BaseX-Talk January 2015

basex-talk@mailman.uni-konstanz.de

36 participants
62 discussions

DBA users permissions
by Jérôme Chauveau 09 Jan '15

09 Jan '15

Hi, Here a "bug" I found (tested with the last release snapshot of the day) when using the DBA frontend (my BaseX server is embedded in a Tomcat ): a - I created a new user "myUser" from the DBA frontend b - I granted this one on a DB with local READ permissions Everything was fine until I restarted my Tomcat: the myUser's privileges has been reset to NONE. Hope this feedback helps. Regards. Jérôme. -- Jérôme Chauveau - SAIC-CERTIC - Campus 4 Université de Caen Basse-Normandie

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basexgui.bat doesn't run under Windows Server 2008 R2
by Dave Haans 08 Jan '15

08 Jan '15

Hi everyone, I'm having an issue running the basexgui.bat file under Server 2008 R2. It runs fine on Windows 7 Pro 64-bit. All the other batch files work under Server 2008 and Win 7. I added a pause to the batch file and there's no feedback (no errors) but the BaseX GUI simply does not start up. I need to use the batch file to properly set memory settings to resolve issues we've been having. If there's another way of doing this, please let me know. We're running the latest version of Java, but got the same issue running 1.7. Setting the memory to -Xmx2048m in the Java control panel in Windows did not have the desired effect. Any help would be much appreciated! Cheers, Dave. -- Dave Haans Research and Computing Consultant, Toronto RDC IT Consultant, CRDCN University of Toronto Room 7032, 130 St. George St. Toronto, ON M5S 1A5 Phone: 416-946-8106 Fax: 416-946-8104 Toronto RDC: http://www.utoronto.ca/rdc CRDCN: http://rdc-cdr.ca Is your published RDC research in the CRDCN bibliography? Check here and let me know if it's not there! http://rdc-cdr.ca/publications

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Index cvs error throws "Content is not allowed in prolog"
by Erol Akarsu 08 Jan '15

08 Jan '15

I am trying to index an csv file through basexclient. I issued this command SET INTPARSE false; CREATE DB Properties Properties.csv got these error message in basex server. What shall I do to index csv through basexclient command? [kangadm@kangapp12 javaProcess]$ basexserver -d BaseX 7.9 [Server] Server was started (port: 1984) Creating Database... org.xml.sax.SAXParseException; systemId: file:///home/kangadm/basex/migros/production/javaProcess/Brands.sql.csv; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198) at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177) at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:441) at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:368) at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1436)

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Fwd: Storing sequences of atomic type into BaseX ?
by jean-marc Mercier 08 Jan '15

08 Jan '15

Christian, Excellent ! thanks a lot ! prof:time(local:savebin((1 to 10000000),$binfile)) ,prof:time(local:loadbin($binfile)) output is now 930.71 ms 907.04 ms 2015-01-08 22:11 GMT+01:00 Christian Grün <christian.gruen(a)gmail.com>: > Hi Jean-Marc, > > > 2) However unserialization seems to perform awfully, or I do not know > how to > > do it properly. > > I haven't tried the query, but my guess is that the binary data is > streamed again and again. The stream:materialize function should help > you [1]: > > let $data := stream:materialize(file:read-binary($file)) > ... > > Christian > > [1] http://docs.basex.org/wiki/Streaming_Module > > > > > declare function local:savebin($seq,$file as xs:string) { > > file:write-binary($file,bin:join( (bin:pack-integer(count($seq),4) > ,$seq > > ! bin:pack-integer(.,4)))) > > }; > > declare function local:loadbin($file as xs:string) { > > let $data := file:read-binary($file) > > let $size:= bin:unpack-integer($data,0,4) > > let $seq := for $i in (1 to ($size)) return > > bin:unpack-integer($data,$i*4,4) > > return count($seq) > > }; > > > > prof:time(local:savebin((1 to 100000),"Bin.dat")) > > ,prof:time(local:loadbin("Bin.dat")) > > > > output : > > > > 46.38 ms > > 10775.12 ms > > 100000 > > > > To compare, unserializing a sequence (1 to 10 000 000) stored in a file > as a > > big string using fn:tokenize takes about 10 sec (100 x faster). Did I > > mistake something ? > > > > > > 2015-01-08 16:44 GMT+01:00 Christian Grün <christian.gruen(a)gmail.com>: > >> > >> > This way of doing stores integers as string, then call a cast string / > >> > integer to unserialize it. For large integer list (I am dealing with > >> > lists > >> > of size 134 Mo), it is quite time and mem consuming. > >> > > >> > I was wondering if there exists a more efficient way to store and > >> > retrieve > >> > atomic list into BaseX ? > >> > >> One alternative is to store the integers in a binary file: > >> > >> let $size := 4 > >> let $data := bin:join( > >> for $n in 1 to 100 > >> return bin:pack-integer($n, $size) > >> ) > >> return db:store('db', 'integers.bin', $data) > >> > >> This way, every integer will occupy the supplied number of bytes > >> (here: 4, allowing you to address 2^32 integers). > > > > >

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Storing sequences of atomic type into BaseX ?
by jean-marc Mercier 08 Jan '15

08 Jan '15

Hello, I am currently trying to store precomputed maps. The basic issue is to store a sequence $seq of integers (that are indeed element id, i.e. retrieved using db:node-pre). Actually, I am storing it using db:replace($db,"map",<map>{fn:serialize($seq)}</map>) and retrieve the sequence using using fn:tokenize(db:open($db,"map")/map," ") ! xs:integer(.). This way of doing stores integers as string, then call a cast string / integer to unserialize it. For large integer list (I am dealing with lists of size 134 Mo), it is quite time and mem consuming. I was wondering if there exists a more efficient way to store and retrieve atomic list into BaseX ?

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Reg : Setting Time Out
by Chandrasekhar 08 Jan '15

08 Jan '15

Dear Christian We are optimizing the collection database(5 GB DB SIZE) .After some time(30 minutes) we are getting the below message. org.basex.core.BaseXException: Timeout exceeded. We are not able to setting time out option.We are setting the time out as below mentioned Context context = new Context(); context.globalopts.set(GlobalOptions.TIMEOUT,10); context.globalopts.set(GlobalOptions.SERVERHOST, "localhost"); context.globalopts.set(GlobalOptions.SERVERPORT, 1984); ClientSession ls = new ClientSession(context, "admin", "admin"); Suggest me the right way to setting the time out. Thanks&Regards Chandra The information contained in this e-mail and any accompanying documents may contain information that is confidential or otherwise protected from disclosure. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message, including any attachments. Any dissemination, distribution or other use of the contents of this message by anyone other than the intended recipient is strictly prohibited.

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data protection at rest
by Mansi Sheth 08 Jan '15

08 Jan '15

Hello, I am thinking about my options of protecting BaseXDB's data at rest. We are storing sensitive client data which we need to protect. We would be migrating BaseXDB on an amazon instance, so protection at rest would be a primary concern. What I wish to do is, while inserting data into the database, it should be encrypted and while using XQUERY, we should have a mechanism to decrypt the data and retrieve the information needed. I am aware of the performance hit here. Would evaluate if its acceptable after I could collect some statistics. I looked at the docs: http://docs.basex.org/wiki/Cryptographic_Module#Encryption_.26_Decryption But, I didn't completely understand a use case for this example. Or if it would solve my purpose. I am currently using some Java code to insert files into the database. Has anyone done something on this line ? Please share some use cases. - Mansi

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Database corrupted while inserting big string
by jean-marc Mercier 08 Jan '15

08 Jan '15

Hello, I am trying to insert big string into BaseX, and ended corrupting the whole database. Here a test code , can you reproduce it ? declare updating function local:dbtest($db as xs:string) { db:replace($db,"map",<map>{fn:serialize(1 to 10000000)}</map>) }; local:dbtest("MyDataBase") output : Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 8.0 beta 769b53b Java: Oracle Corporation, 1.8.0_25 OS: Windows 7, amd64 Stack Trace: java.lang.IndexOutOfBoundsException at java.io.RandomAccessFile.writeBytes(Native Method) at java.io.RandomAccessFile.write(Unknown Source) at org.basex.io.random.DataAccess.writeBlock(DataAccess.java:448) at org.basex.io.random.DataAccess.flush(DataAccess.java:49) at org.basex.io.random.DataAccess.close(DataAccess.java:61) at org.basex.data.DiskData.close(DiskData.java:151) at org.basex.core.cmd.Close.close(Close.java:45) at org.basex.query.QueryResources.close(QueryResources.java:110) at org.basex.query.QueryContext.close(QueryContext.java:564) at org.basex.query.QueryProcessor.close(QueryProcessor.java:235) at org.basex.core.cmd.AQuery.query(AQuery.java:129) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:379) at org.basex.core.Command.execute(Command.java:95) at org.basex.api.client.LocalSession.execute(LocalSession.java:132) at org.basex.api.client.Session.execute(Session.java:36) at org.basex.core.CLI.execute(CLI.java:106) at org.basex.BaseX.<init>(BaseX.java:124) at org.basex.BaseX.main(BaseX.java:42)

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Silly XQUERY exception
by Mansi Sheth 08 Jan '15

08 Jan '15

Hello, I feel very stupid and frustrated, not able to fix this error: Below, is a my query code, which I am trying to run. I am passing the value for "contains" clause thru command line and I expect to receive # of xml files matching $cmd xpath. I always get Stopped at /veracode/msheth/BaseXWeb/get_prevalence.xq, 16/12: *[XPST0003] Expecting ':=', found ':'.* When ran thru REST: *[XPST0003] Expecting valid step, found 'd'.* I think, its the way $cmd is being set. I have tried, simple string concat using ||, using concat command, using html entities etc. declare variable $n as xs:string external; declare option output:item-separator "
"; (: let $cmd := concat("/A/*/descendant::C/descandant::*[contains(@name,",$singlequote,$n,$singlequote,")]") :) *let $cmd := "/A/*/descendant::C/descandant::*[contains(@name,'"|| $n ||"')]"* let $aPath := for $db in db:list() let $query := "declare variable $db external; " || "db:open($db)" || $cmd *return xquery:eval($query,* * map { 'db': $db, 'query': $cmd })* let $clients := for $elem in $aPath return db:path($elem) return $n , distinct-values(count($clients)) Lines of code, which are the culprit, are marked in bold above. Any and all suggestions are greatly appreciated. - Mansi

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prof:time and updating expression
by jean-marc Mercier 08 Jan '15

08 Jan '15

Hi all, I was trying to profile updating expression, and the result is [XUST0001] prof:time(value[,cache[,label]]): no updating expression allowed. Is this a desired behavior ? Cheers, Jean-Marc

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BaseX-Talk January 2015