BaseX-Talk October 2012

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40 participants
47 discussions

XQJ: Exception using Saxon9 TransformerFactoryImpl
by David Oguns 06 Oct '12

06 Oct '12

I am trying to perform a basic document insert using the XQJ API communicating with a standalone BaseXServer. I have a lot of dependencies on my classpath (I'm sure this affects JAXP's behavior), including Saxon, Xerces, Xalan, and probably a few versions of some of them. When I set the transformer factor explicitly to Xalan, there is no exception, but otherwise it appears Saxon is being used and it down throw an exception. I have a very high opinion of Saxon so I have my doubts that it's doing anything illegal with respect to the standards, so I thought I should ask what is going on. This is the property I can set to get rid of the problem: System.setProperty("javax.xml.transform.TransformerFactory", "org.apache.xalan.processor.TransformerFactoryImpl"); Here is the exception and stack trace: javax.xml.xquery.XQException: XQJTO013 - Values of 'standalone' and 'omit-xml-declaration' conflict Root Cause: net.sf.saxon.trans.XPathException: Values of 'standalone' and 'omit-xml-declaration' conflict at MyClass.main(MyClass.java:82) at net.sf.saxon.serialize.XMLEmitter.writeDeclaration(XMLEmitter.java:226) at net.sf.saxon.serialize.XMLEmitter.openDocument(XMLEmitter.java:143) at net.sf.saxon.serialize.XMLEmitter.startElement(XMLEmitter.java:303) at net.sf.saxon.event.NamespaceReducer.startElement( NamespaceReducer.java:72) at net.sf.saxon.event.ReceivingContentHandler.startElement( ReceivingContentHandler.java:290) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl$NSContentDispatcher.scanRootElementHook(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) at net.sf.saxon.event.Sender.sendSAXSource(Sender.java:400) at net.sf.saxon.event.Sender.send(Sender.java:154) at net.sf.saxon.IdentityTransformer.transform(IdentityTransformer.java:35) at MyClass.main(MyClass.java:82) And here is the relevant code: XQDataSource xqs = new BaseXXQDataSource(); xqs.setProperty("serverName", "localhost"); xqs.setProperty("port", "1984"); XQConnection conn = xqs.getConnection("admin", "admin"); try { XQStaticContext context = conn.getStaticContext(); XMLStreamReader xmlReader = XMLInputFactory.newInstance().createXMLStreamReader(newFileReader(args[0])); XQPreparedExpression xqpe = conn.prepareExpression("declare namespace output = \"http://www.w3.org/2010/xslt-xquery-serialization\";declare option output:omit-xml-declaration \"no\";declare variable $doc external;\nfn:put($doc,\"jc003.xml\")", context); //xquery doc('oguns/jc001.xml') try{ xqpe.bindDocument(new QName("doc"), xmlReader, conn.createDocumentType()); XQResultSequence xqrs = xqpe.executeQuery(); } finally { xqpe.close(); } } finally { conn.close(); }

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Jetty, locking files with webDAV and the possibility to use other web servers
by France Baril 05 Oct '12

05 Oct '12

Hi, Our context: - Multiple authors create/modify content stored on BaseX concurrently (content is split into multiple small topic files) - Authors access content using Data Source in Oxygen Issue - No locking mechanism to prevent multiple authors to make changes to the same file at once (leads to overwriting of the other author's changes). Research done seems to indicate that Jetty doesn't support webdav locking. - We couldn't get it working. - Talks with Oxygen validated this conclusion: http://www.oxygenxml.com/forum/post22862.html#p22862 Since the documentation says that Jetty is the default server (as opposed to it being the only server?), we are thinking we could maybe use another one. - Did anyone ever attempt that? - What would the steps to doing so be (Documentation only says how to work with Jetty)? - Anything possible/known issues? Compatibility or otherwise? -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com (514) 572-0341

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index:facets()
by Cerstin Elisabeth Mahlow 05 Oct '12

05 Oct '12

Hi, after Andreas recommended using index:facets(), my application speeds up. However, I don't think that this is the best solution. The database, I apply this function to is changing constantly. As the function is using the index, I would have to re-create the index first, is this correct? So that the functions would give wrong results most of the time. And I found another strange thing: I had to delete some nodes and re-created all indexes. However, index:facets() still gives the information from the status *before* the deletion, i.e., it counts nodes that aren't there anymore. Therefore I don't use it. count(//entry/selected[text () = "yes"]) gives the correct result, index:facets("collect", "flat")//element[@name = "selected"]/entry[text() = "yes"]/@count/data() still gives the wrong result, i.e., the result that was correct some days ago. Is this a bug or a feature? Best regards Cerstin -- Dr. phil. Cerstin Mahlow Universität Basel Departement Sprach- und Literaturwissenschaften Fachbereich Deutsche Sprach- und Literaturwissenschaft Nadelberg 4 4051 Basel Schweiz Tel: +41 61 267 07 65 Fax: +41 61 267 34 40 Mail: cerstin.mahlow(a)unibas.ch Web: http://www.oldphras.net

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XSLT import with relative path fails
by Charles Kowalski 04 Oct '12

04 Oct '12

Hi, I am trying to use TEI-to-xhtml stylesheet* provided by the tei consortium using the saxon HE transformer. The importing of xsl dependencies fails with this error: XTSE0165: I/O error reported by XML parser processing file:/../xhtml2/tei.xsl: /../xhtml2/tei.xsl (No such file or directory) The specific file i try to run is The actual href in the xsl:import is <xsl:import href="../../../xhtml2/tei.xsl"/> From the error message it looks as if the relative path: "../../../xhtml2/tei.xsl" is converted to the (non-existent) absolute path: "/../xhtml2/tei.xsl The same transformation works fine if called from the cli with java -jar path/to/saxon9he.jar some-tei.xml path/to/tei-stylesheets/xml/tei/stylesheet/profiles/tei/html/to.xsl Is there some sort of url resolution happening on behalf of basex before the xsl is passed to saxon? I will try to reproduce with a set of less complex xsl files but it seems like the issue lies with relative path resolution. Thanks, Alexandros *You can download the latest stylesheets from sourceforge at: http://sourceforge.net/projects/tei/files/Stylesheets/tei-xsl-6.14.zip/down…

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deleting and updating nodes
by Cerstin Elisabeth Mahlow 03 Oct '12

03 Oct '12

Hi, I encountered strange behavior in the GUI (version from September 30 of 7.5 beta): In my database of collected node-ids ('collect'), I had to remove some thousands, because the documents the nodes where referring to in the main database ('DB') had to be removed as well. So I had a database ('remove') with the documents like this: <list> <item>abc.xml</item> <item>def.xml</item> </list> And then I used this for the 'collect' database: for $i in //entry let $n := $i/node let $d := replace(db:open-id('DB', $n)/base-uri(), 'DB/', '') where db:open('remove')//item[text() = $d] return delete node $i I tested it (it removed the correct nodes) and then applied it to the whole thing and everything worked fine. In a second step, I deleted the respective texts from the original DB (to be precise, I created a new one without some texts and with whitespace chopping OFF, because the whitespace problem was another issue). And then I have to change the node-ids in my 'collect' database, so I tried this: for $node in //entry/node let $id := data($node) let $path := replace(db:open-id('DB', $id)/path(), 'Q\{.*?\}', '*:') let $base := replace(base-uri(db:open-id('DB', $id)), 'DB', 'newDB') let $newid := xquery:eval(concat('db:node-id(doc("', $base, '")', $path, ')')) return replace value of node $node with $newid It worked OKish on my test data: I removed irrelevant nodes first, made a copy and than applied the node-changing. But I got an error message, that some resources would not exist -- the ones I wanted to remove and thus the ones for which no node should be in 'collect' anymore. I created new test data, removed the nodes and immediately applied the changing, and then it worked. For the whole data, I successfully removed the nodes, I thought. And then regardless of using this database or making a copy and using this, I get an error message that a resource would not exist. How can I find out (in the GUI) where exactly the error occurs, i.e., for which $node? In the query info I only see "Stopped at line 1, column 14 in ...xq" Somehow, nodes that should have been deleted seem to still be there. The names of the files I created 'DB' from in the first place included special characters and spaces. The file I list the documents to be removed is a UTF-8 file where the file names appear also with special characters and spaces. Maybe the error is in there: One file name is "Brontë,-Charlotte.xml". Apparently, matching doesn't work. When I list the base-uri the node-ids belong to, I get Brontë,-Charlotte.xml, but the node will not be deleted, so it doesn't match the respective entry in the corresponding list. So how do I deal with this? Best regards Cerstin -- Dr. phil. Cerstin Mahlow Universität Basel Departement Sprach- und Literaturwissenschaften Fachbereich Deutsche Sprach- und Literaturwissenschaft Nadelberg 4 4051 Basel Schweiz Tel: +41 61 267 07 65 Fax: +41 61 267 34 40 Mail: cerstin.mahlow(a)unibas.ch Web: http://www.oldphras.net

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inquiry
by gzdsliujie6 03 Oct '12

03 Oct '12

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slow processing
by Mahlow Cerstin 02 Oct '12

02 Oct '12

Hi, I'm trying to understand why my Basex application is slow. I have a database looking like this: <collection> <entry time="2012-03-04T17:43:29"> <node>4119300</node> <query>[text() contains text ('Bank' ftand 'fallen') using stemming using language "de" distance at most 6 words ordered]</query> <person>marcel</person> <phraseme>Ad0032</phraseme> <selected>no</selected> </entry> <entry time="2012-03-04T17:43:29"> <node>11150403</node> <query>[text() contains text ('Bank' ftand 'fallen') using stemming using language "de" distance at most 6 words ordered]</query> <person>marcel</person> <phraseme>Ad0032</phraseme> <selected>no</selected> </entry> <entry time="2012-03-04T17:43:29"> <node>17335179</node> <query>[text() contains text ('Bank' ftand 'fallen') using stemming using language "de" distance at most 6 words ordered]</query> <person>marcel</person> <phraseme>Ad0032</phraseme> <selected>yes</selected> </entry> </collection> It consists of 97500 entries stored in the database "collect", one third has "yes" as value for <selected>, the other two third have "no". The number of entries will probably double over time. I use a CGI script to produce a HTML page first listing the total number of "yes" entries and the total number of distinct phrasemes, and then listing all entries sorted by <phraseme> where <selected> is "yes" in a table with 4 columns (phraseme, distinct persons, number of entries with this phraseme, link to another CGI-Perl script). Additionally, after the table I show the last timestamp for an entry with <selected> "yes". I use this for controlling purposes, to track progress of the use of the actual Basex search application. I put the relevant CGI code at the bottom. It is not that complex, but it takes 80 to 90 seconds. Which is much to slow! Skipping the timestamp information does not improve the speed. Do you have an idea how to improve this? Is the slow processing due to badly constructed XQueries, due to rendering as HTML table, due to server issues (I have a virtual server, but I don't know who else is using it for what)? my $session = Session->new("localhost", 1984, "admin", "admin"); $session->execute("open collect"); my $evidencecount = $session->execute("xquery let \$results := //selected[text() = 'yes'] return <b>{count(\$results)}</b>"); my @phrasemes = sort split(/\s+/, $session->execute("xquery distinct-values(//entry/phraseme/text())")); $session->close; my $phrasemecount = $#phrasemes + 1; print "<p> <b>$phrasemecount</b> accessed phrasemes with a total of $evidencecount hits</p>"; print "<table>"; print "<tr><th>Phraseme-ID</th> <th>Person</th><th>Count</th></tr>"; my $query =<<EOF; for \$phraseme in distinct-values(//entry/phraseme) let \$nodes := //phraseme[text() = \$phraseme] let \$count := count(\$nodes[../selected[text() = "yes"]]) let \$person := distinct-values(\$nodes/../person) order by \$phraseme return <tr><td>({\$phraseme})</td> <td>{\$person}</td> <td>{\$count}</td> <td><a href="basex-show-phraseme.pl?phraseme={\$phraseme}">show</a></td></tr> EOF my $viewsession = Session->new("localhost", 1984, "admin", "admin"); $viewsession->execute("open collect"); my $xquery = $viewsession->query($query); print $xquery->execute(); $xquery->close(); print "</table>"; # display last timestamp my $timequery = <<EOF; let \$i := //entry/\@time order by \$i/\@time ascending return <p>Last access: {data(\$i[last()])}</p> EOF my $xtimequery = $viewsession->query($timequery); print $xtimequery->execute(); $xtimequery->close(); $viewsession->close(); -- Dr. phil. Cerstin Mahlow Universität Basel Deutsches Seminar Nadelberg 4 4051 Basel Schweiz Tel: +41 61 267 07 65 Fax: +41 61 267 34 40 Mail: cerstin.mahlow(a)unibas.ch Web: http://www.oldphras.net

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BaseX-Talk October 2012