February 2012 - BaseX-Talk - mailman.uni-konstanz.de

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

4 8

Empty Initial Document Inconsistencies
by Dave Glick 05 Jul '12

05 Jul '12

Hello again, I've noticed some inconsistencies with regard to the initial document in an empty database. I understand that it is often treated as an indication that the database is "empty". I.e., if the database has only one node and it's a document at the first pre value, then Data.empty() returns true. The problem arises because the database isn't actually empty - it contains one empty document - and some commands/methods view it as an empty database while others treat it as a database with one empty document. Several examples: - The method Data.doc(name) will return -1 (indicating the document doesn't exist) while Data.docs() will return an array of size 1 with the first value a 0 (indicating there is one document at pre value 0). This is actually my own problem because the API I'm writing relies on these two methods being internally consistent - I can't have one telling me there is one document called "XYZ" but then have the other refuse to give me a pre value for the "XYZ" document I was just told exists. - The GUI shows a single doc node in the tree view but issuing the command "list [database name]" shows the database as having no resources. - I can evaluate the query "insert node 'text' into doc('[initial document name]')" and it executes. I can see the new text node under the initial document in the GUI tree view. Now when I issue the command "list [database name]" I see 1 resource. Having the list command report different numbers of resources before and after a XQuery insertion seems odd. - If I issue the command "ADD TO newdoc <xyz/>", I can see the new doc("newdoc") node with the child <xyz> element in the GUI but the previously empty document is now gone. This also seems odd - I'm not sure how I feel about an ADD command removing data from the database (even if it was just intended to be a placeholder). In the end, I think BaseX should support the notion of a database with one empty document as being valid - there are probably cases where one might want to start their session in that state. I'm not sure what the solution is or should be (or if it's even something that is worth or needs solving). My own preference would be for the internal indication of an empty database to use a different node kind dedicated for that purpose so there is no confusion whether the single node at pre 0 is an empty initial document or an indication of an empty database. At the very least, I think the inconsistencies above should be corrected - if a single empty document node is intended to signify an empty database and is not actually intended to be part of the database, then you should not see it in the GUI, not be allowed to insert content to it, etc. Dave

4 7

deadlock in BaseXServer 6.2.7
by Godmar Back 23 Jun '12

23 Jun '12

Hi, we're observing that our BaseXServer 6.2.7 deadlocks. The stack traces are here: http://top.cs.vt.edu/~gback/bx/deadlock-6.2.7/basex-deadlock.txt Could you take a look to see if these ring any bells? Has this problem been addressed in a more recent version? - Godmar

3 5

Importing two modules from the same package -> "Module is declared twice"
by Charles Duffy 05 Mar '12

05 Mar '12

Howdy -- please see the following example: === expath-pkg.xml <?xml version="1.0"?> <package xmlns="http://expath.org/ns/pkg" spec="1.0" name=" http://dyfis.net/example/ns-test" abbrev="ns-test" version="0.1.136892+build.20120224.105428"> <title>Namespace Trouble Test</title> <xquery> <namespace>http://dyfis.net/example/ns-test/foo</namespace> <file>foo.xq</file> </xquery> <xquery> <namespace>http://dyfis.net/example/ns-test/bar</namespace> <file>bar.xq</file> </xquery> </package> === ns-test/foo.xq module namespace foo = "http://dyfis.net/example/ns-test/foo"; declare function foo:test() { 1 + 1 }; === ns-test/bar.xq module namespace bar = "http://dyfis.net/example/ns-test/bar"; declare function bar:test() { 1 + 1 }; === ...in the basex-gui buffer... import module namespace foo="http://dyfis.net/example/ns-test/foo"; import module namespace bar="http://dyfis.net/example/ns-test/bar"; 1+1 === ...results in... Error: [XQST0047] Module is declared twice: ' http://dyfis.net/example/ns-test/bar'.

2 2

CHOP=false in a POST request ?
by Maud Ingarao 05 Mar '12

05 Mar '12

Hello, I need BaseX not to chop whitespaces while creating DBs out of my XML texts. I found this post : https://mailman.uni-konstanz.de/pipermail/basex-talk/2010-April/000213.html and this documentation : http://docs.basex.org/wiki/Options#CHOP But could someone please show me how to write it as a REST POST request ? I looked at examples here http://docs.basex.org/wiki/REST#Command_Line but always get a "Nodes must belong to "http://www.basex.org/rest"" error... Thanks a lot !! Maud -- Maud Ingarao IHPC (UMR 5037) Institut d’histoire de la pensée classique, de l’Humanisme aux Lumières Ecole Normale Supérieure de Lyon - Site Descartes - Bureau R322 15 Parvis René Descartes - BP7000 - 69342 Lyon CEDEX 07 +33 4 37 37 65 79 - maud.ingarao(a)ens-lyon.fr cerphi.ens-lyon.fr - pensee-classique.ens-lyon.fr institutdesanti.ens-lyon.fr - hyperdonat.ens-lyon.fr mutec-shs.fr - projet-plume.org - ahn.ens-lyon.fr http://www.cahier.paris-sorbonne.fr/ - je suis absente le vendredi - out of office on Fridays -

3 4

Ask about EVENT
by truc.cam＠emotive.de 01 Mar '12

01 Mar '12

Dear BaseX team, I'd like to ask you why my class not run properly. I'm using EVENT to notify changes from xquery. It must print numbers from 1 to 10, 50 times for each number. Why does it skip some numbers in a random manner? How can I do to correct it? Please see my attachment. Thanks in advance.

3 3

Listing packages in machine-readable form w/ versioning info?
by Charles Duffy 01 Mar '12

01 Mar '12

Howdy -- As best I can tell, there are currently two ways to list installed packages: - The REPO LIST command, which returns complete output, but in a format clearly intended for human consumption. - The repo:list() function, which is more programatically accessible but returns only namespaces (no version numbers)... simply repeating a single namespace twice if two versions of that package are installed. A mechanism to access the installed package list which includes versioning and directory info (the latter to allow uninstallation of a specific version using repo:delete) would be useful.

3 5

access control
by Victor Petrov 29 Feb '12

29 Feb '12

Dear BaseX Community, is it possible to restrict user access on a per-document (or even better, per-element) basis? Imagine that multiple users are sharing the same database and the system needs to prevent XPath queries on the documents/elements which the current user doesn't have access to. If not, is there any other way this functionality could be achieved using BaseX? Thank you in advance! Regards, Victor

3 3

Bug#661297: say how to do a perfect HTML round trip, also man page still doesn't mention HTML
by jidanni＠jidanni.org 28 Feb '12

28 Feb '12

X-debbugs-Cc: basex-talk(a)mailman.uni-konstanz.de Package: basex Version: 7.1.1-2 Severity: wishlist We read basex (7.1.1-2) unstable; urgency=low * Allow non well-formed HTML to be parsed if libtagsoup-java is installed. * Updated man page with an example on how to parse HTML. But we find no such example on the man page. Also please add something to http://docs.basex.org/wiki/Parsers ... OK, I added a minimal http://docs.basex.org/wiki/Parsers#HTML_Parsers By the way http://home.ccil.org/~cowan/XML/tagsoup/ says --files Output into individual files, with html extensions changed to xhtml. Otherwise, all output is sent to the standard output. --html Output is in clean HTML: the XML declaration is suppressed, as are end-tags for the known empty elements. --omit-xml-declaration The XML declaration is suppressed. etc. Please mention how we can manipulate these via "declare option...". Also mention how to manipulate the 'SAX features and properties' mentioned. Allow us to attempt a round trip, declare option db:parser "html"; declare option output:method "html"; declare option output:version "4.01"; declare option output:doctype-public "-//W3C//DTD HTML 4.01//EN"; declare option output:doctype-system "http://www.w3.org/TR/html4/strict.dtd"; doc("http://jidanni.org/index.html") Alas, I need to somehow use --html, and also who is putting those shape="rect" into my <a> links?? Ah, maybe --html will fix that too, http://www.xmlplease.com/shaperect . I can accept the fact that comments are stripped, but there should be a way to adjust things so one can get a closer HTML round trip.

1 1

Serialization to image files
by Andreas Karpf 27 Feb '12

27 Feb '12

Hi, I have a question, which sound a little bit strange. Is there away to serialize to image files (png, pdf etc.)? I am graceful fro every hint. I used to use Mac until two months ago. There I serialized to html documents and then used a secondary software to convert these html files to pngs. Unfortunately I can't find anything like that on Linux, with which I am working now. Best regards, Andreas Karpf

2 1