BaseX-Talk December 2012

basex-talk@mailman.uni-konstanz.de

33 participants
46 discussions

Out of memory bug
by Ivan Lagunov 31 Jul '13

31 Jul '13

Hello, I've got 'Out of memory' error and corrupted database again, this time it's for 6.3 version. Steps: 1. Started server, started terminal client, checked there are no text and attribute indexes. 2. Started my Java application that runs several tests on database: querying, adding, removing. 3. Then I forgot to reopen terminal client and used the one that I opened in Step 1. 4. Run optimize command for the collection and got error. 5. Cannot open the collection any more as I'm getting 'Out of memory'. It's clear that I shouldn't have used the terminal client that I opened before execution of my Java application. But sometimes it's hard to remember. And it's completely unacceptable that these actions result in the corrupted database. You really should catch ArrayIndexOutOfBoundsException everywhere in order to save database from being corrupted. Terminal client stacktrace: > optimize Possible bug? Feedback is welcome: basex-talk(a)mailman.uni-konstanz.de BaseX 6.3: java.lang.ArrayIndexOutOfBoundsException: -1 org.basex.data.PathSummary.add(PathSummary.java:68) org.basex.core.cmd.Optimize.stats(Optimize.java:68) org.basex.core.cmd.Optimize.run(Optimize.java:34) org.basex.core.Command.run(Command.java:236) org.basex.core.Command.exec(Command.java:218) org.basex.core.Command.execute(Command.java:66) org.basex.server.ServerProcess.run(ServerProcess.java:161) > open products Out of Main Memory. Best regards, Ivan

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indent parameter
by Hans-Juergen Rennau 28 Jun '13

28 Jun '13

Hello, it seems to me there is a couple of issues concerning the handling of indentation (serialization parameter "indent"). a) Using "indent=no" whitespace-only text nodes between element nodes are removed b) Using "indent=yes" the content of elements with xml:space="preserve" is indented, too I suppose both behaviors are in contraction to the spec ( http://www.w3.org/TR/xslt-xquery-serialization/#xml-indent ). As a particular consequence, (a) seems to preclude making an exact copy of a document (fragment) - all whitespace-only text nodes vanish. And as a consequence of (b) one has no possibility to locally protect the whitespace used in the source document, as required for example when reusing "programlisting" elements of docbook. Or did I overlook something? Kind regards, Hans-Juergen

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Best practices for concurrency
by The Trainspotter 19 Jun '13

19 Jun '13

Hi, I've read through the online example on server concurrency, however, currently I'm not running a BaseXServer instance I'm just running things locally. I want multiple threads in my application to be able to query the database at once without treading on each others toes. What's the best approach for doing this? I have tried querying the database using different threads but I keep getting internal BaseX errors which leads me to think I'm going about this the wrong way. Cheers Gary

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invalid collection name?
by C. M. Sperberg-McQueen 27 May '13

27 May '13

Using the GUI interface to BaseX 7.2, when I select Database / Open and Manage ..., I get a list of the databases I have built over the time I've been using BaseX. When I try to open the collection named MEP.bigbooks, though, I get an error box saying "Name 'MEP.bigbooks' is invalid." In the "Manage Databases" dialog box, the information about the collection appears normal and plausible (at least, the size is about what I expect, and so on). It's only when I try to open the collection that I run into the error. I get similar errors on other collections which have . in their name; I do not get errors when opening other collections built (as far as I can remember) at the same time from the same data, if their name does not include a full stop. When I try renaming the collection without the full stop, I get the same error message. When I try to issue the command ALTER DATABASE MEP.bigbooks MEPbigbooks from the server command area of the GUI, I get a short syntax summary in the Query Info area complaining about the syntax of the command. When I replace MEP.bigbooks with MEP\.bigbooks and "MEP.bigbooks", I also get syntax errors. If I close the GUI and just rename the directory within my BaseXData directory, the database appears to open normally. I think I have two questions: Q1 is just renaming the directory a safe way (assuming no server is currently working with the data) to rename a collection? Should I do the same for all the other collections I have that don't currently open? I assume that if the 7.2 GUI won't let me rename them, it also will have trouble deleting them, so a related question is: is just deleting a sub-directory of BaseXData a safe way to delete a collection? Q2 Did the rules for names of collections change? Or is there some other cause? Speaking for myself, I guess that as a user I haven't thought much about what characters should be allowed in collection names, but I may have assumed that if they are not unrestricted, they would be restricted to being legal NCNames. I do kind of like using dots in names, so you can count this as one vote for relaxing the naming rules at some convenient moment. It's not a really important point, of course. best, Michael -- **************************************************************** * C. M. Sperberg-McQueen, Black Mesa Technologies LLC * http://www.blackmesatech.com * http://cmsmcq.com/mib * http://balisage.net ****************************************************************

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Changing content through Data Source/Oxygen
by France Baril 17 Jan '13

17 Jan '13

Hi, Our .xqm uses a configuration file that is stored in a DB called AppResources. When we use the GUI to create/upload the content for AppResources, we can access our restxq pages and the result is based on our config. If we access the config file in Oxygen and change anything, even a space, it's like the .xqm cannot access the information anymore. We tried: - Updating/optimize the index/paths. - Stopping/starting the server. The file is saved properly. If we save it on disk from Oxygen and reload AppResources with the config file, we are able to access the information in the file again. So the issue is really the fact that the change occurs through webdav. What are we missing here? Regards, France -- France Baril Architecte documentaire / Documentation architect france.baril(a)architextus.com (514) 572-0341

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Query slow via PHP
by Mayer, Jonathan 11 Jan '13

11 Jan '13

Hi, Hope you can help a very novice basex/xquery user! I have the following query to get the complete XML of the "Links.xml" document in the "project" collection. for $doc in collection('project') where matches(document-uri($doc), '^Links.xml') return $doc When running this command in basex on linux it completes in around 2.5 seconds (acceptable speed given the size of the XML file) but when I run it via PHP using the client from the website, it takes around 15 seconds: $session = new Session("localhost", $host, $username, $password); $input = "for \$doc in collection('project') where matches(document-uri(\$doc), '^Links.xml') return \$doc"; $query = $session->query($input); $xml = $query->execute(); Any idea why it might take so long, or whether rewriting my query in a different way would speed up the response? Thanks, Jon.

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XQuery update: updating inside a closure & how to modify a node and insert it in a DB
by Daniel Kvasnička 10 Jan '13

10 Jan '13

Hi folks, I'm trying to implement a secure RESTXQ service like this: declare %rest:path("api/users/init") %restxq:PUT("{$data}") %output:method("text") function page:init-user($data) { sec:secure(function() { let $profile := json:parse-ml(convert:binary-to-string($data)) return ( insert node attribute id { sec:get-current-user-id() } into $profile, insert node $profile as last into db:open("db")/s:root ) }) }; And I have two problems: - when executing it like this, inside of a closure, nothing happens. No modifications of the database and no errors (%updating missing) either - which is weird. Is this construct supported in 7.5? - when I remove the sec:secure call and leave only the rest (adding %updating to the declaration) the second insert runs but the first one doesn't - the node is saved without a "id" attribute. Does this have something to do with the PUL order? (http://docs.basex.org/wiki/Update#Example) Thanks for your hints! I feel like I'm overlooking something obvious... Daniel -- danielkvasnicka.net

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Re: [basex-talk] how to pass raw bytes intact?
by jidanni＠jidanni.org 02 Jan '13

02 Jan '13

Our mission today is to use Basex to remove tags injected right between the bytes of multibyte UTF-8 characters. http://www.couchsurfing.org/group_read.html?gid=430&post=13986932 >>>>> "CG" == Christian Grün <christian.gruen(a)gmail.com> writes: CG> Have you tried method=raw, as mentioned in our documentation CG> (http://docs.basex.org/wiki/Serialization)? Sorry. Try it yourself: echo '<A>你好</A>'|perl -pwle 's![^[:ascii:]]!$&<wbr/>!'|basex -q ' declare option db:parser "html"; declare option output:method "raw"; doc("/dev/stdin")//*:wbr/..' There is no way to cleanly restore the shattered UTF-8. I would also like to try declare option output:encoding "RAW"; or "BYTES" or "NONE" but on http://docs.basex.org/wiki/Serialization it just says "all encodings supported by Java" So one is supposed to look at http://www.google.com/search?q=all+encodings+supported+by+Java etc. etc. Why doesn't basex have a command that would output the current "all encodings supported by Java" that it is using.

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Initial xquery for full text and geospatial search of ISO 19115 docs
by David Stuebe 31 Dec '12

31 Dec '12

Hi Basex Folks I have written a simple minded xquery script which can be used in a post to search ISO 19115 metadata documents. As I am a newbie to xquery and basex I expect that is much that I could do to improve performance, but currently searches take up to 15 seconds. The server hardware is not blazing fast and we are running inside tomcat… but that is certainly not acceptable for a database which is still quiet small. Initially it was fine, responding in less than a second, but when we expanded from less than 100 docs to about 35000 the time grew at least linearly. I am hoping this is due to my poor xquery programming or a setting on the server. Here is the query we are running using a post request with the declared variables at the bottom filled in by the UI: https://github.com/asascience-open/glos_catalog/blob/master/queries/full_se… Here are some of the ISO xml documents that we have in our basex DB: https://github.com/asascience-open/glos_catalog/tree/master/ISOs It is used by this site: http://explorer.glos.us/ To provide geospatial metadata search. Fill in a text value like "water" or "temperature" in the search box in the top right… The server is here: http://64.9.200.113:8080/BaseX73/ User Name: user Password: glos ACL: read only I am hoping it is as simple as a setting on the basex server. Here is the current server info: info database Database Properties Name: glos Size: 422 MB Nodes: 17045388 Documents: 34922 Binaries: 0 Timestamp: 27.12.2012 00:58:03 Resource Properties Timestamp: 22.12.2012 01:43:05 Encoding: UTF-8 Whitespace Chopping: ON Indexes Up-to-date: true Text Index: ON Attribute Index: ON Full-Text Index: ON The index info is available here: https://github.com/asascience-open/glos_catalog/blob/master/queries/glos_in… David Stuebe Scientist & Software Engineer – RPS ASA 55 Village Square Drive South Kingstown, RI 02879-8248 Tel: +1 (401) 789-6224 Email: David.Stuebe(a)rpsgroup.com<mailto:David.Stuebe@rpsgroup.com> www: asascience.com<http://www.asascience.com/> | rpsgroup.com<http://www.rpsgroup.com/> A member of the RPS Group plc

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Re: [basex-talk] http server ... outsider localhost
by pw＠themail.co.uk 31 Dec '12

31 Dec '12

Hi Christian I just downloaded the BaseX 7.5 zip archive and ran the httpserver.bat file ... On the local machine I was able to access using the localhost or machine name as URLs, but access from elsewhere on the network got to the Jetty server (it logged "access denied") but apparently no further. Peter Hi Peter, the combination of BaseX and Jetty is successfully applied in many productive client/server environments. Can you provide us with some more details on how to reproduce the issue? Thanks, Christian ___________________________ > hello list --- Happy Christmas & New Year > > If I run the http server (Basex 7.5) then I can access through Jetty. > When I try to access the same across the network I get nothing > through and "Access denied" in the Basex logs. What's the solution? > > Many thanks > Peter > > _______________________________________________ > BaseX-Talk mailing list > BaseX-Talk(a)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

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BaseX-Talk December 2012