 11:16 PM, Mark Boon <mboon(a)blueplanetsoftware.com> wrote: > OK, I enter the following commands in the BaseX UI. > create database test > insert node <Ontology/> into doc('test') > replace node collection('test')/Ontology with <Ontology > xmlns="http://www.w3.org/2002/07/owl#" > xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" > xml:base="http://www.w3.org/2002/07/owl#"> > <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/> > <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/> > <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/> > <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/> > <SubClassOf> > <Class IRI="http://ar#boat"/> > <Class IRI="http://ar#vehicle"/> > </SubClassOf> > </Ontology> > Now, if I do > collection('test') > it shows me that the element was in fact inserted as it prints: > <Ontology xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" > xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > xmlns="http://www.w3.org/2002/07/owl#" > xml:base="http://www.w3.org/2002/07/owl#"> > <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/> > <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/> > <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/> > <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/> > <SubClassOf> > <Class IRI="http://ar#boat"/> > <Class IRI="http://ar#vehicle"/> > </SubClassOf> > </Ontology> > However, if I enter: > collection('test')/Ontology > it's empty. Isn't that unusual? I do note that in the "Query Info" panel it > prints: > - removing unknown tag/attribute "Ontology" > although it doesn't do so in my larger example. > When I try to execute the same 'replace...' command again, it tells me: > Error: [XUDY0027] Replace target must not be empty. > Mark Boon > > On Jan 20, 2011, at 11:39 AM, Christian Grün wrote: > > Hi Mark, > > I'm sorry, but I think I need some more information to find a helpful > answer. Do you have a little example (sscce) that allows us to > reproduce the issue? > > Christian > ___________________________ > > On Thu, Jan 20, 2011 at 10:27 PM, Mark Boon > <mboon(a)blueplanetsoftware.com> wrote: > > OK, I tried with BaseX 6.5. Now I don't get an error, but now my Ontology > > element remains empty. > > This is the output of the query: > > Query: replace node collection('bm_test_iam')/BOT-L/Ontology with <Ontology > > xmlns="http://www.w3.org/2002/07/owl#" > > xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > > xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > > xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" > > xml:base="http://www.w3.org/2002/07/owl#"> > > Compiling: > > - pre-evaluating collection("bm_test_iam") > > Result: replace node document-node { "bm_test_iam" }/*:BOT-L/*:Ontology with > > element { "Ontology" } { attribute { "xml:base" } { > > "http://www.w3.org/2002/07/owl#" }, element { "Prefix" } { attribute { > > "name" } { "rdf" }, attribute { "IRI" } { > > "http://www.w3.org/1999/02/22-rdf-syntax-ns#" } }, element { "Prefix" } { > > attribute { "name" } { "rdfs" }, attribute { "IRI" } { > > "http://www.w3.org/2000/01/rdf-schema#" } }, element { "Prefix" } { > > attribute { "name" } { "xsd" }, attribute { "IRI" } { > > "http://www.w3.org/2001/XMLSchema#" } }, element { "Prefix" } { attribute { > > "name" } { "owl" }, attribute { "IRI" } { "http://www.w3.org/2002/07/owl#" } > > }, element { "SubClassOf" } { element { "Class" } { attribute { "IRI" } { > > "http://ar#boat" } }, element { "Class" } { attribute { "IRI" } { > > "http://ar#vehicle" } } } } > > Query plan: > > <Replace> > > <IterPath> > > <document-node() name="bm_test_iam"/> > > <IterStep axis="child" test="*:BOT-L"/> > > <IterStep axis="child" test="*:Ontology"/> > > </IterPath> > > <CElem> > > <Item value="Ontology" type="xs:QName"/> > > <CAttr> > > <Item value="xml:base" type="xs:QName"/> > > <Item value="http://www.w3.org/2002/07/owl#" type="xs:string"/> > > </CAttr> > > <CElem> > > <Item value="Prefix" type="xs:QName"/> > > <CAttr> > > <Item value="name" type="xs:QName"/> > > <Item value="rdf" type="xs:string"/> > > </CAttr> > > <CAttr> > > <Item value="IRI" type="xs:QName"/> > > <Item value="http://www.w3.org/1999/02/22-rdf-syntax-ns#" > > type="xs:string"/> > > </CAttr> > > </CElem> > > <CElem> > > <Item value="Prefix" type="xs:QName"/> > > <CAttr> > > <Item value="name" type="xs:QName"/> > > <Item value="rdfs" type="xs:string"/> > > </CAttr> > > <CAttr> > > <Item value="IRI" type="xs:QName"/> > > <Item value="http://www.w3.org/2000/01/rdf-schema#" > > type="xs:string"/> > > </CAttr> > > </CElem> > > <CElem> > > <Item value="Prefix" type="xs:QName"/> > > <CAttr> > > <Item value="name" type="xs:QName"/> > > <Item value="xsd" type="xs:string"/> > > </CAttr> > > <CAttr> > > <Item value="IRI" type="xs:QName"/> > > <Item value="http://www.w3.org/2001/XMLSchema#" type="xs:string"/> > > </CAttr> > > </CElem> > > <CElem> > > <Item value="Prefix" type="xs:QName"/> > > <CAttr> > > <Item value="name" type="xs:QName"/> > > <Item value="owl" type="xs:string"/> > > </CAttr> > > <CAttr> > > <Item value="IRI" type="xs:QName"/> > > <Item value="http://www.w3.org/2002/07/owl#" type="xs:string"/> > > </CAttr> > > </CElem> > > <CElem> > > <Item value="SubClassOf" type="xs:QName"/> > > <CElem> > > <Item value="Class" type="xs:QName"/> > > <CAttr> > > <Item value="IRI" type="xs:QName"/> > > <Item value="http://ar#boat" type="xs:string"/> > > </CAttr> > > </CElem> > > <CElem> > > <Item value="Class" type="xs:QName"/> > > <CAttr> > > <Item value="IRI" type="xs:QName"/> > > <Item value="http://ar#vehicle" type="xs:string"/> > > </CAttr> > > </CElem> > > </CElem> > > </CElem> > > </Replace> > > Timing: > > - Parsing: 0.87 ms > > - Compiling: 1.21 ms > > - Evaluating: 2.33 ms > > - Printing: 0.14 ms > > - Total Time: 4.55 ms > > When I now do collection('bm_test_iam')/BOT-L/Ontology the "Text" panel just > > contains: > > <Ontology/> > > where I expected it to contain the XML I just inserted. > > Mark Boon > > > On Jan 20, 2011, at 11:13 AM, Mark Boon wrote: > > On Jan 20, 2011, at 11:09 AM, Christian Grün wrote: > > Mark, > > thanks for your mails. Just a short one.. Does the same error occur > > with the latest version of BaseX (6.5)? > > Christian > > Actually, I just picked up this work where I left it a few weeks ago. Some > > reorganization at work made me change e-mail so I hadn't followed this list > > either. So I missed that a new version came out. I'll try it immediately. > > I'll get back with the result. > > Mark > > _______________________________________________ > > BaseX-Talk mailing list > > BaseX-Talk(a)mailman.uni-konstanz.de > > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > > > >

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Transform table to tree
by Erdal Karaca 21 Jan '11

21 Jan '11

I have a table that is to be transformed to a tree: <entry id="entry1" parentId="parentOfThisEntry" /> <entry id="entry2" parentId="parentOfThisEntry" /> <entry id="entry3" parentId="parentOfThisEntry" /> <entry id="entry4" parentId="parentOfThisEntry" /> The tree structure can be constructed by the id/parentId relation. I failed to achieve this... :-( I am using basex 6.5.

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Query corrupts my database
by Mark Boon 20 Jan '11

20 Jan '11

I've been trying to keep an OWL ontology in the BaseX database. It's a little contrived but I thought it should work. But whenever I insert the ontology it corrupts my entire collection. I have a single Ontology node, that initially is just an empty element. Then I perform the following query: replace node collection('bm_test_iam')/BOT-L/Ontology with <Ontology xmlns="http://www.w3.org/2002/07/owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:base="http://www.w3.org/2002/07/owl#"> <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/> <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/> <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/> <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/> <SubClassOf> <Class IRI="http://ar#boat"/> <Class IRI="http://ar#vehicle"/> </SubClassOf> </Ontology> I get an error. Same thing when I run this query from the BasX UI. This is what I see in the "Query Info" panel: Query: replace node collection('bm_test_iam')/BOT-L/Ontology with <Ontology xmlns="http://www.w3.org/2002/07/owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:base="http://www.w3.org/2002/07/owl#"> <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/> <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/> <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/> <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/> <SubClassOf> <Class IRI="http://ar#boat"/> <Class IRI="http://ar#vehicle"/> </SubClassOf> </Ontology> Error: Possible bug? Feedback is welcome: basex-talk(a)mailman.uni-konstanz.de BaseX 6.3.2: java.lang.RuntimeException: Possible bug? Feedback is welcome: basex-talk(a)mailman.uni-konstanz.de BaseX 6.3.2: Data Access out of bounds [pre:699, indexSize:5, access:5 > 4] org.basex.util.Util.notexpected(Util.java:46) org.basex.io.TableDiskAccess.cursor(TableDiskAccess.java:323) org.basex.io.TableDiskAccess.read1(TableDiskAccess.java:92) org.basex.data.Data.kind(Data.java:324) org.basex.query.item.DBNode$4.next(DBNode.java:272) org.basex.query.path.IterStep$1.next(IterStep.java:45) org.basex.query.iter.NodeIter.next(NodeIter.java:1) org.basex.query.path.IterPath$1.next(IterPath.java:66) org.basex.query.path.IterPath$1.next(IterPath.java:1) org.basex.query.up.Replace.item(Replace.java:59) org.basex.query.expr.ParseExpr.iter(ParseExpr.java:47) org.basex.query.QueryContext.iter(QueryContext.java:360) org.basex.query.QueryContext.iter(QueryContext.java:324) org.basex.query.QueryContext.eval(QueryContext.java:282) org.basex.query.QueryProcessor.execute(QueryProcessor.java:104) 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:245) org.basex.core.Command.exec(Command.java:227) org.basex.core.Command.execute(Command.java:66) org.basex.gui.GUI.exec(GUI.java:383) org.basex.gui.GUI$5.run(GUI.java:346) Note: the XML I try to insert is created by Pellet, so I have little control over it. Not only does the query fail, but any subsequent query on the same collection now gives me a "Possible Bug?" message. Any ideas would be greatly appreciated. Mark Boon

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Editorial change in wiki - XQuery 3.0 and GroupBy
by Jan Vlčinský (CAD) 19 Jan '11

19 Jan '11

Hi Reading http://docs.basex.org/wiki/XQuery_3.0 <http://docs.basex.org/wiki/XQuery_3.0>I found, that third code listing telling You can see this effect by changing the return statement to: return element {$income} {count($ppl)} is exactly the same return statement as in first code listing and shall be probably changed into return element {$income} {$ppl} I tried to tell that directly on wiki, but I got no permission to do that, so I use this mailing list for it. Jan PS: I did not test the sample, I only know, it shall differ from the first one and this is my estimation.

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Importing CSV fles (BaseX 6.5)
by Jan Vlčinský (CAD) 18 Jan '11

18 Jan '11

Hi *BaseX 6.5 incl. rewritten web site is impressive*. Really. I go through it feature by feature and test it. Trying to import CSV file I have a problem 1. Creation of new database from xsv file or directory does not work (using default options, no changes) Reports "Line 1: Content is not allowed in prolog" 2. Adding document by Database - Add documents results in the same message 3. Trying to SET PARSER CSV did not change anything 4. Trying to add header with field names into imported file does not help Questions 1. How to import CSV fle 2. What CSV format is expected 1. tab, coma, semicolon? 2. header with field name allowed/expected? With best regards Jan

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FileGuru: Important Note About Submission Of BaseX 6.5
by FileGuru 17 Jan '11

17 Jan '11

Hi,Thanks for submitting your software BaseX 6.5 We will review your software within 2 weeks and you will be notified via email if your software has been accepted. To speed up your submission please place a link to us on any page of your website and let us know. By linking to our site you can greatly improve the position of your listing in our archive. Linking back to us will also ensure a speedy review of your software. Here is linking code which you can use to link back to our site. Software Downloads at FileGuru If you prefer image, you can find nice buttons here Best Regards, FileGuru http://www.fileguru.com © 2000-2010, FileGuru.

1 0

Update BaseX - OK.
by basex-talk＠mailman.uni-konstanz.de 17 Jan '11

17 Jan '11

Dear Developer, Thank you for submitting BaseX to http://www.softviewer.com Submission details: Software: BaseX Version: 6.5 Author: BaseX Page: http://www.basex.org/ Download: http://files.basex.org/BaseX.jar URL: http://www.softviewer.com/download_detail.php?softid=221864 Submit: http://www.softviewer.com/submit_soft.php Submit type: Update Submit date: 2011-01-17 16:32:15 If you would like to provide a link to SoftViewer from your site, you can find a nice buttons at http://www.softviewer.com/link_to_us.html You can link to http://www.softviewer.com/download_detail.php?softid=221864 or our homepage: http://www.softviewer.com Best Regards, SoftViewer - http://www.softviewer.com

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Release of BaseX 6.5, Homepage Relaunch
by Christian Grün 17 Jan '11

17 Jan '11

Dear all, We are excited to announce the relaunch of our homepage, which now includes commercial offerings such as professional support, individual software solutions, and training courses: http://basex.org/ Next, we have released Version 6.5 of BaseX, which offers the following new features: = Storage - Text compression, shrinking text nodes up to 50% - Enhanced collection support - Backup functionality - Built-in importers: HTML, Text, CSV = XQuery - XQuery 3.0 features, including GROUP BY and SWITCH statements - New file, HTTP, database and full-text functions - Built-in Lucene and Snowball Stemming for XQuery Full Text = GUI - New TreeView visualization - Improved database management = APIs - JAX-RX now supports hierarchical paths and external variables - Language Bindings extended with query iterators Thanks to your continuous feedback on BaseX! You can be sure that the project itself will remain Open Source, no matter what. We are looking forward to your responses, Christian BaseX Team 2011

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Extremely serious issue with magically disappearing databases
by Charles F. Munat 17 Jan '11

17 Jan '11

I have an embedded (soon to be unembedded) Base-X database supporting a website written in Scala. I have a very basic caching mechanism. The structure of the DB is such: <data> <cache> <page>...</page> <page>...</page> </cache> <somethings> <something>...</something> </somethings> <otherthings> <otherthing>...</otherthing> </otherthings> </data> I have a huge (1000+ lines) XQuery that takes all the somethings and otherthings recursively and constructs a <page> item that includes the html content of the page thus: <page uri="/" expires=""> <name>home</name> <content> <html> <head>...</head> <body>...</body> </html> </content> </page> This page is then saved into /data/cache. The way this works is simple. The main XQuery checks /data/cache/page[@uri=$uri] If it finds an unexpired page, it returns it. If it doesn't, it looks to see if such a page exists (in pieces) in the DB. If it does, it constructs the html page, inserts it into a <page> element along with some metadata (expires, etc.) and returns that. If no such page exists, it returns a 404 error page. Beauty, eh? And it works extremely well. Until I have an error in my XQuery, which, naturally, happens all the time during development. Just to make clear, here is the Scala that runs the query (from a Circumflex web app): get("(.)*".r) = { response.contentType("text/html") val url = uri.get(0).getOrElse("/") val out = executeQuery(Rx.pageQry(url)) match { case "" => "<p>Houston, we have a problem.</p>" case page if (page.substring(0,2) == "<p") => executeQuery("delete node /data/cache/page[@uri='" + url + "']") executeQuery("insert node " + page + " into /data/cache") executeQuery(Rx.pageQry(url)) case out => out } "<!DOCTYPE html>\n" + out } What this does is very simple. executeQuery simply runs the supplied query. Rx.pageQry just loads the huge query from a file and adds the call "local:getPage('/')" with the url inserted as a parameter. Right? Then the match looks to see if nothing at all comes back (case ""), or if a page that begins "<p" comes back (meaning a newly constructed query). The default is to spit the thing out. So in case one, we're screwed. In the default case, we serve the right page *or* a 404 error page. And in case two, we get the <page> for caching. In that instance, we delete any old page that might be in the cache with that URI, then insert the new page. Then we pull the html from the newly inserted page and serve that. I hope this is clear even if you don't write Scala. HERE IS THE PROBLEM: When I make an error in the big XQuery (the one loaded by Rx.pageQry), I get an error message from Base-X with the line number and the type of error. Beauty! So I fix the error and rerun the query AND MY DATABASE IS EMPTY. That's right: the entire database has been wiped. Running a / query gives me back <data> </data>. OUCH! If this happens in production (and this app is running in production right now), I might as well step in front of a bus. What, please, could be causing the database to dump itself? This has happened dozens of times! I'm willing to send the huge query off-list if anyone thinks that would help, but I don't see how the query *failing* and destroying the database could have anything to do with the query itself. I've looked at the Scala a million times and maybe I'm missing something, but the delete XQuery is /data/cache/page[etc.]. How can this destroy anything outside of /data/cache ? As for the insert query, how can inserting *anything* into /data/cache destroy things outside of /data/cache ? Am I missing something really basic, or is there a nasty bug in Base-X? Hopefully the former, but if it's the latter, I thought you should know. Could this be related to the embedded nature of the database? Thanks! Chas.

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Is op:divide-dayTimeDuration function implemented?
by Jan Vlčinský (CAD) 16 Jan '11

16 Jan '11

Hi I am trying to use function op:divide-dayTimeDuration as declared at http://www.w3.org/TR/xquery-operators/#func-divide-dayTimeDuration <http://www.w3.org/TR/xquery-operators/#func-divide-dayTimeDuration>BaseX tells me either unknown namespace op, or unknown function. Is this supported by BaseX, or I shall find my own implementation written in XQuery? Jan

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