April 2011 - BaseX-Talk - mailman.uni-konstanz.de

Document questions
by Csaba Dery 26 Apr '11

26 Apr '11

Hi, Two questions about documents: 1. Is it possible to replace the whole content of a document stored in the database with newer content that's in raw XML format? Right now I'm deleting the document which is straightforward, and then adding it back again with the new content which is not really atomic. I have tried with XQUF but it won't accept raw XML. 2. Is it possible to retrieve the content of a document without using XQuery? I'm thinking of something similar to the Delete command where the path to the document is needed. Is there a command that by specifying the path to a document returns the XML content stored under that path? Thanks!

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Re: [basex-talk] XQuery from console error
by Andreas Weiler 25 Apr '11

25 Apr '11

Right, this one works for me (Mac Terminal): java -cp BaseX.jmin -Padmin -c'xquery let $i := 10 return $i' -- Andreas > > Am 19.04.2011 um 21:24 schrieb Imsieke, Gerrit, le-tex: > >> Might have sth to do with shell interpolation? If you use single quotes around the -c option's argument, the shell won't try to expand $i to (presumably) the empty string. >> >> Jan's example might have worked because he used another type of shell. >> >> Gerrit >> >> On 2011-04-19 21:14, Andreas Weiler wrote: >>> Hi Hector, Hi Jan, >>> >>> i can reproduce the error with BaseX 6.6.1...strange. >>> >>> java -cp BaseX.jar org.basex.BaseXClient -Uadmin -Padmin -c"xquery let >>> $i := 10 return $i" >>> Error: Stopped at line 1, column 12: >>> Syntax: XQUERY [query] >>> Evaluate XQuery. >>> >>> We will have a look at it. >>> >>> -- Andreas >>> >>> Am 19.04.2011 um 20:27 schrieb Jan Vlčinský (CAD): >>> >>>> Hi Hector >>>> I run query like you, only using my existing database name and >>>> counting my elements, which exists there and I had no problem. I >>>> suspected that before : shall be a space, but this is not the case, it >>>> makes no difference in my test: >>>> >>>> D:\opt\BaseX>java -cp BaseX.jar org.basex.BaseXClient -Uadmin -Padmin >>>> -c"open ISO;xquery <results>{ let $total:=count(//LOCT) return >>>> <total>{$total}</total>}</results>" >>>> <results> >>>> <total>1487</total> >>>> </results> >>>> >>>> I use BaseX version 6.6.1 >>>> >>>> 1. What version of BaseX do you use? >>>> 2. Are you sure you run the same version for server and for the >>>> client? Once I had troubles mixing different versions. >>>> >>>> >>>> With best regards >>>> >>>> Jan >>>> 2011/4/19 Hector Diaz <hectordanieldg(a)gmail.com >>>> <mailto:hectordanieldg@gmail.com>> >>>> >>>> Hello, >>>> I am trying to run some Xqueries from command line but I am >>>> getting the following error: >>>> $ java -cp "C:\Program Files\BaseX\BaseX.jar" >>>> org.basex.BaseXClient -Uadmin -Pa >>>> dmin -c"open dbname;xquery <results>{ let >>>> $total:=count(//callRecords/*) return <t >>>> otal>{$total}</total>}</results>" >>>> Error: Stopped at line 1, column 30: >>>> [XPST0003] Expecting "}", found ":". >>>> If I run the query from the GUI it runs correctly, but here I am >>>> always getting this error. >>>> I tried running other dummy queries that work in the GUI but here >>>> I get an error like this: >>>> $ java -cp "C:\Program Files\BaseX\BaseX.jar" >>>> org.basex.BaseXClient -Uadmin -Pa >>>> dmin -c"open dbname;xquery let $total := count(//callRecords/*) >>>> return $total" >>>> Error: Stopped at line 1, column 23: >>>> Syntax: XQUERY [query] >>>> Evaluate XQuery. >>>> Any idea of how to solve this? >>>> Is it possible to use let in queries from command? >>>> Thanks in advance for your help. >>>> Hector >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>>> >>>> >>>> -- >>>> *Ing. Jan Vlčinský* >>>> CAD programy >>>> Slunečnicová 338/3, 734 01 Karviná Ráj, Czech Republic >>>> tel: +420-597 602 024; mob: +420-608 979 040 >>>> skype: janvlcinsky; GoogleTalk: jan.vlcinsky(a)gmail.com >>>> <mailto:jan.vlcinsky@gmail.com> >>>> http://cz.linkedin.com/in/vlcinsky >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >>> _______________________________________________ >>> BaseX-Talk mailing list >>> BaseX-Talk(a)mailman.uni-konstanz.de >>> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk >> >> -- >> 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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Returning variable-length results
by Sony Vijay 22 Apr '11

22 Apr '11

Hi, Is there a way to return variable-length results using xquery ? Consider the following xml file (document name: doc1) <feed> <title>feed1</title> <entry> <id>1</id> <title>entry 1 title *match*</title> <content>entry 1 content *match* </content> </entry> <entry> <id>2</id> <title>entry 2 title *match*</title> <content>entry 2 content *match* </content> <author> <name>entry 2 author *match* </name> </author> </entry> </feed> Consider that there are multiple xml files in my database. I am trying to run an xquery which would perform a search across all the xml files in the database which contain entires with the matching key. Then for each matching document, return all the entry nodes with at least one match, followed by a list of nodes with the match. Say the match key word is: "match", the desired result is the following: - document name (doc1), id (1), *[**title (entry 1 title match), content (entry 1 content match)], *document name(doc1), id (2),* [title (entry 2 title match), content (entry 2 content match), author: name (entry 2 author match)]* Please note that the first entry(id=1) contains two matching nodes whereas the second entry(id=2) contains 3 matching nodes. Returning a variable length result as shown above would help me identify the next matching document name and entry id. Currently, I perform this action by splitting the task into 2 sub-tasks: - Return the document name and entry id with at least one match using one xquery - Return the list of matching child nodes for each of the above entries using a second xquery Is there a better way to do this? Thanks, Sony

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Execute methods in ClientSession are marked protected...
by Meredith Gregory 21 Apr '11

21 Apr '11

Dear BaseXers, The execute methods in ClientSession are marked protected. So, the examples from the wiki page seem odd to me. What is the preferred approach? Should i implement my own version of ClientSession? Should i use something other than execute? Best wishes, --greg -- L.G. Meredith Managing Partner Biosimilarity LLC 7329 39th Ave SW Seattle, WA 98136 +1 206.650.3740 http://biosimilarity.blogspot.com

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Renaming of documents
by Thomas Kaltofen 21 Apr '11

21 Apr '11

Hi, why is it not possible to rename a document in a database with an update XQuery? Thanks for helping out! Regards, Thomas

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XQuery from console error
by Hector Diaz 19 Apr '11

19 Apr '11

Hello, I am trying to run some Xqueries from command line but I am getting the following error: $ java -cp "C:\Program Files\BaseX\BaseX.jar" org.basex.BaseXClient -Uadmin -Pa dmin -c"open dbname;xquery <results>{ let $total:=count(//callRecords/*) return <t otal>{$total}</total>}</results>" Error: Stopped at line 1, column 30: [XPST0003] Expecting "}", found ":". If I run the query from the GUI it runs correctly, but here I am always getting this error. I tried running other dummy queries that work in the GUI but here I get an error like this: $ java -cp "C:\Program Files\BaseX\BaseX.jar" org.basex.BaseXClient -Uadmin -Pa dmin -c"open dbname;xquery let $total := count(//callRecords/*) return $total" Error: Stopped at line 1, column 23: Syntax: XQUERY [query] Evaluate XQuery. Any idea of how to solve this? Is it possible to use let in queries from command? Thanks in advance for your help. Hector

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how to dump an basex database
by Immanuel Normann 19 Apr '11

19 Apr '11

Hi, is there an easy way to dump an basex database, either on the command line or in the interactive mode of the basexserver. Immanuel

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Invalid permissions
by Immanuel Normann 18 Apr '11

18 Apr '11

Hello, I wanted to let a user insert nodes into a database. Three related questions about that: 1) why does the user need "CREATE" permissions and not just "WRITE" permissions? 2) why does the pattern "grant create on <db> to <user>" yield the error "Invalid permissions specified", whereas "grant create to <user>" works? 3) how could I let user manipulate (e.g. inserting a node) only a specific database? Thanks for help Immanuel

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should BXCollection.listResources always throw an exception?
by Meredith Gregory 17 Apr '11

17 Apr '11

Dear BaseXers, So far, BaseX has been a lot of fun to work with! Thanks for all your efforts on this codebase. i've got a couple of questions, though. - Whether i've got no documents in a freshly created BXCollection, or i've ensured that there is at least one document present, a call to listResources always throws an IndexOutOfBounds exception. Is that the intended behavior? - The reason i'm using this API is that i need to be able to update a single document in a collection guaranteed to have exactly one document. So, i thought i would simply ask the BXCollection to list it's resources, grab the first one (since there should only be one) and then use the id from the list returned by that API in subsequent queries. Maybe that's not the preferred approach? Is there a better one? Any help would be greatly appreciated. Best wishes, --greg override def getCollection( createIfMissing : Boolean )( xmlCollStr : String ) : Option[Collection] = { try { // BUGBUG -- LGM the semantics of BXCollection a little // different than createIfMissing; and requires catching the // database not found exception Some( new BXCollection( xmlCollStr, true ) ) } catch { case e : XMLDBException => { val bxColl = new BXCollection( xmlCollStr, false ) val document = bxColl.createResource( null, XMLResource.RESOURCE_TYPE ).asInstanceOf[XMLResource] document.setContent( "<database></database>" ) bxColl.storeResource( document ) Some( bxColl ) } case _ => None } } override def update( xmlCollStr : String )( cnxn : CnxnCtxtLabel[Namespace,Var,String] ) : Unit = { for( xmlColl <- getCollection( true )( xmlCollStr ) ) { val resourceList : Array[String] = xmlColl.listResources if ( resourceList.size == 0 ) { val document = xmlColl.createResource( null, XMLResource.RESOURCE_TYPE ).asInstanceOf[XMLResource] document.setContent( xmlIfier.asXML( cnxn ).toString ) xmlColl.storeResource( document ) } else { val cnxnElem = xmlIfier.asXML( cnxn ) cnxnElem match { case cElem : Elem => { delete( xmlCollStr, resourceList( 0 ) )( cElem ) insert( xmlCollStr, resourceList( 0 ) )( cElem ) } case _ => { throw new Exception( "record is not an XML element" ) } } } } } <tweet>storing to db : org.basex.api.xmldb.BXDatabase@77dc754 pair : record(contactMeUsing(email), {"com.biosimilarity.lift.model.store.MonadicTermTypes_-Ground":{"v":{"@class":"string","$":"for the win Mikail.Mauz@gmail.com"},"_-outer":{"@class":"com.biosimilarity.lift.model.store.PersistedMonadicTS$TheMTT$"}}}) in coll : Squibble</tweet> java.lang.IndexOutOfBoundsException at java.io.RandomAccessFile.readBytes(Native Method) at java.io.RandomAccessFile.read(RandomAccessFile.java:322) at java.io.RandomAccessFile.readFully(RandomAccessFile.java:381) at org.basex.io.DataAccess.cursor(DataAccess.java:225) at org.basex.io.DataAccess.readToken(DataAccess.java:147) at org.basex.data.DiskData.txt(DiskData.java:213) at org.basex.data.DiskData.text(DiskData.java:181) at org.basex.api.xmldb.BXCollection.listResources(BXCollection.java:128) at com.biosimilarity.lift.model.store.xml.BaseXCnxnStorage$$anonfun$update$1.apply(BaseXXMLPersist.scala:313) at com.biosimilarity.lift.model.store.xml.BaseXCnxnStorage$$anonfun$update$1.apply(BaseXXMLPersist.scala:312) at scala.Option.foreach(Option.scala:185) at com.biosimilarity.lift.model.store.xml.BaseXCnxnStorage$class.update(BaseXXMLPersist.scala:312) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction.update(PersistedMonadicTermStore.scala:321) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction$$anonfun$putInStore$3$$anonfun$apply$12$$anonfun$apply$13.apply(PersistedMonadicTermStore.scala:468) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction$$anonfun$putInStore$3$$anonfun$apply$12$$anonfun$apply$13.apply(PersistedMonadicTermStore.scala:459) at scala.Option.foreach(Option.scala:185) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction$$anonfun$putInStore$3$$anonfun$apply$12.apply(PersistedMonadicTermStore.scala:459) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction$$anonfun$putInStore$3$$anonfun$apply$12.apply(PersistedMonadicTermStore.scala:458) at scala.Option.foreach(Option.scala:185) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction$$anonfun$putInStore$3.apply(PersistedMonadicTermStore.scala:458) at com.biosimilarity.lift.model.store.PersistedTermStoreScope$PersistedMonadicGeneratorJunction$$anonfun$putInStore$3.apply(PersistedMonadicTermStore.scala:458) at scala.util.continuations.package$.run(package.scala:30) at scala.concurrent.cpsops$$anonfun$spawn$1.apply$mcV$sp(cpsops.scala:9) at scala.concurrent.FJTaskRunners$FJTaskRunner$$anon$1.compute(FJTaskRunners.scala:21) at jsr166y.forkjoin.RecursiveAction.exec(RecursiveAction.java:247) at jsr166y.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:286) -- L.G. Meredith Managing Partner Biosimilarity LLC 7329 39th Ave SW Seattle, WA 98136 +1 206.650.3740 http://biosimilarity.blogspot.com

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Can not generate fulltext search indexes for wikipedia XML dB
by Erol Akarsu 14 Apr '11

14 Apr '11

Ok, I was able to run full text search with another XML Database. I am primarily interested in how Basex will play with big XML file Wikipedia. Actually, Database create of wikipedia is fine. But when I add full tet search and indexes for it, it always throws out of memory exception error. I have changed -Xmx with 6GB that is still not enough to generate indexes for Wikipedia. Can you help me on how to generate indexes with a machine that case 6GB for Basex process? Thanks Erol Akarsu On Sun, Apr 10, 2011 at 4:07 AM, Andreas Weiler < andreas.weiler(a)uni-konstanz.de> wrote: > Hi, > > the following query could work for you: > > declare namespace w="http://www.mediawiki.org/xml/export-0.5/"; > for $i in doc("enwiki-latest-pages-articles")//w:sitename > return $i[. contains text "Wikipedia"]/.. > > -- Andreas > > Am 09.04.2011 um 20:43 schrieb Erol Akarsu: > > Hi > > I am having difficulty in running full text operators. This script gives > siteinfo below > declare namespace w="http://www.mediawiki.org/xml/export-0.5/"; > let $d := fn:doc ("enwiki-latest-pages-articles") > return ($d//w:siteinfo)[1] > > But return $d//w:siteinfo[w:sitename contains text 'Wikipedia'] does NOT > give same node > Why "contains" ft operator behave incorrectly? I remember it was working > fine. I just dropped and recreated database and turn all indexes. Can you > help me? > Query info is here: > > Query: declare namespace w="http://www.mediawiki.org/xml/export-0.5/"; > Compiling: > - pre-evaluating fn:doc("enwiki-latest-pages-articles") > - adding text() step > - optimizing descendant-or-self step(s) > - removing path with no index results > - pre-evaluating (())[1] > - binding static variable $res > - pre-evaluating fn:doc("enwiki-latest-pages-articles") > - binding static variable $d > - adding text() step > - optimizing descendant-or-self step(s) > - removing path with no index results > - simplifying flwor expression > Result: () > Timing: > - Parsing: 0.46 ms > - Compiling: 0.42 ms > - Evaluating: 0.17 ms > - Printing: 0.1 ms > - Total Time: 1.15 ms > Query plan: > <sequence size="0"/> > > > > <siteinfo xmlns="http://www.mediawiki.org/xml/export-0.5/" xmlns:xsi=" > http://www.w3.org/2001/XMLSchema-instance"> > <sitename>Wikipedia</sitename> > <base>http://en.wikipedia.org/wiki/Main_Page</base> > <generator>MediaWiki 1.17wmf1</generator> > <case>first-letter</case> > <namespaces> > <namespace key="-2" case="first-letter">Media</namespace> > <namespace key="-1" case="first-letter">Special</namespace> > <namespace key="0" case="first-letter"/> > <namespace key="1" case="first-letter">Talk</namespace> > <namespace key="2" case="first-letter">User</namespace> > <namespace key="3" case="first-letter">User talk</namespace> > <namespace key="4" case="first-letter">Wikipedia</namespace> > <namespace key="5" case="first-letter">Wikipedia talk</namespace> > <namespace key="6" case="first-letter">File</namespace> > <namespace key="7" case="first-letter">File talk</namespace> > <namespace key="8" case="first-letter">MediaWiki</namespace> > <namespace key="9" case="first-letter">MediaWiki talk</namespace> > <namespace key="10" case="first-letter">Template</namespace> > <namespace key="11" case="first-letter">Template talk</namespace> > <namespace key="12" case="first-letter">Help</namespace> > <namespace key="13" case="first-letter">Help talk</namespace> > <namespace key="14" case="first-letter">Category</namespace> > <namespace key="15" case="first-letter">Category talk</namespace> > <namespace key="100" case="first-letter">Portal</namespace> > <namespace key="101" case="first-letter">Portal talk</namespace> > <namespace key="108" case="first-letter">Book</namespace> > <namespace key="109" case="first-letter">Book talk</namespace> > </namespaces> > </siteinfo> > > On Mon, Apr 4, 2011 at 7:31 AM, Erol Akarsu <eakarsu(a)gmail.com> wrote: > >> I imported wikipedia xml into basex and tried to search it. >> >> But searching it takes longer. >> >> I tried to search one element that is first child of whole document and it >> took 52 sec. >> I know the XML file is very big 31GB. How can I optimize the search? >> >> declare namespace w="http://www.mediawiki.org/xml/export-0.5/"; >> >> let $d := fn:doc ("enwiki-latest-pages-articles")//w:siteinfo >> return $d >> >> Database info: >> >> > open enwiki-latest-pages-articles >> Database 'enwiki-latest-pages-articles' opened in 778.49 ms. >> > info database >> Database Properties >> Name: enwiki-latest-pages-articles >> Size: 23356 MB >> Nodes: 228090153 >> Height: 6 >> >> Database Creation >> Path: /mnt/hgfs/C/tmp/enwiki-latest-pages-articles.xml >> Time Stamp: 03.04.2011 12:29:15 >> Input Size: 30025 MB >> Encoding: UTF-8 >> Documents: 1 >> Whitespace Chopping: ON >> Entity Parsing: OFF >> >> Indexes >> Up-to-date: true >> Path Summary: ON >> Text Index: ON >> Attribute Index: ON >> Full-Text Index: OFF >> > >> >> >> Timing info: >> >> Query: declare namespace w="http://www.mediawiki.org/xml/export-0.5/"; >> Compiling: >> - pre-evaluating fn:doc("enwiki-latest-pages-articles") >> - optimizing descendant-or-self step(s) >> - binding static variable $d >> - removing variable $d >> - simplifying flwor expression >> Result: element siteinfo { ... } >> Timing: >> - Parsing: 1.4 ms >> - Compiling: 52599.0 ms >> - Evaluating: 0.28 ms >> - Printing: 0.62 ms >> - Total Time: 52601.32 ms >> Query plan: >> <DBNode name="enwiki-latest-pages-articles" pre="5"/> >> >> >> >> Result of query: >> >> <siteinfo xmlns="http://www.mediawiki.org/xml/export-0.5/" xmlns:xsi=" >> http://www.w3.org/2001/XMLSchema-instance"> >> <sitename>Wikipedia</sitename> >> <base>http://en.wikipedia.org/wiki/Main_Page</base> >> <generator>MediaWiki 1.17wmf1</generator> >> <case>first-letter</case> >> <namespaces> >> <namespace key="-2" case="first-letter">Media</namespace> >> <namespace key="-1" case="first-letter">Special</namespace> >> <namespace key="0" case="first-letter"/> >> <namespace key="1" case="first-letter">Talk</namespace> >> <namespace key="2" case="first-letter">User</namespace> >> <namespace key="3" case="first-letter">User talk</namespace> >> <namespace key="4" case="first-letter">Wikipedia</namespace> >> <namespace key="5" case="first-letter">Wikipedia talk</namespace> >> <namespace key="6" case="first-letter">File</namespace> >> <namespace key="7" case="first-letter">File talk</namespace> >> <namespace key="8" case="first-letter">MediaWiki</namespace> >> <namespace key="9" case="first-letter">MediaWiki talk</namespace> >> <namespace key="10" case="first-letter">Template</namespace> >> <namespace key="11" case="first-letter">Template talk</namespace> >> <namespace key="12" case="first-letter">Help</namespace> >> <namespace key="13" case="first-letter">Help talk</namespace> >> <namespace key="14" case="first-letter">Category</namespace> >> <namespace key="15" case="first-letter">Category talk</namespace> >> <namespace key="100" case="first-letter">Portal</namespace> >> <namespace key="101" case="first-letter">Portal talk</namespace> >> <namespace key="108" case="first-letter">Book</namespace> >> <namespace key="109" case="first-letter">Book talk</namespace> >> </namespaces> >> </siteinfo> >> >> >> >> Thanks >> >> Erol Akarsu >> >> > _______________________________________________ > BaseX-Talk mailing list > BaseX-Talk(a)mailman.uni-konstanz.de > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > > >

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