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

Version 8.5 for Ubuntu 16.04
by Alex R. Loayza 30 Oct '16

30 Oct '16

Hello, I'd like to install BaseX 8.5 on Ubuntu 16.04 (Xenial). However, in https://launchpad.net/ubuntu/+source/basex I see that the only binary available for 16.04 is basex_8.2.3-1_all.deb, which is older. I see on the same address that for Ubuntu 16.10 (Yakkety) BaseX 8.5 is available from deb file basex_8.5.1-1_all.deb. Is it possible to download this deb and install it on Xenial? Any potential issues? By the way, 16.04 is a LTR. Shouldn't we expect updated packages to become available for it as well? Best regards. Alex

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A BaseX/DITA use case...
by France Baril 29 Oct '16

29 Oct '16

For those who are interested in the use of XML content for publishing, this presentation is about using BaseX to power a slideshow editing tool that builds slides from existing DITA documentation/training content... https://www.brighttalk.com/community/content-marketing/ webcast/9273/209719?utm_campaign=community-live-recorded&utm_content=&utm_ source=brighttalk-portal&utm_medium=web&utm_term= - France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com

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Download hinter Firewall funktioniert nicht
by Schindler Wolfgang Dr. 27 Oct '16

27 Oct '16

Hallo, der Download der aktuellen Version des BaseX Windows Installers auf einen Rechner, der über Proxy (hinter einer betrieblichen Firewall) aufs Web zugreift, funktioniert nicht. Warum weiß ich nicht genau, könnte aber vermuten, dass an der Art der URI http://files.basex.org/releases/8.5.3/BaseX853.exe liegt. Gibt es eine andere Methode an den Download zu kommen. Danke fürs Helfen und noch einen schönen Tag! Beste Grüße, Wolfgang Schindler

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Check if server is running, silently
by Bram Vanroy 27 Oct '16

27 Oct '16

Hi all To make clear to users which corpora are currently available and which aren't, I'm checking to see if a BaseX server instance exists and then check if a specific database exists. Testing for the database is done with db:query (as I learned through this mailinglist), but I'm not sure how I can silently test for the server in PHP. All BaseX examples use try-catch blocks, which makes sense to catch errors that go wrong, and do something with them. If I'm not mistaken these errors are automatically logged by Apache (maybe also by other webservices). This means that if I'm only checking the existence of a server with the code below (variables left out), I will always write an error to a log file. Obviously, that is not what I want because I know that the error 'Cannot communicate with server' is to be expected when the server does not exist! try { $session = new Session($dbhost, $dbport, $dbuser, $dbpwd); // db:exists returns a string 'false', still need to convert to bool $corpusExists = toBoolean($session->query("db:exists('$databaseName')")->execute()); $session->close(); if ($corpusExists) { $availabilityArray[] = $databaseName; } } catch (Exception $e) { // } This script works perfectly fine, but I do not want the errors to be logged (for this case) to prevent my error log to be full of the same error. Is there another way to test for a BaseX instance only? For instance, a way to return false when the server does not exist, I could do something like: $session = new Session($dbhost, $dbport, $dbuser, $dbpwd); If ($session) { // db:exists returns a string 'false', still need to convert to bool $corpusExists = toBoolean($session->query("db:exists('$databaseName')")->execute()); $session->close(); if ($corpusExists) { $availabilityArray[] = $databaseName; } } Thank you in advance Bram Vanroy

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Some GUI suggestions
by Andy Bunce 27 Oct '16

27 Oct '16

Hi, Here are some suggestions for future GUI enhancements: Project window: * Add recent locations button, similar to the editor (recent files) Editor window: * use scrollable run of tabs rather than multi row see [1]. Ideally with dropdownlist to select any item as with Eclipse, Firefox etc. * more tab close options. E.g "close all", "close others" Query info window Very useful but typically, at any one time, I am only interested in a particular section from: Compiling,Optimized Query,Query,Result,Timing,Query plan. Maybe checkbox config for which are shown or links to sections or tabs for sections Map/tree/folder windows All these views are rooted at a document. There are times when I would like a collection based root here, as shown on database>properties>resources Cheers /Andy [1] http://docs.oracle.com/javase/7/docs/technotes/guides/swing/1.4/tabbedPane.…

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Re: [basex-talk] Text resources
by Kendall Shaw 27 Oct '16

27 Oct '16

Err… I mean: convert:binary-to-string(db:retrieve(‘some’,’some.txt’)) Can I skip the base64 part? Kendall From: <basex-talk-bounces(a)mailman.uni-konstanz.de> on behalf of Kendall Shaw <kendall.shaw(a)workday.com> Date: Wednesday, October 26, 2016 at 5:05 PM To: "basex-talk(a)mailman.uni-konstanz.de" <basex-talk(a)mailman.uni-konstanz.de> Subject: [basex-talk] Text resources Is this how I should retrieve text that is stored using db:store, within xquery? stream:materialize(db:retrieve(‘some’,’some.txt’)) ? Kendall

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Text resources
by Kendall Shaw 26 Oct '16

26 Oct '16

Is this how I should retrieve text that is stored using db:store, within xquery? stream:materialize(db:retrieve(‘some’,’some.txt’)) ? Kendall

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Adding UIDs to all the elements in a collection
by Graydon Saunders 19 Oct '16

19 Oct '16

HI -- In the process of trying to find the differences between two collections of schemas (the XML differences, as opposed to the not-semantically-meaningful differences in the order of the definitions), I find myself wanting to stick UIDs on everything. (So I can go "oh, this element node is different, but it has descendant elements UIDs also in the list of differences, I don't want this one, the descendants are more precise" (because if I don't do something like this, I'm getting xsd:schema every time...)) I haven't done anything with updating expressions before. By itself, in the GUI, for $x in /descendant-or-self::* return insert node(attribute UID {generate-id($x)}) into $x works. Since I would like everything in one query, with a little flailing I've got as far as let $new as document-node()+ := for $each in db:open($newName) return copy $temp := $each modify ( for $x in $temp/descendant-or-self::* return insert node(attribute UID {generate-id($x)}) into $x ) return $temp return $new And there are all the elements with UID attributes associated with them. Is there a better way to do this? Thanks! Graydon

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Compiler issue?
by Marco Lettere 17 Oct '16

17 Oct '16

Dear BaseX team, running the following two queries [1,2] (which should be semantically equivalent to my eyes) I get different results. In particular [2] sometimes return multiple results or empty sequence which is pretty odd, isn't it? I've tried on 8.5.3 and on a recent snapshot labeled 8.5.4 (beta 6e9bf7c). Regards, Marco. [1] let $domain := for $record in (1 to 100) where $record mod 5 = 0 return $record let $index := 1 + random:integer(count($domain)) return $domain[$index] [2] let $domain := for $record in (1 to 100) where $record mod 5 = 0 return $record return $domain[1 + random:integer(count($domain))]

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Creating more than a million databases per session: Out Of Memory
by Bram Vanroy | KU Leuven 17 Oct '16

17 Oct '16

Hi all I've talked before on how we restructured our data to drastically improve search times on a 500 million token corpus. [1] Now, after some minor improvements, I am trying to import the generated XML files into BaseX. The result would be 100,00s to millions of BaseX databases - as we expect. When doing the import, though, I am running into OOM errors. We put our memory limit on 512MB. The thing is that this seems incredibly odd to me: because we are creating so many different databases, which are all really small as a consequence, I would not expect BaseX to need to store much in memory. After each database is created, the garbage collector can come along and remove everything that was needed for the previously generated database. A solution, I suppose, would be to close and open the BaseX session on each creation but I'm afraid that (on such a huge scale) the impact on speed would be too large. How it is set up now, in pseudo code: ---------------------------------------------------------------------------- ---- $session = Session->new(host, port, user, pw); # @allFiles is at least 100,000 items For $file (@allFiles) { $database_name = $file . "name"; $session->execute("CREATE DB $database_name file "); $session->execute("CLOSE"); } $session->close(); ---------------------------------------------------------------------------- ---- So all databases are created on the same session which I believe causes the issue. But why? What is still required in memory after ->execute("CLOSE")? Are the indices for the generated databases stored in memory? If so, can we force them to write to disk? ANY thoughts on this are appreciated. Enlightenment on how what is stored in a Session's memory is useful as well. Increasing the memory should be a last resort. Thank you in advance! Bram [1]: http://www.lrec-conf.org/proceedings/lrec2014/workshops/LREC2014Workshop-CML C2%20Proceedings-rev2.pdf#page=20

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executing xquery on basex
by Wang, Genneva 16 Oct '16

16 Oct '16

Hi We have seen some weird issue with basex only when executing xquery via java client (the basexclient.java from https://github.com/BaseXdb/basex/blob/master/basex-examples/src/main/java/o…) . And I was wondering if you would have any tips. The issue is happening when executing xquery to execute the function fn:current-dateTime() We have logs the queries that we are sending prior to calling the execute method in BasexClient.java, so we know that the xquerys are constructed correctly. However, we have been receiving inconsistent results from execute this xquery. Below are some examples of the basex logs. 05:42:40.907 172.16.0.43:51776 admin REQUEST XQUERY fn:current-dateTime() 0.11 ms 05:42:40.908 172.16.0.43:51776 admin OK Query executed in 0.18 ms. 0.77 ms 05:42:44.787 172.16.0.35:56245 admin REQUEST Ìº°Ì±ïERY fn:current-dateTime() 10000.3 ms 05:42:44.787 172.16.0.35:56245 admin ERROR Stopped at , 1/6: Unknown command: Ìº°Ì±ïERY. Did you mean 'ALTER'? 0.03 ms In this basex log, as you can see, that the first time that the query "XQUERY fn:current-dateTime()"went successful, and somehow the second time the the query was being altered (in red above) and the query was not able to recognize the query from basex. We were not able to reproduce this issue consistently. We have cross check the log on our applications so we know that the query has been constructed the same prior to making calls to basex. Any thoughts would be greatly appreciated. Thanks. Regards, -Genneva

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Re: [basex-talk] Large CSV File (~1M rows)
by Shaun Flynn 16 Oct '16

16 Oct '16

Hello there, The parsing runs out memory. I also tried doubling the memory to 1024MB, and still the same issue. Kind regards On 16 Oct 2016 09:15, "Christian Grün" <christian.gruen(a)gmail.com> wrote: Hi Shaun, > I do this through the MS DOS prompt, but -Xmx does not appear to be a > parameter any more, If you work with the ZIP distributions of BaseX, you can adjust the memory setting in the start scripts (in the bin directory). Otherwise, you’ll need to pass it to to java, not BaseX itself. > Is there a better method for parsing large CSV files? I then want to add the > resulting file tlk.xml to a new database. Did you check if it’s the CSV parsing or the fn:put call that causes the error? Christian [1] http://docs.basex.org/wiki/Database_Module#db:add

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Making connections to a database
by Thomas Daly 16 Oct '16

16 Oct '16

Hello, I'm developing an application server with node.js. When the server starts, it creates a single connection to a BaseX database, to allow subsequent user queries to the database. I notice that when I connect separately to the BaseX database with the BaseXClient command line tool, the application server connection dies with a 'broken pipe' error. Am I doing this correctly, or should the application server connect then immediately disconnect from BaseX to serve each individual user query (in the same way that PHP works with MySQL)? Thanks Thomas

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(no subject)
by Shaun Flynn 16 Oct '16

16 Oct '16

Hello there, I am trying to parse a large CSV file into XML by the following xquery: let $file := fetch:text("D:\BPLAN\tlk.txt") let $convert := csv:parse($file, map { 'header' : true(), 'separator' : 'tab'}) return fn:put( <tlks> {for $row in $convert/csv/record return <tlk>{$row/*}</tlk> }</tlks>, "D:\BPLAN\tlk.xml" ) Using the GUI, it runs out of memory -- when I click on the bottom right hand corner (where the memory usage is shown), it says to increase memory, restart using -Xmx <size>. I do this through the MS DOS prompt, but -Xmx does not appear to be a parameter any more, Is there a better method for parsing large CSV files? I then want to add the resulting file tlk.xml to a new database. Kindest Regards Shaun Connelly-Flynn

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retrieve a sequence of all values within an attribute index
by Alex Muir 10 Oct '16

10 Oct '16

Greetings, I need to generate a list of all the distinct values within an index. Is there a way to retrieve a sequence of all values within an attribute index? Regards Alex tech.jahtoe.com bafila.jahtoe.com

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http:send-request POST xml body is inheriting the http-client namespace
by chrisis 10 Oct '16

10 Oct '16

I'm using BaseX 8.4 but have recreated the issue with 8.5.4 beta 8d90b66 I'm POSTing xml files to a RESTXQ function using the following script let $fpath := 'C:\incoming\SAQD\mo' let $targetBasex := 'http://localhost:8984/saqd/mo/' let $list := sort(file:list($fpath), function($fname) {fn:analyze-string($fname,'.*_(.*?)\.xml$')/fn:match/fn:group[@nr="1"]/string()}) for $file in $list let $abspath := $fpath||'\'||$file let $body := try {fetch:xml($abspath, map { 'chop': true() }) } catch * {()} return if ( not(empty($body)) ) then (http:send-request(<http:request href="{$targetBasex||$file}" method='POST'> <http:body media-type="text/xml">{$body}</http:body> </http:request>), file:move($abspath,$fpath||'\processed\'||$file) ) else () The XML file has no namespace declarations. The RESTXQ function does a db:update using the body received and the http-client namespace has been added to the root node. If I POST to the same function using curl the stored document is unchanged. The function is as follows. declare %rest:path("/saqd/mo/{$fname}") (: %rest:consumes("application/xml", "text/xml") :) %rest:POST("{$body}") %updating function saqd:mo($fname, $body as document-node()) { try {(db:replace('SAQD', '/MO/'||$fname, $body ), db:output(http:send-request(<http:request href="{' http://example.org:8082/home/VALIDSCHEMA/xml/current/Metoffice_Data/'||$fname }" method='PUT' username='validuser' password='validpassword' send-authorization='true'> <http:body media-type='text/xml'>{$body}</http:body> </http:request>)) ) } catch * {db:output( <rest:response> <http:response status="500" message="{$err:code||' : '||$err:description}"> </http:response> </rest:response>)} }; The file PUT inside the db:output statement also gets the namespace added i.e. it happens even when the file was POSTed with curl so the recieved document still had no namespaces. Is this expected behaviour, a bug, or am I using http:send-request incorrectly? Regards, chris sweeney

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Make BXElem return also namespace declarations
by Erdal Karaca 09 Oct '16

09 Oct '16

Hi, I am accessing the DOM tree of the collections in the embedded mode. Now, I need to process the DOM node returned by a query. For this, Item.toJava() returns a DOM Element (for my specific case/query). When calling Element#getAttributes(), I only get "direct" attributes, i.e. no namespace declarations are included in the list of attributes. Are the namespace declarations omitted intentionally? How can I make the BXElem also report them in the resulting attributes list? Thanks.

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embedded mode thread-safe?
by Erdal Karaca 09 Oct '16

09 Oct '16

Hi all, Is the embedded mode thread-safe? I mean, once I have the Context object and opened a database, is it safe to access (read/write) it from multiple threads? Will the same transaction mechanism apply as if the server mode would be used? Thanks.

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copy attributes of one node to another
by Erdal Karaca 09 Oct '16

09 Oct '16

Hi, I am trying to copy attributes of one node to another: copy $x := <test a="b" c="d"></test>, $y := parse-xml('<o a="x" c="y"></o>') modify ( delete nodes $x/@*, insert nodes $y/@* into $x ) return $x Unfortunately, the resulting $x is an empty <test/> node. I expected it to have the attributes of the parsed node. Am I using parse-xml() properly? Thanks!

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problem getting -somit-xml-declaration=no to work
by Regine I. Heberlein 07 Oct '16

07 Oct '16

Hello all, I wonder whether someone could help me with what I'm sure is just some newbie error on my part. I'm running an XQuery Update using BaseX from the command line over an XML document, and I want the XML declaration to be preserved. My input is: basex -uVwsomit-xml-declaration=no <input xQuery Update file> That looks correct to me per the documentation, but when I run it, I lose the XML declaration nevertheless. (The xQuery Update executes correctly.) I've tried the following, all to no avail: --split out the -s flag, putting it as the first and last flag, respectively --setting the value to "yes" (well, I knew that wasn't going to work, but I had to check, right?) --upper case NO (ditto...) --adding the following two lines to my xQuery file: declare namespace output = "http://www.w3.org/2010/xslt-xquery-serialization"; declare option output:omit-xml-declaration "no"; I know this question has come up before, but I couldn't find an approach that worked for me in the list archives. Obviously, at this point I'm just throwing darts at the problem. I'd be grateful for any pointers! Sincerely, Regine Heberlein Principal Cataloger and Metadata Analyst, Rare Book Collections Princeton University Library One Washington Road Princeton, NJ 08540 609-258-6156

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Cannot insert node into empty db/collection
by Erdal Karaca 06 Oct '16

06 Oct '16

Hi, When creating an empty database, then trying to insert a node into its root, I get the following error message: Command: create db test XQuery: insert node <test></test> into / Error: [XUDY0027] Insert target is an empty sequence. How can I populate an empty database? - I am using basex 8.5.3. Thanks!

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Get DBPATH variable
by Bram Vanroy 05 Oct '16

05 Oct '16

Hi all, it's me again Another day, another question! I'm still working in Perl on BaseX 7.9. This time I am trying to check if a database is already build. I thought a good way would be to check if the path to the database already exists on the file system. However, not wanting to hard-code each single path for each different basex instance, I was wondering if there is a way to get the DBPATH variable that is set in the .basex file. Note that I need to retrieve this information before opening the database itself: when running a Session, I need to check if a database exists on the DBPATH as specified in that Session's variables. I've been looking in the methods of the BaseX client for Perl, and in the available commands on the wiki but I cannot find a way to retrieve these 'Session Globals'. Is there a way? Or any other way to check if the database already exists? Thank you in advance Bram

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Content is not allowed in prolog
by Bram Vanroy 04 Oct '16

04 Oct '16

Hi all This error has been handled with a lot, but always concerns CSV. I am dealing with simple XML. I am writing a Perl script that first generates a XML file, and then imports it into a BaseX database. Unfortunately, I get the error message: "." (Line 1): Content is not allowed in prolog. At /BaseXClient.pm line 126 I have tried many things and have been debugging with perl, but as far as I can see the created files are valid XML. The error implies that a connection to the BaseX server is established. Something's wrong with the XML file but I do not know what and how to prevent it. I added the script on pastebin as to not waste space in this email. [1] The XML is created in the sub createXml. That routine returns the path to the created file, which on line 24 is imported into BaseX. Or at least, that is the goal. But that's where the error occurs. I attached example XML output. The script as well as the output and input are in UTF8. Thank you in advance Kind regards Bram Vanroy [1]: http://pastebin.com/MhA8eBJf

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One database instance per user
by Erdal Karaca 01 Oct '16

01 Oct '16

Hi, I intend to use one database for each user of the business domain (web application). Does anyone have experiences with lots of 'small' databases vs. one 'big' database regarding performance/scalability/stability? Thanks! Best regards, Erdal

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safe to have multiple clients call user:update-info ?
by Maximilian Gärber 30 Sep '16

30 Sep '16

Hi, could not verify in the BaseX source code, so can I assume this is safe, since it is a file on the file system (users.xml)? Background: I want to add locking information there, so everytime an user requests to checkout a file, it should be saved there. At the same time, I have to be sure nobody else can write at the same time. Regards, Max

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