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

Log4j vulnerability CVE-2021-44228
by Marc Coenegracht 13 Dec '21

13 Dec '21

Does Basex (9.x or 8.x) use Log4j in any of its components? If not, should one still worry about the JRE? Regards, Marc

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Changing BaseX GUI preferences is not restored after restart
by Kristian Kankainen 13 Dec '21

13 Dec '21

Hello, I have a strange behaviour with BaseX on MacOS X. I have multiple downloads of BaseX ZIP edition on my mac. They are in different folders. When I start the BaseX GUI from one of these folders (either with opening the basex.jar or running the bin/basexgui script) and inspect the Preferences General tab, I see the Database and Repository paths stating the wrong paths. Trying to open a database yields in a message stating there are no databases and asks whether I want to create one (I choose not to). If I choose the correct paths to the database and repository folders and choose quit from the menu and start the GUI again, then the values have been reverted to the old and wrong ones. Is there a way I can change these paths? Best regards, Kristian Kankainen

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How can I find the document a specific node belongs to?
by Timothée 12 Dec '21

12 Dec '21

Hello, I am trying to build a web application, powered by data served through BaseX. One of the use cases I have is that I want to find all "documents" that match a xquery. I have the following in a RESTXQ file: declare %rest:path("filter_by_author") %rest:GET %rest:query-param("name", "{$name}") function page:by_author($name as xs:string) { let $docs := db:node-id(db:open("sp")//head/meta[@name='author' and contains(lower-case(@content), lower-case(web:decode-url($name)))]) return <response> {for $node_id in distinct-values($docs) return <title value="{$node_id}" />} </response> }; As expected, this does not work because it returns the node IDs. How can I get the "document ID" or "document path" from a node? I understand XQuery does not know about files in a collection (I found the following thread / message in the archives about it: https://mailman.uni-konstanz.de/pipermail/basex-talk/2010-July/000499.html) - but is there a "db" function that would allow me to do it? Thanks for your help, - Tim

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Authentication in server protocol
by Ben Engbers 08 Dec '21

08 Dec '21

Hi Christian, All my previous packages for RBaseX were based on using a blocking socket. Every attempt to use a non-blocking socket failed because I couldn't authenticate. In R each read-operation on a blocking socket uses a timeout of at least 1 second. Consequence was that executing 53 tests on my pacakge took at least 116 seconds on my machine. I finally managed to use a non-blocking socket. Execution of the same tests now take 3.8 seconds. It showed that the crucial needed step was to introduce a sleep/wait between sending the authentication nonce and checking the statusbyte: code <- md5(paste(md5(code), nonce, sep = "")) %>% charToRaw() # send username + code auth <- c(charToRaw(username), as.raw(0x00), code, as.raw(0x00)) writeBin(auth, private$conn) ==> Sys.sleep(.1) Accepted <- readBin(conn, what = "raw", n = 1) ==0 My knowledge of working with sockets is limited so maybe you can answer my question. Does the need of using a sleep means I need to fix a bug in the R code or should I use a setting in BaseX that takes into account the required delay? Ben Engbers

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Re: [basex-talk] BaseX-Talk Digest, Vol 144, Issue 4
by Rob Stapper 08 Dec '21

08 Dec '21

Hi Bachir, I’m afraid I’m not much of a help because the whole docker-sharade is new to me. I did encounter the same problems as you. Can’t say that it is a bug , it is more the combination: OS, docker and BaseX concerning ownership of the mounted docker files. I got it running by logging in as superuser in the docker container as described in previous mail and running: - docker exec -u 0 -it <myrunningcontainer> bash - chown -R basex:basex basex This changed the ownership of the file for me. I also optimized the database-files through the BaseX’s DBA-webapplication. This is all the help I can get you. Have fun, Rob Sent from Mail for Windows From: basex-talk-request(a)mailman.uni-konstanz.de Sent: Wednesday, December 8, 2021 12:00 PM To: basex-talk(a)mailman.uni-konstanz.de Subject: BaseX-Talk Digest, Vol 144, Issue 4 Send BaseX-Talk mailing list submissions to basex-talk(a)mailman.uni-konstanz.de To subscribe or unsubscribe via the World Wide Web, visit https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk or, via email, send a message with subject or body 'help' to basex-talk-request(a)mailman.uni-konstanz.de You can reach the person managing the list at basex-talk-owner(a)mailman.uni-konstanz.de When replying, please edit your Subject line so it is more specific than "Re: Contents of BaseX-Talk digest..." Today's Topics: 1. reply to 2. docker basexhttp wrong owner of /srv/basex/* (scbh) (Rob Stapper) 2. Re: reply to 2. docker basexhttp wrong owner of /srv/basex/* (scbh) (scbh) ---------------------------------------------------------------------- Message: 1 Date: Tue, 7 Dec 2021 12:37:00 +0100 From: Rob Stapper <r.stapper(a)lijbrandt.nl> To: "basex-talk(a)mailman.uni-konstanz.de" <basex-talk(a)mailman.uni-konstanz.de> Subject: [basex-talk] reply to 2. docker basexhttp wrong owner of /srv/basex/* (scbh) Message-ID: <fe337fd0-5751-11ec-aee6-005056998788(a)smtp.kpnmail.nl> Content-Type: text/plain; charset="utf-8" Hi Bach, Login as super-user[1] in your running container to change ownerschip. [1] docker exec -u 0 -it <myrunningcontainer> bash Succes, Rob Sent from Mail for Windows -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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reply to 2. docker basexhttp wrong owner of /srv/basex/* (scbh)
by Rob Stapper 07 Dec '21

07 Dec '21

Hi Bach, Login as super-user[1] in your running container to change ownerschip. [1] docker exec -u 0 -it <myrunningcontainer> bash Succes, Rob Sent from Mail for Windows -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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Didn't know ....
by Marco Lettere 07 Dec '21

07 Dec '21

Hi all, Just because "abc" || () returns "abc", it felt natural to me that <x attr="abc{()}"/> should return <x attr="abc"/> but I get <x attr=""/> instead. This is on a 9.6.1. I can't recall whether this has always been like that thus it's one of my xquery shortcomings or if actually something strange is going on here ... Thanks for clarifications. Marco.

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Output script-element with javascript source code
by Kristian Kankainen 07 Dec '21

07 Dec '21

Hi all, Can I somehow control the serialization of element contents? I want to use Xquery to generate parts of source code for javascript and put the generated code inside a script element on the webpage. Basically this: define function web:display-graph($term) { <script> { string-join(( 'd3.select("#graph").graphviz().renderDot(', "'digraph {a -> b}'", ');' ), out:nl()) } </script> } But it doesn't work as the > character gets replaced with its corresponding HTML entity >. Is there a way to circumvent this behaviour? Best regards Kristian Kankainen

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FW: creating basex jar-file in eclipse
by Rob Stapper 06 Dec '21

06 Dec '21

Hold yours horses. Just managed to build the jar-file with maven outside eclipse. There seems to be an issue with maven in version 2021-09. It is working now. Cheers, Rob Sent from Mail for Windows From: Rob Stapper Sent: Monday, December 6, 2021 4:42 PM To: basex-talk(a)mailman.uni-konstanz.de Subject: creating basex jar-file in eclipse Hi Cristian, I’m trying to build a basex jar file with eclipse under windows 10. But I can’t figure out how. I’m working with EclipseIDE 2021-09 under Windows. I’ve downloaded the BaseX-source from the git-repository. I’ve edited some code. I’m able to run basex with this new piece of functionality within Eclipse. But I have no clue how to build a jar-file in Eclipse. Any suggestions? Thanx in advance. Rob Stapper Sent from Mail for Windows -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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docker basexhttp wrong owner of /srv/basex/*
by scbh 06 Dec '21

06 Dec '21

Hi, I'm new here, but i work since a few years on a vuejs client which is using basex as api. I had a docker environement running very well until recently, but now my basex container is launching correctly any more. In the basex container all folders inside /srv/basex are own by 1000:users instead of basex:basex, so basex gives permissions error. It's like if the line ```chown -R basex /srv``` of docker file is never fired ``` bash-4.4# echo "$PWD" /srv/basex bash-4.4# ls -ls total 12 4 drwxr-sr-x 2 1000 users 4096 Jul 26 11:38 data 4 drwxr-sr-x 2 1000 users 4096 Jul 26 11:38 repo 4 drwxr-sr-x 3 1000 users 4096 Dec 6 13:56 webapp ``` here are the logs of a simple ```docker run --name basexhttp --publish 1984:1984 --publish 8984:8984 basex/basexhttp:latest``` https://figureslibres.io/zerobin/?4e8c389730a39e67#Hzw8dqCkTuVvia8t3YimhLLd… i'm stuck with this problème for days now, please help thank you very much ! ps : the main project is here https://figureslibres.io/gogs/bachir/docker-gdp bach

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creating basex jar-file in eclipse
by Rob Stapper 06 Dec '21

06 Dec '21

Hi Cristian, I’m trying to build a basex jar file with eclipse under windows 10. But I can’t figure out how. I’m working with EclipseIDE 2021-09 under Windows. I’ve downloaded the BaseX-source from the git-repository. I’ve edited some code. I’m able to run basex with this new piece of functionality within Eclipse. But I have no clue how to build a jar-file in Eclipse. Any suggestions? Thanx in advance. Rob Stapper Sent from Mail for Windows -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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R-client RBaseX version 0.9.2
by Ben Engbers 06 Dec '21

06 Dec '21

Hi, I have completely rewritten my R-client for BaseX. This new version can be downloaded from https://cran.r-project.org/web/packages/RBaseX/index.html or https://github.com/BenEngbers/RBaseX. This version should comply more with the server specification. Compared to the previous version, there are (only) a few changes to the interface. Ben Engbers

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RumbleDB
by Ben Pracht 02 Dec '21

02 Dec '21

I don't mean any ill will with this question but value the XQuery opinions of this group. Has any BaseX users tried RumbleDB? I've been intrigued with the scalability OOTB with the Spark. However, I used Spark in a previous job and found pure Spark to be a pain to set up, complex and worst (to me anyway), written in Scala. Also, at a glance it looks like the XQuery library is a bit spartan by comparison to BaseX. Regards, Ben

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Keeping DB in sync with local directory?
by Eliot Kimber 02 Dec '21

02 Dec '21

I’m using BaseX for ad-hoc analysis of content managed in a git repo, so I’m just using the GUI to import the cloned directory into a DB. I know I can write a script to iterate over the docs in the DB to reload them from disk but I’m wondering if that’s already provided for somewhere? I didn’t find anything in the docs but I didn’t spend a huge amount of time looking for it. Thanks, Eliot _____________________________________________ Eliot Kimber Sr Staff Content Engineer O: 512 554 9368 M: 512 554 9368 servicenow.com<https://www.servicenow.com> LinkedIn<https://www.linkedin.com/company/servicenow> | Twitter<https://twitter.com/servicenow> | YouTube<https://www.youtube.com/user/servicenowinc> | Facebook<https://www.facebook.com/servicenow>

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Predicate referring to following-sibling::node()[1]/self::text() incorrectly optimized
by Imsieke, Gerrit, le-tex 02 Dec '21

02 Dec '21

Hi Christian, I wrote a query for a customer who wants to analyze their legacy ISO 12083 math formulas, in this case for detecting multiple subsequent <roman> elements of length >= 3 with only whitespace in between. This is a synthetic test document: <doc> <formula><roman>tan</roman> <roman>tan</roman></formula> <formula><roman>sin</roman> 2 <roman>sin</roman></formula> <formula><roman>cos</roman>3 <roman>cos</roman></formula> </doc> And this is the query I wrote: let $rms := //(formula | dformula)//roman[string-length() gt 2] [ following-sibling::node()[1]/self::text()[not(normalize-space())] ] [ following-sibling::*[1]/self::roman[string-length() gt 2] ]/.., $docs := for $rm-context in $rms let $path := db:path($rm-context) group by $path return <doc path="{$path}">{ $rm-context }</doc> return <result count="{count($rms)}" docs="{count($docs)}">{ $docs }</result> BaseX (up to version 9.6.3) erroneously reports all three <formula> elements as a result, while only the first should be reported. This can be remedied by using parentheses, as in (following-sibling::node())[1]/self::text() and (following-sibling::*)[1]/self::roman. But this is inefficient, and the original query should just work™. In the optimized original query there is following-sibling::text()[fn:position() = 1] and following-sibling::roman[fn:position() = 1]. These are incorrect optimizations of following-sibling::node()[1]/self::text() and following-sibling::*[1]/self::roman. Gerrit -- Gerrit Imsieke Geschäftsführer / Managing Director le-tex publishing services GmbH Weissenfelser Str. 84, 04229 Leipzig, Germany Phone +49 341 355356 110, Fax +49 341 355356 510 gerrit.imsieke(a)le-tex.de, http://www.le-tex.de Registergericht / Commercial Register: Amtsgericht Leipzig Registernummer / Registration Number: HRB 24930 Geschäftsführer / Managing Directors: Gerrit Imsieke, Svea Jelonek, Thomas Schmidt

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Oxygen integration limitations?
by Zimmel, Daniel 02 Dec '21

02 Dec '21

Hi, while the BaseX GUI is really great, there are times I want to use Oxygen (for its features or even for a silly reason like "hey why is there no dark mode in BaseX-GUI I need a dark mode now because I have eye strain!"). According to the wiki, there is no way to get 3.1 support in Oxygen because of the limitation of the XQJ interface? So when I add a scenario with BaseX as transformer I can get Oxygen to respect any BaseX modules (and care for adding else instructions even if they are empty), but in the end it will always give me "invalid syntax, does not pass static validation". Or is there some button I have been missing? Thanks, Daniel

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Attribute index
by Johannes Bauer 01 Dec '21

01 Dec '21

Hi, I want to use the attribute index to access attribute nodes. The following calls in the DBA web interface are working as expected: db:attribute('db', ('6LE007573', '6DC007573'), 'book') db:attribute('db', ('6LE007573', '6DC007573')) They return the attribute nodes with the given values. The attribute index exists and is uptodate. But in the context of a RESTXQ service the first one does not work. It does not return any attribute. The second one works strangely. Any ideas? Regards Johannes

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docker, creating and deploying the dba docker-image
by Rob Stapper 29 Nov '21

29 Nov '21

Hi Christian, I’m fiddling with docker-images and containers now and I’m trying to build an deploy rhe dba-docker axample shipped with the basex-distribution. Docker is running under windows-10. So far I’ve been able to pull, build, deploy images and containers. It all work fine but I got stuck with the dba-example. I’ve mounted ‘c:/Program Files (x86)/basex/data’ on ‘/srv/basex/data’ But I’m confused what directories to mount on: ‘/srv/basex/repo’ and ‘/srv/basex/webapp’? I can’t find the docker-run example for this. Can you shine some more light on the issue. Thanx in advance, Rob Stapper Sent from Mail for Windows -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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encrypting my xquery-files and modules
by Rob Stapper 26 Nov '21

26 Nov '21

Hi Christian, Related to the previous question: Is possible to run encrypted xquery-files? Cheers, Rob Sent from Mail foNNr Windows -- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus

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HTTP server stop working during long time process
by Sebastian Guerrero 25 Nov '21

25 Nov '21

Hi team! I'm enjoying using BaseX more than a year ago, thank you very much for all your help. But then, suddenly, the HTTP server instance stops working while I'm executing a long time duration process: around 4 hours to generate some indexes. ( the process just crash and I have to restart it ). This process was running daily for the last 14 months, without any problem. My doubt is this: *where or how may I get some information about what caused the problem?* Checking files inside */data/.logs* I see only the RESTXQ calls and other minor logs, but nothing to give me a clue about the reason for the server crash. I'm running BaseX 9.4 beta on a *Debian* machine. Here you have my settings: https://imgur.com/ucngBhY Any suggestions?

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Help dealing with slow API responses
by Bridger Dyson-Smith 24 Nov '21

24 Nov '21

Hi all - I have the sneaking suspicion that the answer to this plea for help will be something like, "Use RESTXQ!!" or something similar, but let me describe the problem: I'm pulling data back from an OAI-PMH endpoint that is slow; i.e. response times are ~1/minute. Embarrassingly, I think I've spent several hours trying to figure out if my requests were buggy before I realized that the API endpoint was just *slow* (at least compared to others that I use regularly). I typically use the IntelliJ plugin or the BaseX GUI for the vast majority of my XQuery work, but these requests effectively build up a sequence of responses (as files) and then serialize them all to disk when the requests have finished. When the requests are answered quickly, there's prompt feedback (my script finishes quickly, I can see serialized files, etc), but when the requests are answered slowly, I'm left waiting (and then thinking, "Oh no - I've mistyped the endpoint URL." or something similar). Initially I think I have two requests for guidance: 1. Is there a better way, using the BaseX GUI (or the command line), to get feedback on a querying process like this? Something... asynchronous, or something clever with builtin functions in the `jobs` or `xquery` modules? 2. If this can be addressed relatively directly with RESTXQ, I'm game to (finally) get more comfortable with it, but does anyone have any examples, applications, scripts, etc they would be willing to share? I want to say that several examples and ideas have been shared before here on the list, but I'm having a terrible time finding them. I've attached a simple SSCCE, where the basic idea is: query an API for some data, and get a response like so: <example> <stuff>...</stuff> <resumptionToken>abc123</resumptionToken> </example> then take the text() of the resumptionToken, and resubmit a request to the API, which would return: <example> <stuff>...</stuff> <resumptionToken>def456</resumptionToken> </example> The full responses are written to the temp directory on your system (file:temp-dir()), with a date-stamp name. The endpoint in my attached example has a fairly small response from what I've selected, but the idea would be: how let me (or another user) know that the query is active and running, not hung up or failing? I understand that given the functional nature of XQuery these sorts of things can be a bit more complicated, so I would appreciate any thoughts, opinions, links, etc. Many thanks for your time and trouble. Best, Bridger PS the endpoint in the example doesn't necessarily exhibit the same slow behavior that is the basis for my woes -- for some list readers it may be very fast indeed -- but I felt like it might be apropos to use this particular endpoint for an illustration.

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Module imports are not transitive?
by Andy Bunce 24 Nov '21

24 Nov '21

Hi, "Module imports are not transitive—that is, importing a module provides access only to function and variable declarations contained directly in the imported module. For example, if module A imports module B, and module B imports module C, module A does not have access to the functions and variables declared in module C." https://www.w3.org/TR/xquery-30/#id-module-import I have noticed before that BaseX does not appear to implement this see [1] My case was a conflict in a module that was imported internally within an EXpath Package and the same namespace used as a module in an application. I have just seen another example today where the current behavior was regarded as a "good" feature. I don't remember ever seeing any discussion on this. Is this something that might be implemented at some point? /Andy [1] https://gist.github.com/apb2006/9702104456e5ee2c48f4ff4f9eba5c1b#file-main-…

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Question about ft:normalize
by Tim Thompson 24 Nov '21

24 Nov '21

Hello, I have a question about the BaseX ft:normalize function. What kind of Unicode normalization is performed by this function, and how might it be implemented using standard XPath functions? Thanks in advance! Tim -- Tim A. Thompson (*he, him*) Librarian for Applied Metadata Research Yale University Library www.linkedin.com/in/timathompson timothy.thompson(a)yale.edu

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random items not sorted
by Tom De Herdt 24 Nov '21

24 Nov '21

Hi, While doing some tests, I noticed an unexpected query result in Basex 9.6.3 (on Windows 10). This query: let $ids := for $i in 1 to 10 return random:uuid() for $id in $ids order by $id return $id ... returns 10 UUIDs, but they are /not/ sorted. Information from the Info pane in the GUI: Compiling: - rewrite range expression to range sequence: (1 to 10) - rewrite simple map to util:replicate(items,count[,multiple]): (1 to 10) ! random:uuid() -> util:replicate(random:uuid(), 10, true()) - inline for $i_1 in (1 to 10) - simplify FLWOR expression: util:replicate(random:uuid(), 10, true()) - inline let $ids_0 := util:replicate(random:uuid(), 10, true()) - rewrite fn:sort(items[,collation[,function]]) to util:replicate(items,count[,multiple]): sort(util:replicate(random:uuid(), 10, true())) -> util:replicate(random:uuid(), 10, true()) - inline for $id_2 in util:replicate(random:uuid(), 10, true()) - simplify FLWOR expression: util:replicate(random:uuid(), 10, true()) Optimized Query: util:replicate(random:uuid(), 10, true()) In Basex 9.3.2 (on another Windows machine) items are sorted alphabetically, as I would expect them to be – but I may be overlooking something. Any ideas? Thanks, Tom De Herdt

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how to redirect http error 404 to root
by Günter Dunz-Wolff 16 Nov '21

16 Nov '21

Hi all, how can I handle it, that in my RESTXQ-App every request, where the response is an 404-error, will be redirected to the index-page / Thanks in advance Guenter

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