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Indexes creation fails on big database
by Erdal Karaca 23 Apr '13

23 Apr '13

Hi all, I have downloaded/started the latest dev snapshot of 7.7. My database consists of an extract of the OpenStreetMap data (only Germany) which is 29GB in size (xml/OSM format). I have managed to load the file into the database but the indexes creation procedure fails. I have tried -Xmx4g, but if the progress bar of the GUI is right, I would need the 10x of heap space to create the attribute indexes. Any ideas/workarounds to create the attribute indexes for such a big database? Thanks!

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Geospatial indexing
by Erdal Karaca 23 Apr '13

23 Apr '13

Hi all, Just noticed that basex supports geospatial queries since 7.6. But, how do I index geospatial data in my database? Or is that a missing feature? Thanks! Best regards, Erdal

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inserting ampersand
by marco fregonese 23 Apr '13

23 Apr '13

Hi there, I have the following xquery function: *declare updating function local:insert ($a) { insert node <title>{$a}</title> into /web }; local:insert ("&")* but if I try to insert an apersand, basex says "invalid entity '&' ". So, my question: is there any way to insert an ampersand? Thank you.

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Full-Text search, how to mark whole phrases
by Bartosz Marciniak 19 Apr '13

19 Apr '13

Hi, I have placed small document in database with enabled full-text index: <text> Text with hello world phrase. </text> The following expression: ft:mark(db:open('simple')//*[text() contains text 'hello world']) produces: <text>Text with hello world phrase.</text> Is it possible to enclose result in one element hello world ? Regards Bartosz Marciniak

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Fwd: whitespace around comments
by Wendell Piez 19 Apr '13

19 Apr '13

Oops -- just sent this to Christian only, when it was meant for the list -- ---------- Forwarded message ---------- From: Wendell Piez <wapiez(a)wendellpiez.com> Date: Tue, Apr 16, 2013 at 11:15 AM Subject: Re: [basex-talk] whitespace around comments To: Christian Grün <christian.gruen(a)gmail.com> Hi, Thanks to Cerstin for once again urging that CHOP not be set by default, and to Liam for reminding readers that this is *not* a new issue in markup processing -- indeed it was in view of problems with whitespace in earlier technologies (can anyone say "pernicious mixed content"?) that the XML Rec says what it does -- including section http://www.w3.org/TR/REC-xml/#sec-white-space. And thanks also to Christian for reminding us why much of the time, whitespace chopping is innocuous and helpful. Personally, I'm in an uneasy place with respect to these issues. I wholeheartedly agree with Cerstin and Liam that chopping should not be on by default. Leaving it on by default is wrong and non-conformant. However, I'm also working with an application in which it's very convenient to have it -- not only is the data highly structured and controlled -- no mixed content here -- but also part of its job is to offer clean representations of external data that is much dirtier and cruftier. It is supposed to clear bad data away and clean it up, so managing the whitespace on ingest is just part of what we are doing. For both scaling and usability issues (as Christian has suggested), whitespace chopping is nice to have. Yet at the same time, we are already calling XSLT for uses in which the chopping is destructive, and the day is not very far off when we will have mixed content in our primary data set too. Liam points out something very important: it is possible in principle to distinguish between whitespace that can be safely discarded (by design) and whitespace that can't -- if you have a schema or other specification that represents this design. As he notes, the XML Rec distinguishes between "significant" and "insignificant" whitespace by reference to content models that do and don't include #PCDATA (that is, whitespace that appears in "element content" or "mixed content"; cf http://www.w3.org/TR/REC-xml/#dt-elemcontent) If your content model for div says (p+), then whitespace between the 'p' element children of a 'div' (but not inside them) may often be judged safe to discard. (At least in a system in which a schema is used as a warrant of fitness for processing.) When technologies such as XQuery or XSLT are designed to work with and without schemas, however -- or where schemas cannot be considered as reliable indicators of markup semantics -- even relying on this mechanism can't solve the problem (to say nothing of deciding which schema languages you support). However, it can help to mitigate it. Then too, even XSLT 1.0 has strip-space and preserve-space configuration to indicate to a processor where it can "chop" whitespace. While it's a bit crude (it treats all elements with the same name the same), it can be useful. Over the longer term, therefore, I think that (1) CHOP needs to be "false" by default, (2) it should be possible to turn it on (just as I am learning how to turn it off), and also (3) that we also need more flexible and configurable means for discriminating how it should work, with and without schemas to reference. Cheers, Wendell On Sat, Apr 13, 2013 at 7:05 AM, Christian Grün <christian.gruen(a)gmail.com> wrote: > I’d like to add some more info on why we initially decided to chop > whitespaces, and why a sudden change of the default value may break > existing applications (if you know the details, simply skip this > section..): > > Many XML documents contain whitespace-only text nodes for properly > indenting elements. In highly structured data (i.e., when not working > with mixed content), these nodes are in fact completely irrelevant. > For example, if the following document… > > <xml> > <a>X</a> > </xml> > > …is parsed with CHOP set to true, we will get a document with a single > text node. The following query… > > for $t in //text() > return replace node $t with 'x' > > …will generate the following result: > > <xml> > <a>x</a> > </xml> > > If we set CHOP to false, the document will have three text nodes, two > of them whitespace-only, and the same query will create the following > result document: > > <xml>x<a>x</a>x</xml> > > This is just one example to demonstrate that a sudden change of the > default for chop would most probably lead to unwanted side effects in > existing applications. Another side effect: databases are expected to > increase in size, as all whitespace nodes will get their own node ids, > will be fully stored and indexed, etc. > > However, I completely agree that the removal of whitespaces may lead > to serious changes in mixed contents, and I easily admit that we > haven’t been aware of all the implications some years ago when we > started off designing the database. While I still believe that our > storage copes pretty well with nowaday’s requirements, I would love to > have some weeks off to completely rebuild it, and include > optimizations for all kinds of features that are relevant today > (including larger ranges for node ids and namespaces, or support for > other tree formats such as json). > > Thanks for reading, > Christian > ___________________________ > > On Sat, Apr 13, 2013 at 8:28 AM, Liam R E Quin <liam(a)w3.org> wrote: >> On Fri, 2013-04-05 at 11:31 +0200, Dirk Kirsten wrote: >> >>> So if you could point out some details as why this is not conforming >>> behaviour, this would be interesting. >> >> It's a requirement in the XML Spec that the XML parser pass all >> whitespace back to the application. Some whitespace may be marked as not >> significant - that is only possible if there's a DTD and the space is in >> a context where only elements would be valid, not #PCDATA. There's no >> formal specification, although constructing an XDM instance from an >> infoset, and constructing an infoset from XML, does not entail >> discarding these spaces: >> Chopping internal whitespace nodes in mixed content contexts is not >> sanctioned by any version of any XML specification, with any setting of >> xml:space. I think the onus would be on you to justify the non-standard >> behaviour. >> >> On the other hand I can see its uses too. But I don't want it, and >> always turn it off with BaseX :-) >> >> Best, >> >> Liam >> >> -- >> Liam Quin - XML Activity Lead, W3C, http://www.w3.org/People/Quin/ >> Pictures from old books: http://fromoldbooks.org/ >> Ankh: irc.sorcery.net irc.gnome.org freenode/#xml >> >> _______________________________________________ >> BaseX-Talk mailing list >> BaseX-Talk(a)mailman.uni-konstanz.de >> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > _______________________________________________ > BaseX-Talk mailing list > BaseX-Talk(a)mailman.uni-konstanz.de > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk -- Wendell Piez | http://www.wendellpiez.com XML | XSLT | electronic publishing Eat Your Vegetables _____oo_________o_o___ooooo____ooooooo_^ -- Wendell Piez | http://www.wendellpiez.com XML | XSLT | electronic publishing Eat Your Vegetables _____oo_________o_o___ooooo____ooooooo_^

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java.lang.NoClassDefFoundError while deploying on Tomcat server
by Carlos MARCOS LAGUNAR 19 Apr '13

19 Apr '13

Hi, I've downloaded last BaseX version from the download page and what I've done it is just put the BaseX76.war into webapps deployment directory of Tomcat. As far as I know, it has deployed correctly, since I can make REST requests successfully like http://MiServer/BaseX76/rest?command=show+users. The problem comes when I try to access it from my Java Application, where I've tried with two methods: JavaClient and XQJ. With JavaClient it works, but with XQJ the response is always the same (log from [TOMCAT_DEPLOYMENT_DIRECTORY]/BaseX76/data/.logs): 13:32:40.053 172.24.41.93:59521 admin ERROR Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.6 Java: Oracle Corporation, 1.7.0 OS: Linux, i386 Stack Trace: java.lang.NoClassDefFoundError: org/basex/index/value/DiskValues org.basex.data.DiskData.<init>(DiskData.java:88) org.basex.core.cmd.Open.open(Open.java:70) org.basex.core.cmd.Open.run(Open.java:36) org.basex.core.Command.run(Command.java:342) org.basex.core.Command.exec(Command.java:321) org.basex.core.Command.execute(Command.java:78) org.basex.server.ClientListener.run(ClientListener.java:145) 453.12 ms The block of Java code where the Exception is thrown is the following (for the case of XQJ): log.debug("[BaseX] executing query:"+query); XQDataSource xqs = new BaseXXQDataSource(); xqs.setProperty("databaseName", dbName); xqs.setProperty("serverName", serverNameBaseX); xqs.setProperty("port", portBaseX); xqs.setProperty("user", usuario); xqs.setProperty("password", clave); xqs.setLogWriter(new PrintWriter(System.out, true)); XQConnection xqc = xqs.getConnection(); ß Here is where the Exception is thrown XQExpression xqe = xqc.createExpression(); XQSequence xq = xqe.executeQuery(query); StringBuilder res = new StringBuilder(); while (xq.next()) { res.append(xq.getItemAsString(null)); } log.debug("[BaseX] result:"+res); xqc.close(); It seems that it is not finding the jars inside the WAR where DiskData class is located, but I've entered into the Tomcat directory where the WAR has been deployed (/BaseX76/WEB-INF/lib) and all of them are there: -rw-rw---- 1 2558399 2013-02-05 18:22 basex-7.6.jar -rw-rw---- 1 295821 2013-01-30 11:42 basex-xqj-1.2.3.jar -rw-rw---- 1 58160 2013-01-30 11:42 commons-codec-1.4.jar -rw-rw---- 1 59590 2013-01-30 11:42 commons-fileupload-1.2.2.jar -rw-rw---- 1 109043 2013-01-30 11:42 commons-io-1.4.jar -rw-rw---- 1 153115 2013-01-30 11:42 jdom-1.1.jar -rw-rw---- 1 794991 2013-01-31 15:34 jts-1.13.jar -rw-rw---- 1 410933 2013-01-30 11:42 milton-api-1.7.2.jar -rw-rw---- 1 119180 2013-01-30 11:42 mime-util-2.1.3.jar -rw-rw---- 1 23445 2013-01-30 11:42 slf4j-api-1.5.8.jar -rw-rw---- 1 5284 2013-01-30 11:42 slf4j-nop-1.5.8.jar -rw-rw---- 1 9260 2013-01-30 11:42 xmldb-api-1.0.jar -rw-rw---- 1 7188 2013-01-30 11:45 xmlpull-1.1.3.1.jar -rw-rw---- 1 24956 2013-01-30 11:45 xpp3_min-1.1.4c.jar -rw-rw---- 1 4578 2013-01-30 11:42 xqj2-0.1.0.jar -rw-rw---- 1 16221 2013-01-30 11:42 xqj-api-1.0.jar -rw-rw---- 1 481672 2013-01-30 11:42 xstream-1.4.2.jar Any ideas?. Other projects deployed into that server worked without any problem. I know that I could use JavaClient method for accessing but then the problem is that I cannot recover the result of the query execution, while with XQJ I can: JavaClient: log.debug("[BaseX] executing query:"+query); ClientSession cSes = new ClientSession(serverNameBaseX, Integer.valueOf(portBaseX), user, pass); cSes.setOutputStream(System.out); ClientQuery cQuery = cSes.query(query); cQuery.execute(); String res = cQuery.info(); ß This res only stores the execution time and not the result of the query, so it is useless (for me :-) ) cQuery.close(); XQJ: XQSequence xq = xqe.executeQuery(query); ß Instead, this do stores the result of the query (exactly what I want) Thank you and best regards, C. Carlos Marcos Lagunar Health Technical Consultant Research & Innovation carlos.marcos(a)atosresearch.eu <mailto:carlos.marcos@atosresearch.eu> Valladolid - Spain www.atosresearch.eu <http://www.atosresearch.eu/> es.atos.net ------------------------------------------------------------------ This e-mail and the documents attached are confidential and intended solely for the addressee; it may also be privileged. If you receive this e-mail in error, please notify the sender immediately and destroy it. As its integrity cannot be secured on the Internet, the Atos group liability cannot be triggered for the message content. Although the sender endeavours to maintain a computer virus-free network, the sender does not warrant that this transmission is virus-free and will not be liable for any damages resulting from any virus transmitted. Este mensaje y los ficheros adjuntos pueden contener informacion confidencial destinada solamente a la(s) persona(s) mencionadas anteriormente pueden estar protegidos por secreto profesional. Si usted recibe este correo electronico por error, gracias por informar inmediatamente al remitente y destruir el mensaje. Al no estar asegurada la integridad de este mensaje sobre la red, Atos no se hace responsable por su contenido. Su contenido no constituye ningun compromiso para el grupo Atos, salvo ratificacion escrita por ambas partes. Aunque se esfuerza al maximo por mantener su red libre de virus, el emisor no puede garantizar nada al respecto y no sera responsable de cualesquiera danos que puedan resultar de una transmision de virus. ------------------------------------------------------------------

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Running and configuring update operations outside the GUI
by Wendell Piez 18 Apr '13

18 Apr '13

Hi, I too have a question about database updates, in particular Fabrice's remark that "The GUI may not be the best place to run updates, did you try the basex command line tools ?" I have an update that is working okay from the GUI, but I wouldn't mind it if it were faster. :-) Is simply invoking the same XQuery using RUN from the command line all I have to do to get the benefits of using the CL? In addition: my update query is configured with a bit of XML, something like declare variable $build-db := <build db="new"> <source db="old1"/> <source db="old2"/> <source db="old3"/> </build>; (Of course it's more complicated than this but you get the essence.) But I can't pass this XML into a function to perform the updates, since I can't put update operations into a function at all. (So the XML is piled into a global variable, which the update operations reference.) Do you have any suggestions for how I can encapsulate the updating logic and also make it configurable externally like this? And run it from the command line or a script for speed and efficiency? Thanks, Wendell -- Wendell Piez | http://www.wendellpiez.com XML | XSLT | electronic publishing Eat Your Vegetables _____oo_________o_o___ooooo____ooooooo_^

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Adding millions of XML files
by freesoft 18 Apr '13

18 Apr '13

Hi, I'm new to BaseX and to XQuery. I already knew XPath. I'm evaluating BaseX to store our XML files and make queries on them. We have to store about 1 million of XML files per month. The XML files are little (~1 KB to 5 KB). So our case is: High number of files, little size. I've read that BaseX is scalable and has high performance, so it is probably a good tool for us. But, in the tests I'm doing, I'm getting an "Out of Main Memory" error when loading high number of XML files. For exaple, if I create a new database ("testdb"), and add 3 XML files, no problem occurs. Files are stored correctly, and I can make queries on them. Then, if I try to add 18000 XML files to the same database ("testdb") (by using GUI > Database > Properties > Add Resources), then I see how the coloured memory bar grows and grows... until an error appears: Out of Main Memory. You can try to: - increase Java's heap size with the flag -Xmx<size> - deactivate the text and attribute indexes. The text and attribute indexes are disabled, so it is not the cause. And I increased the Java size with the flag -Xmx<size> (by editing the basexgui.bat script), and same error happens. Probaly BaseX loads all files to main memory first, and then dumps them to the database files. That shouldn't be done in that way. For each XML file, it should be loaded into main memory, then procesed and then dumped to the db files. For each file, independently from the rest. So I have two questions: 1. Do I have to use an special way to add high number of XML files? 2. Is BaseX sufficiently stable to store and manage our data (about 1 million of files will be added per month)? Thank you for our help and for your great software, and excuse me if I am asking for recurrent questions.

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timezone formatting
by Marco Lettere 17 Apr '13

17 Apr '13

Hi again, when, in Basex 7.6, formatting a datetime with format-dateTime(current-dateTime(), "[Y0001][M01][D01][h01][m01][s01][Z0000]") I was expecting something like 20130314035118+0100 for my area (Central Europe) and instead I get 201303140351180060. Looks like minutes are not translated to hours and the sign is missing. For documentation I'm referring to http://www.w3.org/TR/xpath-functions-30/#rules-for-datetime-formatting. Thanks, M.

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Re: [basex-talk] Adding millions of XML files
by pw＠themail.co.uk 17 Apr '13

17 Apr '13

Responding to the last question about querying over collections: I had the same issue and Lukas Kircher provided the answer - http://www.mail-archive.com/basex-talk@mailman.uni-konstanz.de/msg0210 0.html > > > >---- Original Message ---- >From: kqfhjjgrn(a)yahoo.es >To: christian.gruen(a)gmail.com, fetanchaud(a)questel.com >Subject: Re: [basex-talk] Adding millions of XML files >Date: Mon, 15 Apr 2013 13:12:55 +0100 (BST) > >>Worked! :-) >> >>I have uninstalled 7.6 and installed 7.7 beta. Then, created the >empty db, added the 3 files, run the "set addcache true" command, >added the 17828 files... and no "out of memory" error, just the >processing info: >> >> Path "everything" added in 462943.7 ms. >> >>that is ~8 minutes (in my development machine, not in our server). >> >>Now I'm going to do some more tests (both for adding and for >quering), and I'm going to try the "basex" command, in order to add >XML files automatically to the db. >> >>Anyway I would ask some more questions: >> >>1. Is 7.7 beta sufficiently stable to be used in our production >server? Shoud I wait for the final 7.7 release? >> >>2. Is the "addcache" property value permanently saved to the db? >Should I run the "set addcache true" command everytime I add files? >> >>3. Should I keep disabled the Text & Attribute indexes? Is the >"addcache=on" option sufficient to allow the adition of XML files, so >I can enable those indexes? Will my queries be slow with those >indexes disabled? >> >>4. Should I run Optimize after every massive insertion (even with >"addcache=on")? >> >>Thank you for the information on limits, it is very useful. In >particular, the following limits: >> >>FileSize: 512 GiB >>#Files: 536,870,912 >> >>mean a medium value of exactly 1 KB/file. Since my files are bigger >than 1 KB (in medium), then the size limit will be reached first (512 >GiB). So my Perl scripts will have to detect the size of the db, and >if it is bigger than ~500 GB, then they will create a new db and add >new XML files to it. >> >>Please show me an easy example of how to use several databases in >the same query. Perhaps something like: >> >> for $doc in (collection("db1"), collection("db2")) >> for $node in $doc/$a_node_path >> etc... >> >>Well, thank you very much for your help. And excuse me for the huge >amount of questions from a newbie like me :-) >> >> >>freesoft >> >> >> >>________________________________ >> De: Christian Grün <christian.gruen(a)gmail.com> >>Para: Fabrice Etanchaud <fetanchaud(a)questel.com> >>CC: freesoft <kqfhjjgrn(a)yahoo.es>; >"basex-talk(a)mailman.uni-konstanz.de" ><basex-talk(a)mailman.uni-konstanz.de> >>Enviado: Lunes 15 de abril de 2013 12:12 >>Asunto: Re: [basex-talk] Adding millions of XML files >> >> >>Hi kgfhjjgrn, >> >>I believe that Fabrice already mentioned all details that should >help >>you to build larger databases. The ADDCACHE option [1] (included in >>the latest stable snapshot [2]) may already be sufficient to add >your >>documents via the GUI: simply run the "set addcache true" command >via >>the input bar of the main window before opening the Properties >dialog. >> >>Note that you can access multiple databases with a single XQuery >call, >>so if you know that youll exceed the limits of a single database at >>some time (see [3]), simply create new databases in certain >intervals. >> >>Hope this helps, >>Christian >> >>[1] http://docs.basex.org/wiki/Options#ADDCACHE >>[2] http://files.basex.org/releases/latest/ >>[3] http://docs.basex.org/wiki/Statistics >>_________________________________________ >> >>> The size of your test should not cause any problem to BaseX (18 >000 files >>> from 1 up to 5 KB) >>> >>> >>> >>> 1. Did you try to set the ADDCACHE option ? >>> >>> 2. You should OPTIMIZE your collection after each batch of >ADD >>> commands, even if no index is set. >>> >>> 3. Did you try to unset the AUTOFLUSH option, and explicitly >FLUSH the >>> updates at batchs end ? >>> >>> 4. The GUI may not be the best place to run updates, did you >try the >>> basex command line tools ? >>> >>> >>> >>> Opening a collection containing a huge number of documents may >take a long >>> time from my experience. >>> >>> It seems to be related to the kind of memory data structure used >to store >>> the document names. >>> >>> A workaround could be to insert your documents under a common root >xml >>> element with XQuery Update. >>> >>> >>> >>> >>> >>> >>> Best, >>> >>> Fabrice Etanchaud >>> >>> Questel-Orbit >>> >>> >>> >>> >>> >>> De : basex-talk-bounces(a)mailman.uni-konstanz.de >>> [mailto:basex-talk-bounces@mailman.uni-konstanz.de] De la part de >freesoft >>> Envoyé : lundi 15 avril 2013 10:19 >>> À : basex-talk(a)mailman.uni-konstanz.de >>> Objet : [basex-talk] Adding millions of XML files >>> >>> >>> >>> Hi, I'm new to BaseX and to XQuery. I already knew XPath. I'm >evaluating >>> BaseX to store our XML files and make queries on them. We have to >store >>> about 1 million of XML files per month. The XML files are little >(~1 KB to 5 >>> KB). So our case is: High number of files, little size. >>> >>> I've read that BaseX is scalable and has high performance, so it >is probably >>> a good tool for us. But, in the tests I'm doing, I'm getting an >"Out of Main >>> Memory" error when loading high number of XML files. >>> >>> For exaple, if I create a new database ("testdb"), and add 3 XML >files, no >>> problem occurs. Files are stored correctly, and I can make queries >on them. >>> Then, if I try to add 18000 XML files to the same database >("testdb") (by >>> using GUI > Database > Properties > Add Resources), then I see how >the >>> coloured memory bar grows and grows... until an error appears: >>> >>> Out of Main Memory. >>> You can try to: >>> - increase Java's heap size with the flag -Xmx<size> >>> - deactivate the text and attribute indexes. >>> >>> The text and attribute indexes are disabled, so it is not the >cause. And I >>> increased the Java size with the flag -Xmx<size> (by editing the >>> basexgui.bat script), and same error happens. >>> >>> Probaly BaseX loads all files to main memory first, and then dumps >them to >>> the database files. That shouldn't be done in that way. For each >XML file, >>> it should be loaded into main memory, then procesed and then >dumped to the >>> db files. For each file, independently from the rest. >>> >>> So I have two questions: >>> 1. Do I have to use an special way to add high number of XML >files? >>> 2. Is BaseX sufficiently stable to store and manage our data >(about 1 >>> million of files will be added per month)? >>> >>> Thank you for our help and for your great software, and excuse me >if I am >>> asking for recurrent questions. >>> >>> >>> _______________________________________________ >>> BaseX-Talk mailing list >>> BaseX-Talk(a)mailman.uni-konstanz.de >>> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk >>>

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