November 2024 - BaseX-Talk - mailman.uni-konstanz.de

Upgrading BaseX by several major versions
by Rémy Delanaux 18 Dec '24

18 Dec '24

Hello, I manage a project I've worked on from 2020 to 2022 and have recently come back to (no one has really worked on since then). The project currently runs BaseX 9.4, and we obviously would like to catch up on versions of BaseX. But I'm wondering what is the best way to process here. I don't remember upgrading major versions of BaseX during my time on project (we changed servers so for BaseX 9 we did a fresh install and backup restore) What is the correct way to do this? Should I straight up install the latest version (probably BaseX at the time of writing) and find all blocking migration changes, or gradually install major version after major version (10 then 11 then 12 when available) and ook for smaller migration processes? I wasn't able to find migration guides except for upgrading from 9 to 10 (although there are individual changelogs for each individual module). Thanks! Best, Remy Delanaux

6 10

BaseX freeze
by Jerome Chauveau 16 Dec '24

16 Dec '24

hi, my basex server (11.5) stops responding when too many clients request my rxq application. I've published a little demo to reproduce the bug here : [ https://git.unicaen.fr/chauveau/basex-freeze-app | https://git.unicaen.fr/chauveau/basex-freeze-app ] I don't know if the problem comes from BaseX, Jetty or the Saxon XSLT processor. Thanks for your help Jérôme

2 3

RestXQ OAuth2 permission checks
by Jörn Willhöft 05 Dec '24

05 Dec '24

Hi all, I recently implemented a small OAuth2 / OpenID permission check library in XQuery, complete with a small example page and a docker compose setup, including an identity provider (FusionAuth in this case). I saw this popped up once or twice on the mailing list, but I could not make much use of the provided code, so I hope this might be of interest to anybody. The example project is available on Github: https://github.com/willhoeft-it/basex-oauth2 I would be glad to hear about any opinions or get some feedback. While working on this, I realized that BaseX' permission attributes unfortunately lack a small feature that would be quite useful: The "perm" parameter to the checking function provides the method and the path, but unfortunately not any URL parameters. In my case, I would like to remember the URL (including parameters) the user called before I redirect him to the authorization server to login, so I can afterward redirect him to the page he actually wanted. But in a more general context, I can imagine it would also be useful to do permission checks on the parameters, too. Or maybe I missed something? Kind regards Jörn Willhöft

3 5

BaseX 9.6: The Summer Edition
by Christian Grün 28 Nov '24

28 Nov '24

Dear all, We provide you with a new and fresh version of BaseX, our open source XML framework, database system and XQuery 3.1 processor: https://basex.org/ Apart from our main focus (query rewritings and optimizations), we have added the following enhancements: XQUERY: MODULES, FEATURES - Archive Module, archive:write: stream large archives to file - SQL Module: support for more SQL types - Full-Text Module, ft:thesaurus: perform Thesaurus queries - Fulltext, fuzzy search: specify Levenshtein limit - UNROLLLIMIT option: control limit for unrolling loops XQUERY: JAVA BINDINGS - Java objects of unknown type are wrapped into function items - results of constructor calls are returned as function items - the standard package "java.lang." has become optional - array arguments can be specified with the middle dot notation - conversion can be controlled with the WRAPJAVA option - better support for XQuery arrays and maps WEB APPLICATIONS - RESTXQ: Server-Timing HTTP headers are attached to the response For a more comprehensive list of added and updated features, look into our documentation (docs.basex.org) and check out the GitHub issues (github.com/BaseXdb/basex/issues) Have fun, Your BaseX Team

11 43

Fwd: db-rename unexpected behaviour
by Rob Stapper 25 Nov '24

25 Nov '24

I attached a complete demo project. > ---------- Oorspronkelijk Bericht ---------- > Van: Rob Stapper <r.stapper(a)lijbrandt.nl> > Aan: "basex-talk-owner(a)mailman.uni-konstanz.de" <basex-talk-owner(a)mailman.uni-konstanz.de> > Datum: 23-11-2024 11:17 CET > Onderwerp: db-rename unexpected behaviour > > > Hi Christian, > > It's been a while so I thought it was time to find some trouble, which I did. (;-) > > In my database I want the document-names to be consistent with the id-attribute of its root-element. So, a document named: "test.xml" should have a root--element with @id also: "test.xml". > When renaming a with an updated root-element updated document, I find db-rename not working[1]. > However creating a new with an updated root-element updated document under the new name and deleting the origional document does work[2]. > > I would think that if solution[2] works then also solution[1] would work. In both cases all database updating functions follow the same PUL-order. > Am I missing something here or is db-rename misbehaving? > > > [1] > declare %updating function this:rename-document-alt1 (: does NOT work :) > ( $serverName > , $itemName1 > , $itemName2 > ) > { db:put( $serverName > , this:get-element( $serverName > , $itemName1 > ) > => this:update-element-name( $itemName2 > ) > , $itemName1 (: <------------------------ updates org document with renamed root-element :) > ) > , db:rename( $serverName > , $itemName1 > , $itemName2 > ) > } ; > > [2] > declare %updating function this:rename-document-alt2 (: does work :) > ( $serverName > , $itemName1 > , $itemName2 > ) > { db:put( $serverName > , this:get-element( $serverName > , $itemName1 > ) > => this:update-element-name( $itemName2 > ) > , $itemName2 (: <------------------------ creates new document with renamed root-element :) > ) > , db:delete( $serverName > , $itemName1 > ) > } ; > > mvgr. > > Rob Stapper > mvgr. Rob Stapper

2 1

Question: trying to make a higher-order function in a Java module
by Nico Verwer (Rakensi) 20 Nov '24

20 Nov '24

This is a long question, and quite complicated, at least to me. I am trying to make a Java module, which is included in BaseX as a jar-file in `lib/custom`. The module contains one XQuery function: named-entity-recognition($grammar as item(), $options as map(*)?) as function(item()) as node()* This is a higher-order XQuery function that returns another (anonymous) XQuery function. The returned function is a parser (for named entities), similar to what the `invisible-xml` function returns. The relevant part (I think) is the following Java function: @Requires(Permission.NONE) @Deterministic @ContextDependent publicFuncItem namedEntityRecognition(Object grammar, Map<String, String> options) throwsQueryException { // Types of the arguments of the generated function. finalVar[] generatedFunctionParameters= { newVarScope().addNew(newQNm("input"), SeqType.ITEM_O, queryContext, null) }; // Type of the generated function. finalFuncType generatedFunctionType= FuncType.get(SeqType.NODE_ZM, generatedFunctionParameters[0].declType); // The generated function. NamedEntityRecognitionFunction nerf= newNamedEntityRecognitionFunction(grammar, options, generatedFunctionType, queryContext); // Return a function item. returnnewFuncItem(null, nerf, generatedFunctionParameters, AnnList.EMPTY, generatedFunctionType, generatedFunctionParameters.length, null); } The NamedEntityRecognitionFunction has a public Value value(final QueryContext qc) function that does the actual parsing. It starts by getting the value of its (only) parameter: Value inputValue = arg(0).value(qc); // Java The namedEntityRecognition function works fine when I use it like this (XQuery): let $ner-parse := ner:named-entity-recognition($grammar, map{}) return $input => $ner-parse() However, is does not work when the parsing function is put into a declared variable, like declare variable $ner-parse as function(item()) as node()* := ner:named-entity-recognition($grammar,map{}); $input => $ner-parse() In this case, the parameter value obtained by arg(0).value(qc) is null. When I debug this expression, it turns out that the parameter ($input) is not on the stack. The stack (which is qc.stack) is all nulls, and the begin and end indexes of the stack are both 0, meaning that the stack is empty.. This probably means that the query context of a local (let) variable is different from the query context of a global (declare) variable. Maybe I need to indicate that the namedEntityRecognition function returns a higher order function (but how)? The code for this can be found at https://github.com/nverwer/basex-ner-xar. If anyone can shed some light on this, that would be very much appreciated. Best regards, Nico Verwer

2 4

Improper use? Potential bug
by DK Singh 20 Nov '24

20 Nov '24

Hi I am using BaseX version 9.5, i am getting error while doing Query in database below error i am getting 500 Unexpected error: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 9.5 Java: Oracle Corporation, 1.8.0_191 OS: Windows Server 2016, amd64 Stack Trace: java.lang.RuntimeException: Data Access out of bounds: - pre value: 234511809 - table size: 234511809 - first/next pre value: 234511724/234511809 - #total/used pages: 916434/916434 - accessed page: 916433 (916434 > 916433] at org.basex.util.Util.notExpected(Util.java:63) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:474) at org.basex.io.random.TableDiskAccess.read1(TableDiskAccess.java:158) at org.basex.data.Data.kind(Data.java:312) at org.basex.query.value.node.DBNode$2.next(DBNode.java:295) at org.basex.query.value.node.DBNode$2.next(DBNode.java:288) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:38) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:32) at org.basex.query.QueryContext.next(QueryContext.java:352) at org.basex.query... 1567.06 ms ``` I tried to restore database but when any write operation happening then after write operation same issue is occurring Thanks Dharmendra

2 3

Re: [basex-talk] Potential bug in archive:extract-to
by Christian Grün 14 Nov '24

14 Nov '24

Hi (cc to the list), The filenames in your archive may be CP437-encoded, while many newer archives use Unicode. Unfortunately, the standard JDK ZIP library that we use is not smart enough to detect different filename encodings. We could add an $options argument to all Archive Functions that open and create/update archives [1]. For the moment, you will need to… • create archives with Unicode filenames (e.g., with "zip --unicode"), • avoid characters in the 80-FF range from CP437 [2], or • invoke an external unzipper, e.g. via proc:system. Sorry for that, Christian [1] https://github.com/BaseXdb/basex/issues/2344 [2] https://en.wikipedia.org/wiki/Code_page_437 On Thu, Nov 14, 2024 at 12:59 PM Grythe, Thomas Berge < thogry(a)innlandetfylke.no> wrote: > Hi! > > I ran the code you sent me. I then found out the cause of the error. The > reason for the error message 'malput input' is that there was the letter > 'å' in a file name of the zip file (see the attached image). > > When I changed the title "2 klage på vedtak" to "2 klage paa vedtak", the > program worked. > > Is there an easy way to fix this so that the code can handle special > characters like "æ, ø" and "å"? > > Best regards, Thomas. > ------------------------------ > *Fra:* Christian Grün <christian.gruen(a)gmail.com> > *Sendt:* onsdag 13. november 2024 16:11 > *Til:* Grythe, Thomas Berge <thogry(a)innlandetfylke.no> > *Emne:* Re: [basex-talk] Potential bug in archive:extract-to > > > Denne eposten er sendt fra en person utenfor organisasjonen. Ikke klikk på > lenker eller åpne vedlegg før du er sikker på hvem avsender er og at > innholdet er trygt. > > Hi Thomas, > > maybe we can first try to simplify the script. Could you check what the > following code does? > > let $inputpath :="E:\Transfer\vaaler_websak – Kopi\" > for $name in //record//entry/text() > where contains($name, '.bin') > let $input := $inputpath || $name > let $target := $inputpath || substring-before($name, '.') > return archive:extract-to($target, $input) > > If yes, could you possibly send the problematic archive file to me (it > needn’t be shared over the list)? > > Thanks, > Christian > > > On Wed, Nov 13, 2024 at 3:58 PM Grythe, Thomas Berge < > thogry(a)innlandetfylke.no> wrote: > > Hi! > > Thank you for your reply. Attached is the code of my program and also an > image of the extracted files from a zip-file. If I run the program with > this zip -file, I am getting the error message 'malformed input'. > > Can the file -names cause this problem? > > Best regards, Thomas. > ------------------------------ > *Fra:* Christian Grün <christian.gruen(a)gmail.com> > *Sendt:* onsdag 13. november 2024 14:32 > *Til:* Grythe, Thomas Berge <thogry(a)innlandetfylke.no> > *Kopi:* basex-talk(a)mailman.uni-konstanz.de < > basex-talk(a)mailman.uni-konstanz.de> > *Emne:* Re: [basex-talk] Potential bug in archive:extract-to > > > Denne eposten er sendt fra en person utenfor organisasjonen. Ikke klikk på > lenker eller åpne vedlegg før du er sikker på hvem avsender er og at > innholdet er trygt. > > Hi Thomas, > > As Martin indicated, it would be interesting what the xquery:eval function > call does. Could you possibly provide us with a little self-contained > example? > > With BaseX 11 or later, you can simply do: > > archive:extract-to('/path/to/target', '/path/to/archive') > > Best, > Christian > > > On Tue, Nov 12, 2024 at 10:28 AM Grythe, Thomas Berge < > thogry(a)innlandetfylke.no> wrote: > > Hi! > > I am an electronic archivist and I have recently tried to use BaseX to > unzip files in an archive. The two main lines I have used are: > > let $archive := file:read-binary(xquery:eval($filepath-corrected) > return archive:extract-to(xquery:eval($dir_corrected), $archive) > > The variables $dir_corrected and $archive are defined earlier in the > code. But I get the error message 'malformed input off : 10, length : 1' , > indicating that there is an issue with the input data being processed. > > Do you know what can cause this problem? And do you know of a possible > work - around? > > > > Med vennlig hilsen > > *Thomas Berge Grythe* > Rådgiver > Innlandet Fylkesarkiv/IKA Opplandene > > Telefon: 48 99 47 85 > E-post: thogry(a)innlandetfylke.no > > > > > > *Innlandet fylkeskommune* > Telefon: 62 00 08 80 > www.innlandetfylke.no > > > > > >

1 0

10.X Server to produce pretty printed XML results?
by Buddy Kresge 13 Nov '24

13 Nov '24

In BaseX 10.X, is there a way for the DB server to format/pretty-print that resulting XM? It did so by default in the 9.X versions, but as we upgraded to 10.X we are no longer seeing that behavior. Is there something that can be set to turn this on for the server? Thanks in advance! Buddy Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast, a leader in email security and cyber resilience. Mimecast integrates email defenses with brand protection, security awareness training, web security, compliance and other essential capabilities. Mimecast helps protect large and small organizations from malicious activity, human error and technology failure; and to lead the movement toward building a more resilient world. To find out more, visit our website.

2 1

Potential bug in archive:extract-to
by Grythe, Thomas Berge 13 Nov '24

13 Nov '24

Hi! I am an electronic archivist and I have recently tried to use BaseX to unzip files in an archive. The two main lines I have used are: let $archive := file:read-binary(xquery:eval($filepath-corrected) return archive:extract-to(xquery:eval($dir_corrected), $archive) The variables $dir_corrected and $archive are defined earlier in the code. But I get the error message 'malformed input off : 10, length : 1' , indicating that there is an issue with the input data being processed. Do you know what can cause this problem? And do you know of a possible work - around? Med vennlig hilsen Thomas Berge Grythe Rådgiver Innlandet Fylkesarkiv/IKA Opplandene Telefon: 48 99 47 85 E-post: thogry(a)innlandetfylke.no<mailto:thogry@innlandetfylke.no> [cid:cb942b57-4e06-4d32-b529-cd07173c2993] Innlandet fylkeskommune Telefon: 62 00 08 80 www.innlandetfylke.no<https://www.innlandetfylke.no/>

3 2