BaseX-Talk December 2013

basex-talk@mailman.uni-konstanz.de

54 participants
77 discussions

Re: [basex-talk] Local variables holding retrieved data from BaseX
by Christian Grün 12 Dec '13

12 Dec '13

Hi Teena (cc @basex-talk), first of all, thanks for giving us details on your data and queries. To complete this: do you have a complete version of your query that shows us what are the values of $context, $project and $scopeName? As an example, I’m wondering what are the ancestor nodes of the <scopes> elements. > declare function foo:get-node-v1($context as element()?, $project as > element()?, $scopeName as xs:string) as element()? { > if (exists($project) = true()) then ( > $project/scopes/scope[@name=$scopeName]/item > ) > else () > }; The following query is equivalent, by the way (this is the beauty of XPath): declare function foo:get-node-v1($context as element()?, $project as element()?, $scopeName as xs:string) as element()? { { $project/scopes/scope[@name=$scopeName]/item }; If all your data is stored in the same database, it may be faster to open the database within the function. One more optimization could be to directly access the text index: declare function foo:get-node-v1($context as element()?, $project as element()?, $scopeName as xs:string) as element()? { { db:attribute("name-of-your-db", $scopeName, "name")/parent::scope }; You could also check out the latest stable snapshot of BaseX 7.8 [1], which inlines functions and may thus do this automatically. > When we call the first function in another > function and use it for further computation, it is always slower by 40 > seconds (when compared to second variation of the function). > What could be causing this? Difficult to say; we probably need to see your complete function call. > Are we still referencing to baseX document when > we do following instead of getting a local copy? > let $items := foo:get-node-v1($context, $project, $scopeName) Yes, the returned nodes still reference nodes in the database. Hope this helps, Christian [1] http://files.basex.org/releases/latest/

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Throughput Issues
by Jeremy Moseley 12 Dec '13

12 Dec '13

Hi Guys, I am attempting to diagnose some throughput issues we are having with BaseX, and I was hoping to get some input on a couple of thread blocking issues I am noticing. Please see the Gist ( https://gist.github.com/jerezzprime/7901172) containing the thread dumps for reference. These thread dumps were generated while BaseX was handling a large number of requests produced using Apache Benchmark. All requests were being made against the same URL and the thread dumps were gathered over a 30 second period. The most common place for threads to be blocking is at org.basex.io.random.TableDiskAccess.read*. The threads are waiting for other threads to finish, since these method calls are synchronized. Is it possible to concurrently read from disk? Another place threads appear to be blocking is while waiting for the lock to call org.basex.http.RestXqModules.cache (another synchronized method). It seems like this should only be called once to parse the modules, and then all requests afterwards should be retrieved from the cache, but from the thread dumps it appears threads are still re-parsing the xquery modules. Is this expected behavior? Thanks, Jeremy

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Fwd: Client Side transactions
by Charles Foster 12 Dec '13

12 Dec '13

For the purposes of the list. Begin forwarded message: > From: Charles Foster > Subject: Re: Client Side transactions > Date: 12 December 2013 20:47:36 GMT > To: rajeshwar.kamineni(a)neustar.biz > > Hi Raj, > > BaseX doesn't support client side transactions, but does support ACID transactions within the context of 1 query, i.e. all updates / inserts / deletes within the context of one query will either succeed or fail [1]. > > To update a document in place, you can always use XQuery Update Facility [2], or you could overwrite the document by re-inserting it with BaseX XQJ. > > In BaseX XQJ 1.2.x, performing an insert with a URI which already exists in the Database will create duplicate fragments (not good), so you would have to delete the previous document first prior to inserting. As of BaseX XQJ 1.3.x which is scheduled to be released soon, you won't need to worry about any of that. > > Just to help you along, the source code for the XQJ2 interfaces can be found here: > > https://github.com/cfoster/xqj2/ > > Which includes the insertItem [3] method. > > Kind Regards, > > Charles > > [1] http://docs.basex.org/wiki/Transaction_Management > [2] http://docs.basex.org/wiki/XQuery_Update > [3] https://github.com/cfoster/xqj2/blob/master/src/main/java/com/xqj2/XQConnec… > > > > On 12 Dec 2013, at 20:10, rajeshwar.kamineni(a)neustar.biz wrote: > >> Raj Kamineni: >> >> Hi >> >> When using setAutoCommit(false) on a connection, >> I got Client Side transactions are not supported. >> >> Any suggestions on alternative ways? >> >> Also, I am looking for a way to update the entire document in basex using XQJ >> >> xqc = baseXRepository.getConnection(); >> XQItem item = xqc.createItemFromDocument(policyDoc,null,null); >> xqc.insertItem(policy.getPolicyId(),item, null); >> >> How do I go about updating when I inserted a document using the above code. >> >> Thanks >> Raj >> >

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ConnectionPoolXQDataSource
by Charles Foster 12 Dec '13

12 Dec '13

For the purposes of the list. Begin forwarded message: > From: Charles Foster > Subject: Re: ConnectionPoolXQDataSource > Date: 12 December 2013 20:41:44 GMT > To: rajeshwar.kamineni(a)neustar.biz > > Hi Raj, > > There is the class: > > net.xqj.basex.BaseXConnectionPoolXQDataSource > > Which is an implementation of ConnectionPoolXQDataSource [1]. > > However, as far as I'm aware. No Connection Pool Manager yet exists for XQJ. So you would have to write your own. If you were to write your own, then using instances of ConnectionPoolXQDataSource is definitely the way to go. > > I plan to write an XQJ Connection Pool Manager at some point in the future, but it won't be free. If you know of someone who is willing to pay the development of an XQJ Connection Pooler Mechanism, then I'm up for making this a priority of other pieces of work I've got on. > > BaseX supports ACID transactions within the context of a single running XQuery, but doesn't support client transactions. > > Both Sedna and MarkLogic do support client transactions though. > > To find out if an XQJ implementation supports client side transactions, amongst other things, you can inspect at its XQMetaData [2], specifically the "boolean isTransactionSupported()" method. > > Kind Regards, > > Charles > > [1] http://xqj.net/javadoc/javax/xml/xquery/ConnectionPoolXQDataSource.html > [2] http://xqj.net/javadoc/javax/xml/xquery/XQMetaData.html > > On 12 Dec 2013, at 17:29, rajeshwar.kamineni(a)neustar.biz wrote: > >> Raj Kamineni: >> >> Just wondering if there is an implementation of this ConnectionPoolXQDataSource for baseX. >> >> I have background in the JDBC SQL so I am thinking in terms of connection pool to database. >> >> Also, I got an error: Client side transaction are not supported. Is it the baseX that doesn't support it or is it the xqj driver that is unable to handle it now.. >> >> thanks >> Raj >> Sr. Architect >> Neustar. >> >

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basex errors
by Kamineni, Rajeshwar 12 Dec '13

12 Dec '13

I am running basexhttp in service mode. At the same time I was using base client to add/delete some documents. I got this error suddenly. >add /root/policy_testdata/policy_template_6.xml Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7.2 Java: Oracle Corporation, 1.7.0_40 OS: Linux, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException: 3 at org.basex.io.random.TableDiskAccess.flush(TableDiskAccess.java:124) at org.basex.data.DiskData.finishUpdate(DiskData.java:212) at org.basex.core.cmd.Add.run(Add.java:109) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.exec(Command.java:321) at org.basex.core.Command.execute(Command.java:78) at org.basex.server.ClientListener.run(ClientListener.java:145) Then I got this when I exited the basexclient >open neuhub_pdp_store Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7.2 Java: Oracle Corporation, 1.7.0_40 OS: Linux, amd64 Stack Trace: java.nio.channels.OverlappingFileLockException at sun.nio.ch.SharedFileLockTable.checkList(FileLockTable.java:255) at sun.nio.ch.SharedFileLockTable.add(FileLockTable.java:152) at sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1056) at org.basex.io.random.TableDiskAccess.lck(TableDiskAccess.java:183) at org.basex.io.random.TableDiskAccess.sharedLock(TableDiskAccess.java:170) at org.basex.io.random.TableDiskAccess.<init>(TableDiskAccess.java:83) at org.basex.data.DiskData.init(DiskData.java:122) at org.basex.data.DiskData.<init>(DiskData.java:92) at org.basex.core.cmd.Open.open(Open.java:68) at org.basex.core.cmd.Open.run(Open.java:35) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.exec(Command.java:321) at org.basex.core.Command.execute(Command.java:78) at org.basex.server.ClientListener.run(ClientListener.java:145) Then I stopped the server OPTIMIZE Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7.2 Java: Oracle Corporation, 1.7.0_40 OS: Linux, amd64 Stack Trace: java.lang.RuntimeException: Data Access out of bounds: - pre value: 0 - #used blocks: 0 - #total locks: 0 - access: -1 (0 > -1] at org.basex.util.Util.notexpected(Util.java:53) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:488) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:189) at org.basex.data.Data.kind(Data.java:282) at org.basex.index.resource.Docs.docs(Docs.java:87) at org.basex.index.resource.Docs.init(Docs.java:75) at org.basex.index.resource.Resources.init(Resources.java:64) at org.basex.core.cmd.Optimize.optimize(Optimize.java:80) at org.basex.core.cmd.Optimize.run(Optimize.java:42) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.exec(Command.java:321) at org.basex.core.Command.execute(Command.java:78) at org.basex.server.ClientListener.run(ClientListener.java:145) > INSPECT Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7.2 Java: Oracle Corporation, 1.7.0_40 OS: Linux, amd64 Stack Trace: java.lang.RuntimeException: Data Access out of bounds: - pre value: 0 - #used blocks: 0 - #total locks: 0 - access: -1 (0 > -1] at org.basex.util.Util.notexpected(Util.java:53) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:488) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:189) at org.basex.data.Data.kind(Data.java:282) at org.basex.core.cmd.Inspect.inspect(Inspect.java:50) at org.basex.core.cmd.Inspect.run(Inspect.java:27) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.exec(Command.java:321) at org.basex.core.Command.execute(Command.java:78) at org.basex.server.ClientListener.run(ClientListener.java:145) Thanks Raj Kamineni [T] +1 571 434 5463 [M] +1 703 342 9358

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Re: [basex-talk] XPath child::node() axis sequence order
by Christian Grün 12 Dec '13

12 Dec '13

Hi Wendell (cc @basex-talk), thanks for your mail. Yes, there are cases in which the result of an axis step are not returned in document order. One such example is shown as follows: Document Order: <A> <B><c/></B> <c/> </A>//c / parent::node() No document order (when using the map operator): <A> <B><c/></B> <c/> </A>//c ! parent::node() I was using parent::node() instead of child::node() here, but the example can surely be adapted to also include a child step. Hope this helps? Christian ___________________________ On Tue, Dec 10, 2013 at 3:22 PM, Wendell Piez <wapiez(a)wendellpiez.com> wrote: > Dear Christian, > > Since a path expression consists of "one or more steps" > (http://www.w3.org/TR/xquery-30/#dt-path-expression), then isn't > 'child::node()' itself a path expression? > > I'm not asking to be pedantic. To restate the OP's question, "are > there any circumstances in BaseX under which 'child::node()' will > return a sequence of nodes not in document order?" > > If so, this is easily fixed ... child::node()/. ... but does one ever > need to take such care? (In XPath generally, the answer as I > understand it would be "no".) > > Cheers, Wendell > > Wendell Piez | http://www.wendellpiez.com > XML | XSLT | electronic publishing > Eat Your Vegetables > _____oo_________o_o___ooooo____ooooooo_^ > > > On Tue, Dec 10, 2013 at 8:02 AM, Christian Grün > <christian.gruen(a)gmail.com> wrote: >>> In BaseX, is the result of the child::node() axis always in document-order ? >> >> The nodes will be in document order if child::node() is part of a path >> expression (..../....). All the nifty details can be found in the spec >> [1]. >> >> Christian >> >> [1] http://www.w3.org/TR/xquery-30/#id-path-operator >> _______________________________________________ >> BaseX-Talk mailing list >> BaseX-Talk(a)mailman.uni-konstanz.de >> https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk

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Any way to access attributes directly from XQItem class?
by Ando Roy 11 Dec '13

11 Dec '13

Hi all, I have a question regarding the XQItem class from the XQJ apis. Let's say that I have a XQResultSequence obtained from executing a query, with the result sequence containing a number of XQItem objects. If I were to print each of them as strings they would look like: <CUSTOMER UserID="abc" Password="123"/> How can I access the attributes in this XQItem directly? Must I write a parser for this, or is there an easier way? Regards, Roy

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XQuery development and Access through URL
by Mansour Al Akeel 11 Dec '13

11 Dec '13

Hello all, I am new to BaseX. I am using the war file, deployed to tomcat and looking for a way to create an xquery file and execute this query through a URL. For example, under WEB-INF/repo/hello.xq and call it with http://localhost:8080/BaseX/hello Any modification for the xquery file, will be reflected in the next URL request. Does BaseX support something like this ?? Thank you.

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what's wrong with this updating function?
by easy 11 Dec '13

11 Dec '13

hi,all, I have write a restxq service, as following: ------------------------------- module namespace page = 'http://basex.orgs/examples/web-page'; declare %output:method("xhtml") %output:omit-xml-declaration("no") %output:doctype-public("-//W3C//DTD XHTML 1.0 Transitional//EN") %output:doctype-system("http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd") %updating %rest:path("/addehr") %rest:POST('{$ehr}') %rest:GET %rest:form-param("message","{$message}", "(no message)") %rest:header-param("User-Agent", "{$agent}") function page:hello-postman( $ehr, $message as xs:string, $agent as xs:string*) { let $path:=substring('5102108843434',1,3)||'/'||'test' let $test := 'ehr/v1/1382968159350/12001.xml' return for $x in doc($test)//header[id=12001] return db:output('ok,path='||$path), insert node ( 'text', <e>test</e> ) into $x }; -- but still say :undefined variavle $x. how to do ? is there a good way to do insert update operation on a file and return some customzied response? many Thanks. 此致 easy 莫愁前路无知己，天下谁人不识君。

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Alternative to XQDT ?
by jean-marc Mercier 11 Dec '13

11 Dec '13

Hello, I am developing using Eclipse, together with the integrated xquery editor provided by XQDT. This last editor does not seem to support xquery 3.0 syntax. I can survive, but there are a lot of nice functionality that are not working anymore (for instance the outline windows). Does someone know any alternative to XQDT editor that could integrate with eclipse and is xquery 3.0 compliant ? Cheers Jean-Marc

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BaseX-Talk December 2013