- BaseX-Talk - mailman.uni-konstanz.de

Resolver/catalog: can't make it work
by Imsieke, Gerrit, le-tex 24 Jan '11

24 Jan '11

Dear Team (especially Michael), I'm trying to use an XML catalog during import (for the first time admittedly), but the catalog is obviously not being used. I tried to specify a full path in the GUI: c:/cygwin/home/gerrit/Apotheker/BaseX/catalog/catalog-win.xml I also tried to specify SET CATFILE on the command line, when the server was running and the GUI was off: basexclient -Uadmin -Padmin -c "SET CATFILE catalog/catalog-win.xml; set createfilter *.html; create database amt2; open amt2; add Apotheker/AMT" Took ages (never finished), which made me think that the resolver wasn't used. Switched off network connection. Received: Error: www.w3.org Since I was trying to import XHTML files, this is an indication that the catalog hasn't been used. Changed the CATFILE path to Apotheker/BaseX/catalog/catalog-win.xml (because the documents to be imported were apparently considered relative to my home dir or the current dir), to no avail. Also c:/cygwin/home/gerrit/Apotheker/BaseX/catalog/catalog-win.xml didn't work. Here's the server output: $ basexserver -di BaseX 6.5 [Server] Try "help" to get more information. > Creating Database... 62.02 ms (501 KB) Indexing Text... . 63.36 ms (588 KB) Indexing Attributes... . 66.02 ms (621 KB) Creating Database... java.io.IOException: www.w3.org java.net.PlainSocketImpl.connect(Unknown Source) ... Created a CatalogManager.properties in the CLASSPATH before starting the server. But it kept trying to connect to www.w3.org. Current catalog file looks like that: <?xml version="1.0"?> <catalog prefer="system" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog"> <rewriteSystem systemIdStartString="http://www.w3.org/TR/xhtml1/DTD/" rewritePrefix="file:///c:/cygwin/home/gerrit/Apotheker/schema/xhtml1/" /> </catalog> First HTML file that it is trying to import begins with: <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html;charset=utf-8"/> There is a file xhtml1-strict.dtd in the local directory. Altering the catalog file so that it's not well-formed any more doesn't seem to impress the parser. So I think it is not being read, but without a warning. What did I do wrong? If we manage to solve this, you may want to insert an XML Catalog Howto into the documentation wiki. Gerrit -- Gerrit Imsieke Geschäftsführer / Managing Director le-tex publishing services GmbH Weissenfelser Str. 84, 04229 Leipzig, Germany Phone +49 341 355356 110, Fax +49 341 355356 510 gerrit.imsieke(a)le-tex.de, http://www.le-tex.de Registergericht / Commercial Register: Amtsgericht Leipzig Registernummer / Registration Number: HRB 24930 Geschäftsführer: Gerrit Imsieke, Svea Jelonek, Thomas Schmidt, Dr. Reinhard Vöckler

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Invalid arguments...
by Mark Boon 23 Jan '11

23 Jan '11

Just now I spent considerable time figuring out why I get a message like this: [FORG0006] Invalid arguments for com.avatar_reality.ai.OntologyManager.save(...) method. In case you're wondering, it doesn't have anything to do with invalid arguments. It prints this whenever anything is wrong. Anything. It could be the wrong arguments. Or the wrong method name. Or the wrong class-name. Or even better, nothing like that at all, just any uncaught exception thrown by the method (or the class-loader) will cause it to print this error. May kindly I suggest embedding the original cause in the error message? That would save a ton of time figuring out what exactly is the matter. Mark

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BaseX 6.5
by Raymond Meester 21 Jan '11

21 Jan '11

I like 6.5 with the new tree visualization and commercial support. It's stabile and fast. Here is some feedback/feature requests for future development of BaseX: 1) Double click on the blue bar to get a full view (All other views are send to the background. When double clicking the other views appear again) 2) Put a close button on the blue bar 3) Folder view; add entry in the right-click menu to collapse in or out all nodes 4) Add support for intelligent xpath autocompletion in the search bar 5) Possibility in the right click menu to duplicate a node 6) Possibility to place a node in comment /uncomment 7) In text mode highlight a node when the cursor is standing on an opening or ending tag, so that the corresponding pair will be remark 8) Make "Enter" equal to double clicking when navigation in a xml 9) Option to show line numbers in text mode 10) Launch a xml in a browser, xml editor or IDE from the menu In the long run it would be nice to add 1) A XML Grid View (like xmlSpy or Stylus Studio) 2) XSD support for validating and generating schemas 3) XSLT support for transforming a xml db into another xml db and alternative query posibillities 4) Visualizing differences between two databases 5) Export xml to text, csv, xls, json etc 6) XQuery Documentation Generator (XQDoc Support) 7) Use colors to show structure of an xml in the visualization views (this option can be turned on and off) 8) Support for forms (Create forms as a front end for basex and distribute this together with the xml db as a jar file) 9) XML editing mode and read only mode (xacml) 10) Focus on support for adding thousands of xml files into one db Thanks, I will look forward to future releases Ray

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Re: [basex-talk] Query corrupts my database - we shall be happy namespaces are there
by Jan Vlčinský (CAD) 21 Jan '11

21 Jan '11

2011/1/21 Mark Boon <mboon(a)blueplanetsoftware.com> > ...It looks like I got it working using *:Ontology. I must say I never > understood why namespaces must make things so complicated and > counterintuitive. > Hi Mark. Namespaces are a mean, which let you live in quite complex universe, where more spaces are intersecting. You may think of writting XQuery for $x from my_universe return the-thing-I-am-thinking-of($x) (Un)Fortunately, this function was not implemented yet :-) (Are you really sure, what would your thoughts return to you?) But back to intersecting space - if you think of it, you realize, it is very easy to pick up something wrong, or to miss something. And we shall be happy, that in our XML space those separate spaces have names, so we can be enough explicit in telling what we really want. OK, apart from philosophical thoughts, I have simple rules, which helped me using namespaces 1. prefixes are just temporary abbreviations for real namespaces (fully qualified) and the prefixes can change during single XML document 2. imagine, that all prefixes (including the empty one) are replaced by fully qualified namespace name (and you may get rid of xmlns: attribues as they become useless) So for <Traffic xmlns="myone" xmlns:openlr="http://www.openlr.org/openlr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <openlr:OpenLR> <openlr:LocationID>defg123</openlr:LocationID> ...... </openlr:OpenLR> <OpenLR xmlns="http://www.openlr.org/openlr"> <LocationID>defg123</LocationID> </OpenLR> </Traffic> you get <myone:Traffic> <http://www.openlr.org/openlr:OpenLR> <http://www.openlr.org/openlr:LocationID>defg123</ http://www.openlr.org/openlr:LocationID> ...... </http://www.openlr.org/openlr:OpenLR> <http://www.openlr.org/openlr:OpenLR> <http://www.openlr.org/openlr:LocationID>defg123</ http://www.openlr.org/openlr:LocationID> </http://www.openlr.org/openlr:OpenLR> </myone:Traffic> This way it is perfectly clear, what namespaces are effective. I agree, namespaces are not easy to start with, but my feeling is, the complexity of namespace apparatus is balanced with complexity of the problem it should resolve. And once you get it - it will be clear and easy. Wish you the best. Jan

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XQuery Globaler Zähler
by Burkert, Michael 21 Jan '11

21 Jan '11

Hallo ! Will man allen XML-Elementen eine eindeutige Zahl zuordnen, würde man das über einen globalen Zähler lösen. Die globalen Variablen in XQuery lassen sich offenbar nicht hochzählen. Hat XBase eine Lösung für dieses Problem ? Eine Art eigenen Namespace mit eigener Funktionalität ? Es wird zwar eine Funktion angeboten die ähnliches leistet functx:index-of-node( ... ) Nur bremst diese die Bearbeitung beträchtlich. Viele Grüße Michael

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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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