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Fwd: [homebrew] basex 7.7.2 (#23100)
by Jens Erat 07 Oct '13

07 Oct '13

I just bumped BaseX on Homebrew to 7.7.2, patch already got merged. Whoever's using Homebrew is just a brew update; brew upgrade basex away from the newest release. Regards, Jens -- Jens Erat [phone]: tel:+49-151-56961126 [mail]: mailto:email@jenserat.de [jabber]: xmpp:jabber@jenserat.de [web]: http://www.jenserat.de PGP: 350E D9B6 9ADC 2DED F5F2 8549 CBC2 613C D745 722B Anfang der weitergeleiteten Nachricht: > Von: Mike McQuaid <notifications(a)github.com> > Betreff: Aw: [homebrew] basex 7.7.2 (#23100) > Datum: 7. Oktober 2013 16:53:44 MESZ > An: mxcl/homebrew <homebrew(a)noreply.github.com> > Kopie: JensErat <email(a)jenserat.de> > Antwort an: mxcl/homebrew <reply+i-68992688-ffa65db8839fe5d83e9eccef8d1c043a081d3fe5-628441(a)reply.github.com> > > Closed #23100 via f7ace42. > > — > Reply to this email directly or view it on GitHub. >

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xquery replace node adds spaces to inline content
by France Baril 07 Oct '13

07 Oct '13

Hi, I'm getting extra spaces after a node replace. Code: *let **$original* := <div><p>I love flowers (<specify/>).</p> <p>I love flowers: <specify/>.</p></div> *let* *$specify* := <b><i>red, yellow and white ones</i></b> *let* *$new* := *copy* *$copy* := *$original* *modify*(*for **$prompt* *in **$copy*//*specify* *return **replace* *node* *$prompt* *with* * $specify*) *return **$copy* I would expect $new to give: I love flowers (*red, yellow and white ones*). I love flowers: *red, yellow and white ones*. But I get extra spaces inside the parenthesis of the first sentence and before the period of the second sentence: I love flowers (* red, yellow and white ones** *). I love flowers: *red, yellow and white ones** *. You can try my .xqm on BaseX 7.7 1. Create a DB 'test' with chop white spaces to 'no'. 2. Run access http://*localhost:8984*/test-extra-spaces/test-1 from your browser. 3. Look at the .xml in the test DB. It has extra carriage return. It looks like the query assumed that <i> was a block and it felt compelled to add a carriage return and indent. -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com (514) 572-0341

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BaseX 7.7.2
by Christian Grün 07 Oct '13

07 Oct '13

Dear all, a new minor BaseX release is available; it provides the following new features and fixes: XQUERY • a CSV Module and serialization was added • the JSON serializer was updated (more to follow!) • some update checks in the modify clause were fixed • parsing of new map syntax was fixed (ignoring spaces) • tail call handling in built-in higher order functions was fixed API • a Russian translation was added (thanks to Oleksandr Shpak, Max Shamaev) • command-line arguments starting with '<' are interpreted as XQuery INDEXING • a bug was fixed in the updatable index structure (updindex=true) We are looking forward to your feedback, Christian, BaseX Team 2013

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db:list($db) returns raw files, but not db:list($db, $path)
by France Baril 01 Oct '13

01 Oct '13

I'm currently on 7.7. The second function returns files from folders and subfolders at $path, but omits the folders that contain only raw files. -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com (514) 572-0341

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BaseX http running single threaded?
by Joe Templeman 30 Sep '13

30 Sep '13

Hi all, I'm having trouble with the running a restxq API, set up as either a stand alone app (using basexhttp) or running the servlet in jetty. When I make a request, the server will lazily load in the requested content using a small java library that I've built which can take quite a while, and unfortunately it completely blocks waiting for this request to complete. This means that if I make a request for content which is already loaded, which should return in a couple of milliseconds, it instead waits for the downloading of the first request to complete before returning. I'm sure it's something simple that I'm missing in the config somewhere, but I have the threadpool parameters set up in my jetty.xml config file but it doesn't seem to make any difference. Is this expected behavior? I can't imagine any HTTP server would ever be designed to be single threaded... Any help is welcome, I've been trying to figure this out for days now. Thanks, Joe

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Keep index in main memory-performance
by Aravanis, G. 30 Sep '13

30 Sep '13

Hi community, I have created a DB of around 7 GB documents in BaseX (100 first records of Medline) with full text index option enabled (index size 1 GB). I test it locally on my laptop. The problem is that I observe great variations in the free text query times from 8s up to couple of minutes. Main memory is underused (allocated 2 GB) and the processor has quite low utilization. I observe high usage of the hard disk. I have read that the whole db could be loaded in the main memory, but this is not an option for an 100 GB db collection that I would like to have. My question is if there is a possibility to load only the index in the main memory in order to accelerate the process of searching. Any other performance tips are very welcome. Thank you, George Aravanis

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Re: [basex-talk] Set Operator Examples
by Arto Viitanen 26 Sep '13

26 Sep '13

Question was about set operations in BaseX. I had to calculate set difference on a sequence of values. XQuery has operator except, but it works only on nodes. I guess normal code for this is using distinct-values: declare function local:difference-pred($a, $b) { distinct-values($a[not(.=$b)]) }; I used it on big (thousands of values) sets, and it was slow. Then I tried on maps using BaseX map-module : declare function local:difference-map($a, $b) { let $m1 := map:new(for $i in $a return map:entry($i, true())) let $m2 := map:new(for $i in $b return map:entry($i, false())) let $m3 := map:new(($m1, $m2)) return for $i in map:keys($m3) return if ($m3($i)) then $i else () }; Then we found another solution, with only one map: declare function local:difference-map-2($a, $b) { let $m2 := map:new(for $i in $b return map:entry($i, true())) return for $i in $a return if($m2($i)) then () else $i }; When trying them at same sequences: let $a :=for $i in (1 to 100000) return if (random:double() < 0.01) then () else string($i) let $b := for $i in $a return if (random:double() < 0.45) then () else $i return (count($a), count($b), count(prof:time( local:difference-pred($a, $b), true(), 'pred ')), count(prof:time( local:difference-map($a, $b), true(), 'map ')), count(prof:time( local:difference-map($a, $b), true(), 'map2 '))) This gives times (on BaseX 7.6 running on OpenSUSE on VMWare virtual machine on a PC). pred: 80468.68ms map: 261.23 ms map2: 253.77 ms That is: map2 is 317 times faster than distinct-values version. I did not measure memory usage. Also on different size sequences, each one of the functions can be fastest! -- Arto Viitanen Finland

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Issue with linebreak using REST since 7.7.1
by Yoann Maingon 25 Sep '13

25 Sep '13

Hi, I've got a simple node move PHP script (sorry for my terrible code, I'm an electronician!) 1. // get the node 2. $xquery = "XQUERY //noteitem[@id='$movedID']"; 3. $saveNode = $session->execute($xquery); 4. 5. // delete the node 6. $xquery = "XQUERY delete node //noteitem[@id='$movedID']"; 7. $content = $session->execute($xquery); 8. // insert the node 9. if ($nextID == 'last') { 10. $xquery = "XQUERY insert node ($saveNode) as last into //meeting[@id='$meetingID']/items " ; 11. $content = $session->execute($xquery); 12. } else { 13. echo $saveNode; 14. $xquery = "XQUERY insert node ($saveNode) before //meeting[@id='$meetingID']/items/noteitem[@id='$nextID'] " ; 15. $content = $session->execute($xquery); 16. } 17. $contentFull = "<MN>$content</MN>"; 18. echo $contentFull; If I look into the content that is saved, deleted and inserted I have the following: <noteitem status="new" commentsCounter="0" created_on="Tue, 24 Sep 13 12:09:29 +0000" modified_on="Tue, 24 Sep 13 12:09:29 +0000" id="MnNo524180f9587c1" genid="MnNo524180f9587c1" owner="1" type="question"> <notecontent>...</notecontent> </noteitem> It worked fine until the latest update. Where apparently the query breaks with the line break. It creates an error saying that the closing </noteitem> tag is missing. Just got back to 7.6 and it works well. any idea? Yoann Maingon CEO - mydatalinx +33664324966

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feature request -- GUI database creation overall progress
by Graydon Saunders 25 Sep '13

25 Sep '13

Hi! Right now, creating a database in the GUI gives a per-file progress, which is accurate but not informative. Any chance of getting, in addition to the per-file progress, the overall progress of creating the database? Thanks! Graydon

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empty tags
by Lars Johnsen 24 Sep '13

24 Sep '13

Hello BaseX developers! When using BaseX scripting to generate HTML, I got a problem with the representation of empty nodes. For example, my code has something like this in it <div> { ... some code...} </div> if ...some code... returns nothing, the div is empty as is labelled <div/>. This causes trouble in HTML, since <div/> is treated as if it was the start tag <div>, and will therefore nest over following divs. Is there a way for BaseX to output <div></div> instead? There is an ad hoc solution which checks if ...some code... is empty and inserts a blank in those cases, preventing the div from collapsing into one tag, but was hoping for a more general solution. All the best, Lars G Johnsen National Library of Norway

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Caching RestXQ responses
by Wendell Piez 24 Sep '13

24 Sep '13

Hi, I'm in over my head on this one, but I have questions about running BaseX behind restXQ, specifically on whether I can have query responses cached. Does this happen already? (How can I determine this?) Does caching responses to queries under restXQ fall outside of BaseX's responsibilities? Is it a Jetty thing? Any advice in general, or links I can go to learn about this? Thanks, Wendell Wendell Piez | http://www.wendellpiez.com XML | XSLT | electronic publishing Eat Your Vegetables _____oo_________o_o___ooooo____ooooooo_^

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Set Operator Examples
by John Best 24 Sep '13

24 Sep '13

Hi all, Where can I find examples using set operators... wrt BaseX. -- Have a nice day JBest

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Snapshoting in baseX
by Simon Görke 23 Sep '13

23 Sep '13

Hi everybody, this is rather a general question than a concrete issue or a bug report: Does baseX provide any snapshoting-alike functionality, i.e. the possibility to automatically save (potentially) affected elements *before* an updating transaction is performed? We have a (existing) GUI which is used to edit data stored in a baseX database. For this GUI, we want to add undo/redo functionality for the user. Snapshoting would be a straightforward approach, but any other hints or ideas are also welcome (maybe using events?). Thanks in advance, Simon

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Uninstall Removes Repo directory!
by James Wright 20 Sep '13

20 Sep '13

AH! Well its my fault. Several weeks of work lost because I uninstalled 7.7 and it removed the repo directory with all my modules! Just wanted to give the fair warning.. Time to get a drink... I was going to put that in Drop Box last week and never got to it!! - James

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Namespace conflict in XQuery update
by alxarch 19 Sep '13

19 Sep '13

While trying to transform an xhtml document I ran into this general case: copy $ul := <ul xmlns="http://www.w3.org/1999/xhtml"> <li>item</li> <li>item</li> </ul> modify ( rename node $ul as QName("http://www.w3.org/1999/xhtml","ol"), insert node attribute class {"a"} into $ul ) return $ul which throws an "[XUDY0024] New namespaces conflict with each other." error. After reading the XQuery update facility recomendation it wasn't clear to me if this is supposed to happen. Do I *have* to use chained copy statements to achieve both renaming a node an inserting an attribute? Thanks, Alex

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Re: [basex-talk] New map syntax issue
by Daniël Knippers 18 Sep '13

18 Sep '13

Thank you for the swift reply Christian. Please do not feel obligated to let me know once this is fixed, it is not a blocking issue for me and I'm sure you can spend your time in better ways :-) I'm already glad it's been picked up this quickly. -- Daniël On Wed, Sep 18, 2013 at 9:28 PM, Christian Grün <christian.gruen(a)gmail.com>wrote: > Hi Daniël, > > the XQuery 3.1 grammar has not been finalized yet, but I agree that > our implementation is not what one would expect. I have tracked your > observation [1] and will let you know when a fix is available. > > Thanks, > Christian > > [1] https://github.com/BaseXdb/basex/issues/755 > > ___________________________ > > 2013/9/18 Daniël Knippers <dknippers(a)gmail.com>: > > Hi, > > > > Using the new map syntax of BaseX 7.7.1, I ran into this: > > > > let $m := { 'key':'val' } > > return $m('key') > > > > [XPST0003] Invalid key, simple expression expected. > > > > As it turns out, a space is required after the closing quote of the key. > > That is, the above example works fine when replacing 'key':'val' by > > 'key'<SPACE>:'val' > > > > This is not the case when using an integer key, i.e. this works fine: > > > > let $m := { 1:'val' } > > return $m(1) > > > > I'm not sure if this behavior is intentional, but I would guess it is not > > :-) > > > > Regards, > > Daniël > > > > _______________________________________________ > > BaseX-Talk mailing list > > BaseX-Talk(a)mailman.uni-konstanz.de > > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > > >

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New map syntax issue
by Daniël Knippers 18 Sep '13

18 Sep '13

Hi, Using the new map syntax of BaseX 7.7.1, I ran into this: let $m := { 'key':'val' } return $m('key') [XPST0003] Invalid key, simple expression expected. As it turns out, a space is required after the closing quote of the key. That is, the above example works fine when replacing 'key':'val' by 'key'<SPACE>:'val' This is not the case when using an integer key, i.e. this works fine: let $m := { 1:'val' } return $m(1) I'm not sure if this behavior is intentional, but I would guess it is not :-) Regards, Daniël

2 1

Re: [basex-talk] (no subject)
by Christian Grün 18 Sep '13

18 Sep '13

Hi Anand (cc @ basex-talk), > Yesterday, in the mailing list you have mentioned certain NEW fixes for > 7.7.1. > I am more concerned about > > CORE > ? OutOfMemory exceptions are avoided when building large databases > > > Can you explain it in details? I mean the size of "large databases"... John Best was so kind to point me to a bug in BaseX 7.7, which hindered the creation of index structures of larger databases (i.e., those document instances the size of which exceeded the system’s main memory). This error occurred whenever a newly built index structure was too large to fit in main memory. In this case, a partial index is written to disk, and the subsequent memory check was too strict and stopped further indexing. Hope this helps, Christian

1 0

fn:format-number()#2 possible bug
by alxarch 18 Sep '13

18 Sep '13

There seems to be an unexpected behaviour whem using fn:format-number() while having declared a default element namespace in the prologue. Example: > declare default element namespace "http://foo.bar"; > format-number(1234, "0000") Throws an [FODF1280] 'Unknown decimal format: Q{http://foo.bar}' Am i missing something or is this a bug in the 2 argument form of fn:format-number? Thanks, Alex

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BaseX 7.7.1, refactored project structure
by Christian Grün 16 Sep '13

16 Sep '13

Dear all, you are invited to check out our minor 7.7.1 release, which contains the following patches and fixes: XQUERY • we have switched to the new map syntax (example: {'key':'value'}) • tail call optimization is now also applied to dynamic functions • fn:subsequence() calls and sequence casts are better optimized • original options are preserved when calling db:optimize() WEBDAV • non-breakable spaces are returned as   CORE • OutOfMemory exceptions are avoided when building large databases The new release can be found at: http://basex.org Next, we have refactored our project structure: all basex repositories have been merged into one single basex repository: https://github.com/basexdb/basex Your feedback is welcome! Have fun, Christian BaseX Team, 2013

1 0

Adding non ".xml" file extension XML files
by Joe Templeman 14 Sep '13

14 Sep '13

I'm trying to add a collection of files which are all valid XML but when I'm doing the add with this command: db:add("db", "/data/xml/docs/", "docs") where /data/xml/docs contains a number of XML files with a .s9ml file extension, nothing gets added to the database, however if I rename that file.xml, it works. Is there somewhere I can set what file extensions should be used? I can't seem to find anything in any of the docs about this. Thanks, Joe

2 1

Exception when using replace - UPDINDEX problem?
by James Ball 14 Sep '13

14 Sep '13

Hello, I've got a collection with about 1.4 million small XML files in it. I can load all these through the GUI with no problems. However really I need to be loading them, a few at a time, through PHP and have code to do this. Because the process involves add, query, add and so on I have set UPDINDEX to true on the database. In most instances everything works fine but sometimes I get the error below (it's not on particular documents, a second run will give the error in different places). Once this error has been received it seems the OPTIMIZE doesn't work properly on the database - giving an array out of range error. I don't understand the stack trace enough to know what the most likely cause is. Can anyone provide me with some guidance? Many thanks, James exception 'Exception' with message 'Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 7.7 Java: Apple Inc., 1.6.0_51 OS: Mac OS X, x86_64 Stack Trace: java.lang.IllegalStateException: Key should not exist at org.basex.index.value.UpdatableDiskValues.index(UpdatableDiskValues.java:79) at org.basex.data.DiskData.indexEnd(DiskData.java:356) at org.basex.data.Data.insert(Data.java:817) at org.basex.core.cmd.Add.run(Add.java:107) at org.basex.core.Command.run(Command.java:345) at org.basex.core.Command.run(Command.java:117) at org.basex.core.cmd.Replace.run(Replace.java:68) 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.core.Command.execute(Command.java:90) at org.basex.server.ClientListener.execute(ClientListener.java:386) at org.basex.server.ClientListener.replace(ClientListener.java:365) at org.basex.server.ClientListener.run(ClientListener.java:106) ' in /Library/WebServer/Documents/ISIS/BaseXClient.php:101 Stack trace: #0 /Library/WebServer/Documents/ISIS/BaseXClient.php(60): Session->sendCmd(12, 'ISIS_IND_BIO/IW...', '<?xml version="...') #1 /Library/WebServer/Documents/ISIS/uploadBioCli.php(79): Session->replace('ISIS_IND_BIO/IW...', '<?xml version="...') #2 {main}Processing file 358 /Users/jb8748/Documents/Data Auditing/ISIS_IND_BIO/IWF/-9458-.xml

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DB ~webdav
by France Baril 14 Sep '13

14 Sep '13

Hi, I deleted the ~webdav DB by error, and now I am getting an Unexpector error with this trace: DB org.basex.core.BaseXException: Database '~webdav' was not found. Doh! Is there a place I can download a copy of this DB? Or can you provide the parameters I should use to recreate it? Thanks, -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com (514) 572-0341

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Query document metadata
by Bodo Hüsemann 14 Sep '13

14 Sep '13

Hi, do we have any means in XQuery or with the Base-X API to query the age of a document? E.g. let's assume we add documents like this: mySession.add(inDocumentRef, new ByteArrayInputStream(inDocument)); Is there any way to query metadata when this document was added to the database (or other metadata, e.g. the size, too)? The background is that I access external content dynamically and I want to refresh data in the DB according to some defined update strategy (e.g. when the document is older than x-days). I want to apply the strategy based on metadata and not on content, so I don't want to query some document specific elements or attributes. Many thanks in advance! Bodo Hüsemann

2 1

BaseX 7.7 error in working with EQNames
by Dimitre Novatchev 11 Sep '13

11 Sep '13

Hi, Given this XML document (in file example.xml): <p xmlns="http://example.com/one" xml:lang="de" author="Friedrich von Schiller"> Freude, schöner Götterfunken,<br/> Tochter aus Elysium,<br/> Wir betreten feuertrunken,<br/> Himmlische, dein Heiligtum.</p> This XQuery expression (in file TesQNametExpression.xquery, in the same directory): let $doc := doc('example.xml') return string-length($doc/Q{ http://example.com/one}p[1]/@Q{http://www.w3.org/XML/1998/namespace}lang) produces: 0 However the correct result (which I get with Saxon 9.5.01) is: 1 Here is the "Query Info" from the BaseX UI: Compiling: - pre-evaluating fn:doc("example.xml") - binding static variable $doc - removing unknown element/attribute Q{http://example.com/one}p - pre-evaluating fn:string-length(()) - removing variable $doc - simplifying flwor expression Query: let $doc := doc('example.xml') return string-length($doc/Q{ http://example.com/one}p[1]/@Q{http://www.w3.org/XML/1998/namespace}lang) Optimized Query: 0 Hope that this information would be useful for identifying and fixing the issue. -- Cheers, Dimitre Novatchev --------------------------------------- Truly great madness cannot be achieved without significant intelligence. --------------------------------------- To invent, you need a good imagination and a pile of junk ------------------------------------- Never fight an inanimate object ------------------------------------- To avoid situations in which you might make mistakes may be the biggest mistake of all ------------------------------------ Quality means doing it right when no one is looking. ------------------------------------- You've achieved success in your field when you don't know whether what you're doing is work or play ------------------------------------- Facts do not cease to exist because they are ignored. ------------------------------------- Typing monkeys will write all Shakespeare's works in 200yrs.Will they write all patents, too? :) ------------------------------------- I finally figured out the only reason to be alive is to enjoy it.

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