BaseX-Talk January 2024

basex-talk@mailman.uni-konstanz.de

19 participants
20 discussions

GUI feature request: paste into search boxes
by Thompson, Timothy 17 Jan '24

17 Jan '24

Hello, In the BaseX GUI, it’s not possible (as far as I can tell) to paste a copied value into search boxes. Not being able to do so can be inconvenient, for example, when searching for a string like a UUID in result output, etc. Is lack of support for pasting intentional, or am I missing something? Thanks in advance, Tim -- Tim A. Thompson (he, him) Librarian for Applied Metadata Research Yale University Library www.linkedin.com/in/timathompson<http://www.linkedin.com/in/timathompson>

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Re: [basex-talk] Corrupt data base not recognized by inspect
by Christian Grün 15 Jan '24

15 Jan '24

Dear Jürgen, The safest/easiest option for now may be to consider a database corrupt if the output does not contain the string “No inconsistencies found”. For more details, feel free to check out the source code [1]. Hope this helps, Christian [1] https://github.com/BaseXdb/basex/blob/main/basex-core/src/main/java/org/bas… On Mon, Jan 15, 2024 at 2:44 PM Jürgen Schwenk Büro < juergen.schwenk(a)gruendler.de> wrote: > Dear Christian, > > thanks a lot for your work. I tried it out and got the answer "Access to > storage failed (java.lang.RuntimeException: java.io.EOFException)." That is > fine. > > One more, perhaps last :-), question: To avoid a crash when opening > database in our application I send the "inspect" command via C-Adapter > basexdbc.c and check the resulting string. This is because the query > command itself is OK, so I have to check the content. Up to now I check the > resulting string if it contains either "Warning: Database is inconsistent." > or "RuntimeException". I hope, these are the only possible failure > responses. Or are there any other? > > Regards, > > Jürgen > Am 15.01.2024 um 11:04 schrieb Christian Grün: > > Dear Jürgen, > > It turned out that the invocation of the INSPECT command raised an > exception that was not caught by the command itself, but was only sent to > stderr. We’ve revised this with the latest snapshot [1]. > > Best (and good luck for your power connection in 2024) > Christian > > [1] https://files.basex.org/releases/latest/ > > > > On Thu, Jan 11, 2024 at 6:07 PM Jürgen Schwenk Büro < > juergen.schwenk(a)gruendler.de> wrote: > >> Hello, >> >> in our application we "produced" a corrupt data base caused by a power >> fail. On restart we check data base using the "inspect" command to detect >> failures, creating new empty data base if found one. The attached data base >> seems OK using "inspect", but accessing the data base we get an exception. >> Perhaps this may help to make "inspect" more reliable. >> >> Thanks a lot, >> >> Jürgen Schwenk >> >> >> Client output: >> >> > list >> Name Resources Size Input Path >> >> ----------------------------------------------------------------------------------- >> VentilutionOnlineDataBaseCorrupt 1 1170 >> VentilutionOnlineDataBase.xml >> >> 1 database(s). >> >> > open VentilutionOnlineDataBaseCorrupt >> Database 'VentilutionOnlineDataBaseCorrupt' was opened in 0.03 ms. >> >> > inspect >> Checking main table (152 nodes): >> - 0 invalid node kinds >> - 0 invalid parent references >> - 0 wrong parent/descendant relationships >> No inconsistencies found. >> 'VentilutionOnlineDataBaseCorrupt' inspected in 0.06 ms. >> >> > xquery //* >> Improper use? Potential bug? Your feedback is welcome: >> Contact: basex-talk(a)mailman.uni-konstanz.de >> Version: BaseX 10.1 >> Java: Eclipse Adoptium, 17.0.4 >> OS: Windows 10, amd64 >> Stack Trace: >> java.lang.RuntimeException: Data Access out of bounds: >> - pre value: 152 >> - table size: 152 >> - first/next pre value: 0/152 >> - #total/used pages: 1/1 >> - accessed page: 0 (1 > 0] >> at org.basex.util.Util.notExpected(Util.java:64) >> at >> org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:477) >> 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$6.next(DBNode.java:402) >> at org.basex.query.value.node.DBNode$6.next(DBNode.java:1) >> at org.basex.query.expr.path.IterStep$1.next(IterStep.java:38) >> at org.basex.query.expr.path.IterStep$1.next(IterStep.java:1) >> at org.basex.query.QueryContext.next(QueryContext.java:375) >> at org.basex.query.expr.path.IterPath$1.next(IterPath.java:48) >> at org.basex.query.scope.MainModule$1.next(MainModule.java:55) >> at org.basex.core.cmd.AQuery.run(AQuery.java:88) >> at org.basex.core.Command.run(Command.java:233) >> at org.basex.core.Command.execute(Command.java:93) >> at org.basex.server.ClientListener.run(ClientListener.java:141) >> >> Query "softwareProjectVentilution" executed in 0.31 ms. >> >> >> -- >> >> >> -- >> >> Jürgen Schwenk >> - R&D Engineer - >> >> >> >> >> Gründler GmbH Tel: +49 (0)7441 40761-14 >> Jaspisstrasse 23 Fax: +49 (0)7441 40761-99 >> 72250 Freudenstadt E-Mail: juergen.schwenk(a)gruendler.de >> -- >> >> >> -- >> >> Jürgen Schwenk >> - R&D Engineer - >> >> >> >> >> Gründler GmbH Tel: +49 (0)7441 40761-14 >> Jaspisstrasse 23 Fax: +49 (0)7441 40761-99 >> 72250 Freudenstadt E-Mail: juergen.schwenk(a)gruendler.de >> > -- > > > -- > > Jürgen Schwenk > - R&D Engineer - > > > > > Gründler GmbH Tel: +49 (0)7441 40761-14 > Jaspisstrasse 23 Fax: +49 (0)7441 40761-99 > 72250 Freudenstadt E-Mail: juergen.schwenk(a)gruendler.de >

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Processing stack traces in XQuery code
by Omar Siam 15 Jan '24

15 Jan '24

Hi, Until 10.6 one could find the stack trace of an error in $err:additional. This feature is now gone from BaseX and the documentation. I made my life much easier with reporting stack traces on errors in RestXQ endpoints. Now I don't see how to get that information anymore. Any advice how to get this functionality back? 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 Bäckerstraße 13, 1010 Wien, Österreich | Vienna, Austria T: +43 1 51581-7295 omar.siam(a)oeaw.ac.at | www.oeaw.ac.at/acdh

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Corrupt data base not recognized by inspect
by Jürgen Schwenk Büro 15 Jan '24

15 Jan '24

Hello, in our application we "produced" a corrupt data base caused by a power fail. On restart we check data base using the "inspect" command to detect failures, creating new empty data base if found one. The attached data base seems OK using "inspect", but accessing the data base we get an exception. Perhaps this may help to make "inspect" more reliable. Thanks a lot, Jürgen Schwenk Client output: > list Name Resources Size Input Path ----------------------------------------------------------------------------------- VentilutionOnlineDataBaseCorrupt 1 1170 VentilutionOnlineDataBase.xml 1 database(s). > open VentilutionOnlineDataBaseCorrupt Database 'VentilutionOnlineDataBaseCorrupt' was opened in 0.03 ms. > inspect Checking main table (152 nodes): - 0 invalid node kinds - 0 invalid parent references - 0 wrong parent/descendant relationships No inconsistencies found. 'VentilutionOnlineDataBaseCorrupt' inspected in 0.06 ms. > xquery //* Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk(a)mailman.uni-konstanz.de Version: BaseX 10.1 Java: Eclipse Adoptium, 17.0.4 OS: Windows 10, amd64 Stack Trace: java.lang.RuntimeException: Data Access out of bounds: - pre value: 152 - table size: 152 - first/next pre value: 0/152 - #total/used pages: 1/1 - accessed page: 0 (1 > 0] at org.basex.util.Util.notExpected(Util.java:64) at org.basex.io.random.TableDiskAccess.cursor(TableDiskAccess.java:477) 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$6.next(DBNode.java:402) at org.basex.query.value.node.DBNode$6.next(DBNode.java:1) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:38) at org.basex.query.expr.path.IterStep$1.next(IterStep.java:1) at org.basex.query.QueryContext.next(QueryContext.java:375) at org.basex.query.expr.path.IterPath$1.next(IterPath.java:48) at org.basex.query.scope.MainModule$1.next(MainModule.java:55) at org.basex.core.cmd.AQuery.run(AQuery.java:88) at org.basex.core.Command.run(Command.java:233) at org.basex.core.Command.execute(Command.java:93) at org.basex.server.ClientListener.run(ClientListener.java:141) Query "softwareProjectVentilution" executed in 0.31 ms. -- -- Jürgen Schwenk - R&D Engineer - Gründler GmbH Tel: +49 (0)7441 40761-14 Jaspisstrasse 23 Fax: +49 (0)7441 40761-99 72250 Freudenstadt E-Mail: juergen.schwenk(a)gruendler.de -- -- Jürgen Schwenk - R&D Engineer - Gründler GmbH Tel: +49 (0)7441 40761-14 Jaspisstrasse 23 Fax: +49 (0)7441 40761-99 72250 Freudenstadt E-Mail: juergen.schwenk(a)gruendler.de

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Improper use error
by DK Singh 12 Jan '24

12 Jan '24

Hi i am executing the simple command uri-collection('SYS_CONTENT_METADATA') and i am getting the below error: 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_151 OS: Windows Server 2012 R2, amd64 Stack Trace: java.lang.ArrayIndexOutOfBoundsException Can you please suggest how to resolve this issue? Thanks Dharmendra Kumar Singh

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basexgui is crashing for me ...
by Jonathan Robie 10 Jan '24

10 Jan '24

Basexgui has been crashing for me. I thought my environment might be messed up, so I uninstalled brew, reinstalled it, and checked my environment. Then I ran basexgui, and got another crash. % basexgui > 2024-01-09 15:09:58.791 java[18502:5023580] WARNING: Secure coding is > automatically enabled for restorable state! However, not on all supported > macOS versions of this application. Opt-in to secure coding explicitly by > implementing > NSApplicationDelegate.applicationSupportsSecureRestorableState:. > # > # A fatal error has been detected by the Java Runtime Environment: > # > # SIGILL (0x4) at pc=0x00007ff80e07cb73, pid=18502, tid=259 > # > # JRE version: OpenJDK Runtime Environment Homebrew (21.0.1) (build 21.0.1) > # Java VM: OpenJDK 64-Bit Server VM Homebrew (21.0.1, mixed mode, sharing, > tiered, compressed oops, compressed class ptrs, g1 gc, bsd-amd64) > # Problematic frame: > # C [AppKit+0xc8fb73] _NSCarbonMenuCrashIfNeeded+0x258 > # > # Core dump will be written. Default location: /cores/core.18502 > # > # An error report file with more information is saved as: > # /Users/jonathan/github/Clear/hs_err_pid18502.log > # > # If you would like to submit a bug report, please visit: > # https://github.com/Homebrew/homebrew-core/issues > # The crash happened outside the Java Virtual Machine in native code. > # See problematic frame for where to report the bug. > # > zsh: abort basexgui > What should I do? Jonathan

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How to invalidate XSD cache without stopping and restarting Jetty Web server?
by ykhabins＠bellsouth.net 10 Jan '24

10 Jan '24

Hello, We are using BaseX 10.8 beta for XML files validation against the XSD. Our XSDs are conformant with the XSD 1.1 that why all necessary Apache Xerces 12.2.2 files are in the lib/custom directory. On top of that we are using Jetty Web server by launching c:\Program Files (x86)\BaseX\bin\basexhttp.bat Eventually, our REST HTTP call is as follow: string REQUESTURL = $"http://{HOST}:{PORT}/rest?run={XQUERY}&$xml={xmlFile}&$xsd={xsdFile}"; Our XQuery validation call is as follows: let $result := validate:xsd-report($xml, $xsd, map { 'http://apache.org/xml/features/validation/cta-full-xpath-checking': true(), 'cache': true() }) Everything is working as expected. :) Here is a question. =================== The validate:xsd-report(...) call is using caching via the 'cache': true() parameter. We are updating XSDs from time to time. Unfortunately, the validation is not picking up a new version of the XSD file on the file system. It is unaware that the *.xsd file was updated. It is still using an old XSD version that is cached in memory. Is it possible to invalidate the XSD cache without stopping and restarting Jetty Web server? IMHO, it is too intrusive. Maybe you can introduce a manual command for XSD cache invalidation in the BaseX GUI? Or some other mechanism to handle the scenario. Regards, Yitzhak Khabinsky

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fiddle certificate error
by Martin Honnen 09 Jan '24

09 Jan '24

Hi, trying to access https://bxfiddle.cloud.basexgmbh.de/ Chrome tells me Your connection is not private Attackers might be trying to steal your information from bxfiddle.cloud.basexgmbh.de (for example, passwords, messages, or credit cards). Learn more NET::ERR_CERT_DATE_INVALID bxfiddle.cloud.basexgmbh.de normally uses encryption to protect your information. When Chrome tried to connect to bxfiddle.cloud.basexgmbh.de this time, the website sent back unusual and incorrect credentials. This may happen when an attacker is trying to pretend to be bxfiddle.cloud.basexgmbh.de, or a Wi-Fi sign-in screen has interrupted the connection. Your information is still secure because Chrome stopped the connection before any data was exchanged. You cannot visit bxfiddle.cloud.basexgmbh.de right now because the website uses HSTS. Network errors and attacks are usually temporary, so this page will probably work later. It seems the certificate expired on Jan 2nd of this (new) year. Anyone can fix this?

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Creating backups manually
by Matthew Dziuban 04 Jan '24

04 Jan '24

Hi all, I'm interested in creating backups manually so I can use a different compression algorithm. Based on the source code[1], it looks like backups are just created by adding each file (excluding upd.basex) in the database directory to a .zip file, so I could do the same using tar and my compression algorithm of choice. Is my understanding correct or am I missing some other logic? Thanks, Matt [1] https://github.com/BaseXdb/basex/blob/main/basex-core/src/main/java/org/bas…

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Help - Regarding Performance Improvement
by Deepak Dinakara 03 Jan '24

03 Jan '24

Hi, Reaching out to get suggestions on improving performance. Using basex to store and analyze around 350,000 to 500,000 XMLs. Size of each XML varies between a few KBs to 5MB. Each day around 10k XMLs get added/patched. I have the following queries 1) What is the optimal size or number of documents in a DB? Earlier I had 1 DB with different collections but inserts were too slow, took more than 30s just to replace a document. So split it up by some category to have around 30 DBs. Inserts are fine but again if there are too many documents in a category, patching that DB slows and querying across all DBs also gets slowed down. Any optimal number for DBs? Can I create many DBs like 1 for every 10K XMLs? I read through https://www.mail-archive.com/basex-talk@mailman.uni-konstanz.de/msg06310.ht…, having 100s of DBs cause query performance degradation? Is there any better solution? 2) Query performance has degraded with more documents in a DB. I also noticed that with/without token/attribute index, there is not much difference to query performance (they are just XML attribute queries). "Optimize" flag after inserts to recreate the index takes too much time and memory. I am not running it now since I didn't find significant improvement with/without index with my tests. Any suggestions for improving this? 3) Is it possible to just run queries against specific XMLs? I will have a pre-filter based on user selection and queries need to be run against only those XMLs. There are a number of filters users can apply and every time it can result in a different set of XMLs against which analysis has to be performed (Hence not feasible to create so many collections). Right now, I am querying against all XMLs even though I am interested only in a subset of XMLs and doing post filtering. I did go through https://mailman.uni-konstanz.de/pipermail/basex-talk/2010-July/000495.html, but again having a regex to include all the interested file paths(sometimes entire set of documents) will slow it down. Thank you, Deepak

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BaseX-Talk January 2024