BaseX-Talk July 2010

basex-talk@mailman.uni-konstanz.de

26 participants
48 discussions

Student project based on BaseX
by Antonis Thomas 22 Aug '10

22 Aug '10

Hello all, we are two master students at the university of Utrecht. We have a DB Architecture class that includes a small project (15%*7.5 ECTS= 1.125 ECTS). So, BaseX looks like a good chance to work on such a project. Our idea so far is based on some benchmarking experiments and small summary on how it works (maybe its relation with Monet) including any experiments we run (5-6 pages). Do you have anything better for us to do (maybe something you can get advantage of yourselves) or any guidelines/hints/whatever? Take into account that out time limit is approximately a week (full-time) and that we cannot do more work that what deserves 2.25ECTS for the 2 of us. I look forward to an answer (so we can decide and start working -the deadline is 9/7-. Best regards, -- Antonis Thomas Information & Computing Sciences Utrecht University Utrecht, The Netherlands

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Data limit?
by judith.risse＠wur.nl 09 Aug '10

09 Aug '10

Hello, I'm trying to load a large dataset (Medline, 16.7 million records, 66Gb data on disk) into BaseX. The input data is divided into 563 files of 30000 records each. When I try to load the data into a database with the following command: create db path/dir medline_full I get the following error message: Error: "medline08n0507.xml" (Line 2620386): Document is too large for being processed. The document itself can be loaded into a seperate database without problems and I also managed to load a merged file containing 1 million records, so the file size itself seems not to be the problem. I used the gui implementation running on a quadcore server with SuSe 10.2 64bit and 8Gb of memory, although the java version is 32bit 1.6.0_18 Therefore my question, does BaseX have a datalimit, either on file-, record- or nodelevel? Or are there hardware limitiations that could result in such an error message? With kind regards Judith

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serialization options with jax-rx
by Maximilian Gärber 02 Aug '10

02 Aug '10

Hi all, I am doing some tests with the jax-rx api - using static html files and a little jquery. I placed the html file in the \basex-api\etc directory and wanted to use the run command to let jetty deliver the html document: http://localhost:8984/basex/jax-rx?run=QueryTest.html&wrap=no&output=media-… The deliverd file will always be text/plain, however. Is there anything I am missing, or will the media-type option currently not affect the response Content-Type? Regards, Max For completeness, this is the ajax call: var data1 = '<query xmlns="http://jax-rx.sourceforge.net"><text>for $f in //file return $f/type</text><parameter name="count" value="5"/><parameter name="wrap" value="yes"/></query>'; var url1 = "http://localhost:8984/basex/jax-rx/Applications"; $.ajax( { url: url1, data: data1, type: "POST", processData: false, contentType: "application/query+xml", timeout: 10000, dataType: "xml", error: function(){ alert('Error loading XML document'); }, success: function(xml){ //alert(xml); $(xml).find('type').each(function(){ var item_text = $(this).text(); $('<li></li>') .html(item_text) .appendTo('#list'); }); } } );

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Refer to a specific document in a BaseX DB using XQuery
by cosmotron+basex＠gmail.com 30 Jul '10

30 Jul '10

If I add two documents to a BaseX DB, let's say normal.xml and normal2.xml, is there a way to refer to each one individually? I know about the doc() function, but it looks at the filesystem for their location, rather than in the database itself. For instance, if I query with this: doc("normal.xml")/name , then I will get an error about normal.xml not being found. I also tried: basex:db("my-db-name")/doc("normal.xml")/name and received the same error. Thanks for any help!

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XML Schema validation
by reference＠gmx.net 29 Jul '10

29 Jul '10

Does anybody know if it possible to enable XML schema validation before store xml documents in the database? Thanks in advance!

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Re: [basex-talk] BaseX download problem
by Andreas Weiler 28 Jul '10

28 Jul '10

Hi Merve, no problem, have fun with BaseX. cheers, Andreas Merve Ayd?nl?lar schrieb: > I have restarted my firefox and now I'm able to download, interesting > thing is I have also tried wget, I must misspelled the link. Sorry for > bothering and thanks for quick reply. > Have a nice day. > > Merve > > > > On Wed, Jul 28, 2010 at 2:00 PM, Andreas Weiler > <andreas.weiler(a)uni-konstanz.de > <mailto:andreas.weiler@uni-konstanz.de>> wrote: > > Hi, > > i just tested it and it worked for me. > What browser, system etc. are you using? > > Kind regards, > Andreas > > maydinlilar7(a)gmail.com <mailto:maydinlilar7@gmail.com> schrieb: > > Hi, > I want to inform you that I can't download BaseX (BaseX61.jar) > from the links you have provided. It redirects me to > sourceforge.net <http://sourceforge.net> and gives the error: > /tmp/NicidWVk.jar.part could not be saved, because the source > file could not be read. > Same problem also exists for direct link option. > _______________________________________________ > BaseX-Talk mailing list > BaseX-Talk(a)mailman.uni-konstanz.de > <mailto:BaseX-Talk@mailman.uni-konstanz.de> > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > > >

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BaseX download problem
by maydinlilar7＠gmail.com 28 Jul '10

28 Jul '10

Hi, I want to inform you that I can't download BaseX (BaseX61.jar) from the links you have provided. It redirects me to sourceforge.net and gives the error: /tmp/NicidWVk.jar.part could not be saved, because the source file could not be read. Same problem also exists for direct link option.

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NullPointerException in XQJ
by Godmar Back 27 Jul '10

27 Jul '10

Hi, before I prepare a self-contained test case, perhaps this description already rings a bell: I'm getting with the latest 6.2.2 this NPE: java.lang.NullPointerException at org.basex.query.up.primitives.UpdatePrimitive.addNode(UpdatePrimitive.java:193) at org.basex.query.up.primitives.UpdatePrimitive.addNode(UpdatePrimitive.java:214) at org.basex.query.up.primitives.UpdatePrimitive.buildDB(UpdatePrimitive.java:133) at org.basex.query.up.primitives.NodeCopy.prepare(NodeCopy.java:47) at org.basex.query.up.Primitives.check(Primitives.java:67) at org.basex.query.up.DBPrimitives.check(DBPrimitives.java:45) at org.basex.query.up.Updates.apply(Updates.java:102) at org.basex.query.QueryContext.iter(QueryContext.java:299) at org.basex.api.xqj.BXQDynamicContext.execute(BXQDynamicContext.java:266) at org.basex.api.xqj.BXQPreparedExpression.executeQuery(BXQPreparedExpression.java:55) This happens when I pass an actual DOM node to bindNode as argument 2. The error does not occur, and the query runs successfully, when I instead pass the node's ownerDocument. The node is the root of its document. Actual code: Works: xqp.bindNode(new QName("entry"), elem.getOwnerDocument(), null); Fails: xqp.bindNode(new QName("entry"), elem, null); Here, 'elem' is the root node of a document created via parseXml <http://top.cs.vt.edu/~gback/bx/b622/Test.java>from a string. It uses the JDK's DOM implementation. I note that in the second bug<http://top.cs.vt.edu/~gback/bx/b622/Test.java>we're discussing, BaseX also shows different behavior for nodes that are the root nodes of their respective documents when passed to bindNode. Which makes me wonder what the correct behavior is. It seems to me that passing a document or its root node to bindNode should result in the same behavior; correct? Thanks. - Godmar

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custom resolver / XML catalogs
by Imsieke, Gerrit, le-tex 27 Jul '10

27 Jul '10

Dear Team, We need to deal with XML that contains a DOCTYPE declaration and named entities. Unfortunately the DTD sometimes isn't available at the system location (e.g., "E:\mydoc.dtd") given in each document's declaration. Is it possible to specify a custom resolver such as org.apache.xml.resolver.tools.CatalogResolver so that the DTD can be found by virtue of a catalog, and consequently the entities can be resolved? If catalogs are not available, we'll have to resolve the entities (and remove the DOCTYPE declaration) in a preprocessing step using xmllint or saxon. This is acceptable, we just need to know how to proceed. Many thanks, Gerrit

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Clinical Trial Magnifier - now 21, 305 subscribers from 157 countries
by Clinical Trial Magnifier 27 Jul '10

27 Jul '10

Dear Colleague, You are invited to subscribe to a new free electronic monthly newsletter, the Clinical Trial Magnifier ( http://t.rs-tk.com/t.aspx/subid/24146128/camid/46345/www.clinicalresearchcl… ). The Magnifier is a free electronic newsletter that was launched in January 2008 by Johan Karlberg, MD, PhD, the Director of the Clinical Trials Centre at the University of Hong Kong. The Magnifier has today 21,305 subscribers representing 157 countries. The next Clinical Trial Conference ( http://t.rs-tk.com/t.aspx/subid/24146128/camid/46345/www.ctmconference.com/… ) will be November 24-26, 2010 in Kota Kingabalu, Sabah (the Land Below the Wind), Malaysia; the main conference theme will be Investigator Incentives for Participation in Industry Sponsored Clinical Trials. There are already 116 registrations by clinical trial professionals from 42 countries and about half have signed up for the pre-conference courses. Details are provided in the June 2010 Magnifier issue. The June 2010 Magnifier Issue has the following contents: Editorial. New Book on Clinical Trials - Reviewing Clinical Trials: A Guide for the Ethics Committee. A case study: Refining Clinical Research Infrastructure. Magnifier Subscriber Survey The Ethics Guide. Interview with 15 Magnifier Subscribers. The Study Site SOP Standardization - 4S - Project. Magnifier Advisory Board Members. The most recent May and June 2010 Industry-sponsored Clinical Trials Registered. Highlights Next Issue - Clinical Trials Overseen by the US FDA. Challenges to FDAs Ability to Monitor and Inspect Foreign Clinical Trials. Clinical Trial Conferences: November 2010, Kota Kinabalu, Malaysia Yours Sincerely Johan PE Karlberg, MD, PhD Clinical Trials Centre The University of Hong Kong P.S. If you have any kind of queries or messages please contact me directly using: EditorialBoard(a)ClinicalTrialMagnifier.com ( ) Delete my email from the Magnifier database. ( http://s.rs-tk.com/Unsubscribe.aspx?sub=24146128&user=4658&campid=46345&typ… )

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BaseX-Talk July 2010