BaseX-Talk

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6 participants
5269 discussions

Attribute cannot be serialized !!
by John Best 02 Apr '14

02 Apr '14

Dear Team, I have downloaded the latest source code of BaseX, by latest I mean just a half hour ago. When I run it through Eclipse, I am getting error - [SENR0001] Attributes cannot be serialized:db:open-pre("docdb",7). This comes when, I try to get ONLY attributes .... -- Have a nice day JBest

4 6

WEBDAV bug when changing admin password in 7.8.1
by Maud Ingarao 02 Apr '14

02 Apr '14

Hi :) We are experiencing a strange bug in 7.8.1 After installing and before changing the admin password is everything ok (client connexion, rest and restxq connexions, webdav connexion...) But as soon as we change the admin password (best practice ? :p), the webdav connexion becomes impossible, and so the restxq connexion with a 404, while the rest connexion remains ok, like the client one. WEBDAV example : With the admin/admin password : mingarao@l100318:~$ cadaver http://localhost:8984/webdav Authentication required for BaseX on server `localhost': Username: admin Password: dav:/webdav/> ls Listing collection `/webdav/': succeeded. Coll: input 0 avril 1 16:49 Coll: my 0 avril 1 16:50 Coll: test 0 avril 1 16:49 dav:/webdav/> After changing the admin password mingarao@l100318:~$ cadaver http://localhost:8984/webdav Could not open collection:*-> doesn't even ask for a login/password* Impossible de s'authentifier auprès du serveur: missing realm in Basic challenge dav:/webdav/? ls The `ls' command can only be used when connected to the server. Try running `open' first (see `help open' for more details). dav:/webdav/? open http://localhost:8984/webdav Could not open collection: Impossible de s'authentifier auprès du serveur: missing realm in Basic challenge dav:/webdav/? Thanks a lot :) Maud -- /« Ne travaillez jamais »/ *Maud Ingarao* IHPC (UMR 5037) Institut d'histoire de la pensée classique, de l'Humanisme aux Lumières Ecole Normale Supérieure de Lyon - Site Descartes - Bureau R322 15 Parvis René Descartes - BP7000 - 69342 Lyon CEDEX 07 +33 4 37 37 65 79 - maud.ingarao(a)ens-lyon.fr /Je suis absente le vendredi | Out of office on Fridays/ http://pensee-classique.ens-lyon.fr | http://institutdesanti.ens-lyon.fr http://ahn.ens-lyon.fr | http://forge.cbp.ens-lyon.fr/ http://www.mutec.huma-num.fr | http://www.projet-plume.org http://www.cahier.paris-sorbonne.fr/

4 6

bug or requirement
by Rob Stapper 30 Mar '14

30 Mar '14

Hi there, In order to maintain consistency in my solution-patterns I seem to end up with the need for cyclicly chained/imported modules: module "A" imports module "B" which imports module "A". Too bad that the "import module" command of Basex can't handle this type of structure. Now I can't access the functionality of "A" within module "B". What are the chances in solving this issue? Have a nice weekend, Rob Stapper --- Dit e-mailbericht bevat geen virussen en malware omdat avast! Antivirus-bescherming actief is. http://www.avast.com

2 1

Runnable jar not running properly..
by John Best 29 Mar '14

29 Mar '14

Dear Christian I have downloaded BaseX source code from BaseX Github. Then imported the source code into Eclipse IDE and configured Maven. When I run the project, it runs properly. Then I export the project to create a runnable jar th rough Eclipse. Jar file is created smoothly, but when I run the jar, GUI is not starting. NO ERROR messages.. !!! Can you put some light on this issue ? -- Have a nice day JBest

2 1

Is there any mechanism of version control of objects, kept in BaseX database?
by Moshe Zuisman 29 Mar '14

29 Mar '14

Hi. I am right now using BaseX to analyse My XML files that keep installations pseudo-code(XMLs of IzPack open source installer). Procedure is quite entangled. I keep my XML source in files.. I periodically recreate BaseX database from folder that contain all my XML files and use it to perform queries, that analyse my data. When I find something I need - I have to go back to file, and perform search there to find once more therexml element . already retrieved at BaseX query. I weight to move from files to BaseX database and keep all info there. But... Here is a catch: Files I can keep in version control system (IBM Rational Cynnergy system) Is there some way to keep versions track of data - kept in BaseX database? Some interface with standard Version control systems, or any other way?

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Accessing DOCTYPE information after DB creation?
by Hondros, Constantine (ELS-AMS) 28 Mar '14

28 Mar '14

Hi all, I would really like to be able to query a large corpus of documents to get names and counts of the DTDs which are declared in the (somewhat old-fashioned now) DOCTYPE declaration: <?xml version="1.0" encoding="utf-8"?> <!DOCTYPE converted-article PUBLIC "-//ES//DTD journal article DTD version 4.5.2//EN//XML" "art452.dtd" [ ]> <converted-article>  Is there any way to get BaseX to preserve this information? Can I rewrite the doctype declaration into some sort of element node as the DB is being created so that this info can be queried? Thanks for any tips, Constantine. ________________________________ Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677, Registered in The Netherlands.

4 4

NullPointerException when executing geo:distance query
by Jesse Clark 27 Mar '14

27 Mar '14

Hi All, I am writing a feature that will rely on geo:distance to give me the distance between two points of latitude and longitude. I am a total n00b to GIS and GML so I may have messed this up, but based on a bit of research to figure out how to define the coordinate system and based on the example query from the BaseX docs I came up with the following query as a test: import module namespace geo = "http://expath.org/ns/geo"; declare namespace gml='http://www.opengis.net/gml'; let $vancouver := <gml:Point srsDimension="2" srsName="http://www.opengis.net/def/crs/EPSG/0/4326"> <gml:pos>49.40 -123.26</gml:pos> </gml:Point> let $seattle := <gml:Point srsDimension="2" srsName="http://www.opengis.net/def/crs/EPSG/0/4326"> <gml:pos>47.68 -122.37</gml:pos> </gml:Point> return geo:distance($vancouver, $seattle) I have this in a file and am trying to execute it from the CLI with: 'RUN [/path/to/file]' It pukes with this error: Stopped at [/path/to/file], 12/21: [GEO:GEO0002] java.lang.NullPointerException I am running off of the zip distribution of BaseX so I believe the geo module should be included. Any guidance would be greatly appreciated. Best, -Jesse

3 4

Re: [basex-talk] Class loading error
by Erol Akarsu 27 Mar '14

27 Mar '14

Sorry, throw this question, that is my fault. I have another question. Until now, I was able to read huge xml file (several Gbytes) through partition it and parse it with basex part by part. Do we have any new utility that can read 3-5G xml file and parse through basex? Thanks Erol Akarsu On Wed, Mar 26, 2014 at 10:16 AM, Erol Akarsu <eakarsu(a)gmail.com> wrote: > Sorry the mail sent incomplete. When I run, I am getting this exception. > Actually, I have added all libs to project and eclipse compiles project > successfully. but when I run, getting exception. I send in previous email > the eclipse project description. > > Exception in thread "main" java.lang.NoClassDefFoundError: BaseXException > Caused by: java.lang.ClassNotFoundException: BaseXException > at java.net.URLClassLoader$1.run(URLClassLoader.java:202) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:190) > at java.lang.ClassLoader.loadClass(ClassLoader.java:306) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) > at java.lang.ClassLoader.loadClass(ClassLoader.java:247) > > > On Wed, Mar 26, 2014 at 10:14 AM, Erol Akarsu <eakarsu(a)gmail.com> wrote: > >> I am trying to run WikiExample coming as examples in eclipse. I moved >> all basex jars into lib folder of eclipse project that includes WikiExample >> basex application. But when I run >> >> >> >

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Fwd: Re: whitespaces in import
by Dirk Kirsten 27 Mar '14

27 Mar '14

Sorry, mail was supposed to be send to the mailing list... Information is the same as in Leos mail -------- Original Message -------- Subject: Re: [basex-talk] whitespaces in import Date: Wed, 26 Mar 2014 17:59:12 +0100 From: Dirk Kirsten <dk(a)basex.org> To: Stefan Sechelmann <sechel(a)math.tu-berlin.de> Hello Stefan, On 26/03/14 17:51, Stefan Sechelmann wrote: Is there some kind of whitespace normalization > going on during import? Yes, it is. Can I set options that influence this behavior or is this a bug? Yes, you can. Set the CHOP option to false (see https://docs.basex.org/wiki/Options#CHOP for details) or start BaseX with the -w flag (which sets CHOP to false). Hope that helps. Cheers, Dirk -- Dirk Kirsten, BaseX GmbH, http://basex.org |-- Firmensitz: Blarerstrasse 56, 78462 Konstanz |-- Registergericht Freiburg, HRB: 708285, Geschäftsführer: | Dr. Christian Grün, Dr. Alexander Holupirek, Michael Seiferle `-- Phone: 0049 7531 28 28 676, Fax: 0049 7531 20 05 22

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Oracle SQL set up for extracting XML Clobs
by Bednar, Scott E 26 Mar '14

26 Mar '14

Just sharing some information I've learned over the past week about using BaseX with Oracle using the SQL Module... in particular, to extract XML out of CLOB fields in Oracle you need to jump through a couple hoops: To get things set up, the following jars need to be on the classpath (I just put them into the BaseX lib directory which gets picked up if you start BaseX using one of the .bat scripts): - ojdbc6.jar - xdb6.jar - xmlparserv2.jar With this last jar, xmlparserv2.jar, there are a few things to watch for. First, you need a later version of the jar. Earlier versions are smaller (the jar for 11g is about 1350KB, the jar you have should probably be at least that big), and the filename isn't different for different versions. Be sure of what you have... you can find it in Oracle distributions here: {ORACLE_HOME}/oracle/produce/{VERSION_NUMBER}/lib/xmlparserv2.jar The jar can also be found under /lib in the Oracle client distributions. Next, you will need to reconfigure the out-of-the-box xmlparserv2.jar to use some standard java components rather than Oracle's: Change the entries in the files in the META-INF/services as follows: - for javax.xml.parsers.DocumentBuilderFactory replace oracle.xml.jaxp.JXDocumentBuilderFactory with com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl - for javax.xml.parsers.SAXParserFactory replace oracle.xml.jaxp.JXSAXParserFactory with com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl - for javax.xml.transform.TransformerFactory replace oracle.xml.jaxp.JXSAXTransformerFactory with com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl The answer on this thread has complete instructions on reconfiguring the jar: http://stackoverflow.com/questions/11853967/errors-with-xmlparserv2-jar-and… Finally, you will need to add the following property setting to the startup script you are using (basex.bat, basexhttp.bat, basexgui.bat): -Doracle.jdbc.getObjectReturnsXMLType="false" This tells Oracle to return the java standard java.sql.SQLXML type that BaseX is expecting rather than the proprietary oracle.xdb.XMLType. See: http://docs.oracle.com/cd/E18283_01/java.112/e16548/jdbcvers.htm#BABGHBCC Here's how I added it to the script: set PROPS=-Doracle.jdbc.getObjectReturnsXMLType="false" java -cp "%CP%" "%PROPS%" %VM% org.basex.BaseX %* Once you have done all of that, you should be able to run an XQuery like this to get XML out of Oracle: sql:init("oracle.jdbc.OracleDriver"), let $conn := sql:connect("jdbc:oracle:thin:@myoracledb.org:1523:mydbsid", "username","password") return sql:execute($conn, "SELECT xmltype(MyXMLClob) from MyTable") If you get escaped XML in you results, you still need to reconfigure your xmlparserrv2.jar as shown above. As a side note: the above configuration is also necessary to make the basexhttp.bat script successfully start the server. If you use the un-configured xmlparserrv2.jar it will not start. Hope this helps! Cheers, Scott Bednar -----Original Message----- From: Bednar, Scott E Sent: Sunday, March 23, 2014 5:43 PM To: 'basex-talk(a)mailman.uni-konstanz.de' Subject: XML clob w/ SQL module I'm trying to extract XML stored in a CLOB from an oracle database using the sql module for BaseX. When I select the clob value, I get this sort of thing: <sql:column name="MSG">oracle.sql.CLOB@49458ef3</sql:column> I've tried casting it to XMLType (similar message) and to char (buffer size too small for the XML I'm dealing with). Is there a way of doing this short of creating a specialized Java module for it? Thanks, Scott

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