BaseX-Talk

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9 participants
5241 discussions

Improving the understanding for counting of entries in data groups
by Markus Elfring 19 Apr '22

19 Apr '22

Hello, I constructed the following XML file for another test of the software “BaseX 9.7”. <?xml version="1.0" encoding="UTF-8" standalone="yes"?> <test_data> <info> <id>12</id> <topics> <topic>Demo1</topic> <topic>Demo2</topic> </topics> </info> <info> <id>23</id> <topics> <topic>Demo1</topic> <topic>Demo2</topic> </topics> </info> <info> <id>34</id> <topics> <topic>Test1</topic> <topic>Test2</topic> <topic>Test3</topic> </topics> </info> <info> <id>45</id> <topics> <topic>Test1</topic> <topic>Test2</topic> <topic>Test3</topic> </topics> </info> <info> <id>56</id> <topics> <topic>Test1</topic> <topic>Test2</topic> <topic>Test3</topic> </topics> </info> <info> <id>67</id> <topics> <topic>Probe1</topic> </topics> </info> </test_data> I tried the following XQuery script out accordingly. declare option output:method "csv"; declare option output:csv "header=yes, separator=|"; for $x in //test_data/info group by $topics := string-join($x/topics/topic/data(), "*") let $incidence := count($topics) order by $incidence descending return <csv> <record> <topic_combination>{$topics}</topic_combination> <incidence>{$incidence}</incidence> </record> </csv> Corresponding test result: topic_combination|incidence Demo1*Demo2|1 Test1*Test2*Test3|1 Probe1|1 I would like to see the numbers “2” and “3” instead at the end of two rows for such a data analysis approach. I would appreciate further advices for this use case. Regards, Markus

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CVE-2022-22965: Spring framework 0-day remote code execution vulnerability
by Bülow, Gilles 14 Apr '22

14 Apr '22

Hi all, to exclude issues with BaseX and the topic in this email-subject (CVE-2022-22965: Spring framework 0-day remote code execution vulnerability<https://securityboulevard.com/2022/04/spring4shell-vulnerability-cve-2022-2…>) I would like to know if BaseX could possibly be affected by the problem discussed and if so, when there is an update scheduled which can solve this problem. Thanks in advance for replies Regards Gilles other links: https://www.dfn-cert.de/aktuell/0day-schwachstelle-spring-framework-apache-… https://tanzu.vmware.com/security/cve-2022-22965 -- Dr.-Ing. Gilles Bülow Project Manager Digitalization Production IT DKE German Commission for Electrical, Electronic & Information Technologies Merianstraße 28 63069 Offenbach am Main Phone: +49 69 6308-294 Fax: +49 69 6308-9294 Mobile: +49 170 5769243 gilles.buelow(a)vde.com<mailto:gilles.buelow@vde.com> http://www.dke.de<http://www.dke.de/> [cid:VDE_Email_Abbinder_VDEHiglights2021_aaf1e897-893b-444a-a4a4-f03d3e97ff22.jpg]<https://www.vde.com/highlights> VDE Verband der Elektrotechnik Elektronik Informationstechnik e. V. VDE Association for Electrical, Electronic & Information Technologies Vorstand / Executive Board: Ansgar Hinz (Vorsitzender / CEO); Dr. Beate Mand (stellv. Vorsitzende / CFO) Rechtsform / Legal form: Eingetragener Verein / Registered association Amtsgericht Vereinsregister / Local court register of associations: Frankfurt am Main / Nr. / No: VR 4884 Sitz der Gesellschaft / Association's registered office: Frankfurt am Main, Germany USt-IdNr. / VAT-ID: DE 114 235 367 Datenschutzinformationen<https://www.vde.com/dsh-vde> Data Protection Information<https://www.vde.com/dpn-vde> Der Inhalt dieser E-Mail (sowie der ggf. enthaltenen Anhänge) ist vertraulich und kann darüber hinaus durch besondere Bestimmungen geschützt sein. Sollten Sie nicht der vorgesehene Empfänger sein, bitten wir Sie, den Versender zu informieren und die Nachricht zu löschen. Die Weitergabe sowie Vervielfältigung, Verwertung und Mitteilung seines Inhalts ist nur mit unserer ausdrücklichen Genehmigung gestattet. Alle Rechte vorbehalten, insbesondere für den Fall der Schutzrechtsanmeldung. This e-mail and any attachments are confidential and may also be privileged. If you are not the intended recipient, please immediately notify the sender and delete this message. Its contents are not to be passed on, duplicated, exploited or disclosed without our express permission. All rights reserved, especially the right to apply for protective rights.

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Closing a socketconnection
by Ben Engbers 14 Apr '22

14 Apr '22

Hi, While reading the basexdbc.c code from Alexander Holupirek, I saw that he explicitly sends the 'exit' command to the server before closing the socket. I couldn't find anything on this command in the client server protocol. Is it necessary to send this command to the server? If so what is the effect of sending this command? Ben Engbers

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BaseX Query Performance
by Darryl Pretto 12 Apr '22

12 Apr '22

Hi, I have a BaseX 9.0 instance running on Jetty 9.4.8 on RHEL 7.9. I run many different types of queries on several thousand XML files, about 10gb total source files. These queries take several hours to complete. While I have been able to rewrite queries here and there to optimize them, I am wondering what is the best way to increase BaseX query performance overall. When I check the server CPU and memory neither of them have high utilization. The CPU use varies but mostly is at 12%. The memory use is similar. I have allocated 8gb of memory to Jetty via the Java options settings: -Xms8g -Xmx8g Are there any other resources I can check or change to increase overall query speed? Thanks, Darryl

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Re: [basex-talk] Checking the display of line breaks in the info view
by Markus Elfring 12 Apr '22

12 Apr '22

> What do you mean with space character? I suggest to take a closer look at the differences from a display like “``["line 1 line 2 line 3"]``” in comparison to the mentioned test example. Would you find any other representation more appropriate here? Regards, Markus

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Basexgui Feature suggestion
by Majewski, Steven Dennis (sdm7g) 11 Apr '22

11 Apr '22

It would be handy if there was a way to bind results to current context for additional inspection/investigation/query of results. Currently, it seems, you would have to save results to a file and then create database from that file to make an additional query on results. That binding would be available from editor or input bar. Or perhaps alternatively, it could include an option to base visualizations on results instead of open database — although I’m guessing the former would be easier to implement than the latter. — Steve Majewski

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User group meeting in Prague?
by Imsieke, Gerrit, le-tex 10 Apr '22

10 Apr '22

Fellow BaseX Users! You might have heard that XML Prague 2022 will take place in June. (Unless the then-prevalent Greek letter makes it impossible even in that time of year, of course.) I asked Christian whether the BaseX team will organize a user group meeting after it had not happened for years now. Christian didn’t seem to be very fond of organizing such a meeting. I asked him whether he would be available to present new features, the roadmap, and for a Q&A session if the users themselves organized such a meeting. He agreed, and therefore I hereby ask the list members whether anyone will join me in organizing this. The plan looks as follows: We will apply for one or two 90-minute slots via the CFP process (https://www.xmlprague.cz/cfp/). We don’t need to have a fixed schedule yet by Dec. 20 (end of CFP date as currently announced – it will be extended anyway). Christian was so kind as to create a new repo, user-group, on Github. We will use one or more of its Wiki pages [1] in order to plan the event. The page will eventually evolve into an agenda if you agree. Looking forward to meeting many of you in Prague in June. And another organizing volunteer (or other volunteers), please come forward. Maybe we can also deal with it in the Wiki [2]. Gerrit [1] https://github.com/BaseXdb/user-group/wiki/2022-06-XML-Prague [2] https://github.com/BaseXdb/user-group/wiki/Members

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Checking the display of line breaks in the info view
by Markus Elfring 10 Apr '22

10 Apr '22

Hello, I tried the following XQuery script out with the software “BaseX 9.7”. let $t1 := ``[line 1 line 2]``, $t2 := ``[line 3 line 4]`` return ('"' || $t1 || '"', "---", '"' || $t2 || '"') I observed the following display then in the info view. “… Optimized Query: ("""line 1
line 2""", "---", """line 3
line 4""") Query: let $t1 := ``[line 1 line 2]``, $t2 := ``[line 3 line 4]`` return ('"' || $t1 || '"', "---", '"' || $t2 || '"') …” May I expect that original line breaks will be preserved in the shown query display? Regards, Markus

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html document retrieval runs out of main memory
by Graydon Saunders 08 Apr '22

08 Apr '22

Hello -- I'm using the basexgui to run (minus some identifying actual values defined previously in the query) (: for each path, retrieve the document :) for $remote in $paths let $name as xs:string := file:name($remote) let $target as xs:string := file:resolve-path($name,$targetBase) let $fetched := http:send-request(<http:request method='get' override-media-type='application/octet-stream' username='{$id}' password='{$pass}' />, $remote)[2] let $use as item() := try { html:parse($fetched) } catch * { $fetched } return if ($use instance of document-node()) then file:write($target,$use) else file:write-binary($target,$use) It works, in that I get exactly 100 documents retrieved. (There are unfortunately 140+ documents in the list.) However, the query fails with an "out of main memory" error when using a recent 10.0 beta or 9.7 with Xmx set to 2g. Setting Xmx to 16g with 9.7 produces the same "out of memory" error in the same length of time (about 5 minutes). java -version says 20:27 test % java -version openjdk version "11.0.14.1" 2022-02-08 OpenJDK Runtime Environment 18.9 (build 11.0.14.1+1) OpenJDK 64-Bit Server VM 18.9 (build 11.0.14.1+1, mixed mode, sharing) It's entirely possible I'm going about fetching files off a web server the wrong way; it's possible there's something there that's rather large, but I doubt it's that large. What should I be doing instead? Thanks! Graydon

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I would like to share some code I use for easier RestXQ development
by Omar Siam 08 Apr '22

08 Apr '22

Hi list, I am using BaseX here at my institution a lot as an XML database that provides data using RESTful APIs [1] or serves HTML, JS and CSS with RestXQ which in turn uses HTTP requests to fetch more data [2]. Our main use of BaseX databases is about TEI/XML encoded dictionaries of various sizes. That means we mainly want to search for, get and change small tei:entry parts in larger TEI/XML documents. BaseXwas amazingly stable (compared to some other open source XML database existing today) over the last few years and has a very solid set of built in functions that almost always are sufficient to get a job done. I also like BaseX because I am pretty sure I always could understand why things did not work and what I can do about it even without doing any Java programming (although I saw some weirdness or the other over the last few years). I created or ported some XQuery modules [3][4][6][7] and a containerization environment [5] that make my life easier and I would like to share them here and maybe have a discussion about my implementations and if others can make use of them and how (for example can these [6][7] be expath packages, I see some obstacles in the way RestXQ annotations work). I will try to give an introduction to each of the modules in some separate mails. Finally, I now write to the list as I have a performance problem with a CRUD API I created [1] for the task mentioned above when using it with a dataset that is about 7GB looking at the BaseX databases that make it up. This API uses many of the modules and techniques I came up with so I thought it might be helpful to first talk about those parts. I hope that they may be useful to others as well. I tried to get creative at finding a way to optimize querying the data without having many long lasting global lock situations and having BaseX using indexes as much as possible (this started before the db:enforceindex pragma was introduced and still works for me as expected without it) while still writing the RESTful API in BaseX' implementation of RestXQ. That is why I created [7]. It heavily uses (abuses?) BaseX' jobs module. It allows me to query in smaller BaseX databases in parallel and present them as if they were one big XML DB, which vastly improves performance on update and reindex, to a point. Still there is a file based lock (or is it even class based?) [8], I think the JVM profiling tells me, that severely limits the number of (read) operations that can be done over the API without the user having to wait so long they think the operation failed. This is a multi threading problem as I see it. Or maybe I overlooked something that would solve my problems without all the creative stuff I tried? That probably will be obvious when I have explained the current implentation in more detail which I intend to do in the next few days. [1] https://vle-curation.acdh.oeaw.ac.at/openapi/, https://github.com/acdh-oeaw/vleserver_basex [2] https://vicav.acdh.oeaw.ac.at/, https://github.com/acdh-oeaw/vicav-app [3] https://github.com/acdh-oeaw/openapi4restxq [4] https://github.com/acdh-oeaw/api-problem4restxq [5] https://github.com/simar0at/heroku-buildpack-basex [6] https://github.com/acdh-oeaw/vicav-app/blob/master/http.xqm, https://github.com/acdh-oeaw/openapi4restxq/blob/master_basex/swagger-ui.xqm [7] https://github.com/acdh-oeaw/vleserver_basex/blob/main/vleserver/util.xqm [8] https://github.com/BaseXdb/basex/blob/master/basex-core/src/main/java/org/b… and other read mehods there Best regards -- Mag. Ing. Omar Siam Austrian Center for Digital Humanities and Cultural Heritage Österreichische Akademie der Wissenschaften | Austrian Academy of Sciences Stellvertretende Behindertenvertrauensperson | Deputy representative for disabled persons Wohllebengasse 12-14, 1040 Wien, Österreich | Vienna, Austria T: +43 1 51581-7295 omar.siam(a)oeaw.ac.at |www.oeaw.ac.at/acdh

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