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

automatic encoding
by Philippe Pons 06 May '21

06 May '21

Hi, This may be more of an xquery question than a BaseX question, but I'm trying to ask it here anyway. I can of course remove it if necessary. However, I have an XML document with a sequence of paragraphs and a CSV spreadsheet (examples 1 and 2 below). The csv gives a list of terms in the first column (present in the XML), and the name of the index in which we want to integrate this term in the second. I use BaseX and XQuery a lot, and I'm looking for a way to automatically encode the terms in the TEI file without success so far. I've tried to rely on the ft:mark function to achieve this, but it doesn't completely fit my need. Maybe you could give me some advice to get the result I'm looking for (example 3)? With kind regards, Philippe Exemple 1, XML : <div> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quis nisl ultrices, viverra erat id, volutpat magna. Mauris cursus tellus non nisi commodo faucibus. Pellentesque condimentum feugiat sem quis interdum. Vestibulum tempus lectus a augue viverra molestie. Ut condimentum vehicula nisi, vel tincidunt mauris accumsan malesuada. Aliquam quis facilisis justo. Proin convallis eget enim vel eleifend. Nullam faucibus ultricies diam, iaculis feugiat odio condimentum non. Cras vitae dignissim lectus, in pellentesque est. Vivamus pharetra semper magna, sed sodales dui porttitor in. Pellentesque eget sodales quam, et dignissim velit. Aliquam vulputate pulvinar cursus. Phasellus commodo nibh a diam imperdiet cursus. Maecenas dui orci, aliquet quis porttitor non, auctor fringilla leo.</p> <p>Vestibulum venenatis velit in imperdiet iaculis. Vivamus consectetur mollis augue, acefficitur nisl ultrices eu. Cras commodo eleifend mi a luctus. Vivamus sed odio maximus, laoreet mauris quis, tincidunt lorem. Duis non elementum tortor. Nam hendrerit dolor ac interdum condimentum. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia curae; Aenean vitae massa commodo, condimentum quam in, malesuada massa. Maecenas finibus convallis erat at aliquet. Aliquam erat volutpat. Praesent ligula nisi, tempus id arcu id, scelerisque condimentum dolor. Sed quis tincidunt sem. Nulla ac ex hendrerit, ullamcorper leo et, sodales nulla.</p> </div> Exemple 2, CSV : Vestibulum, placeName Cras, persName condimentum, persName Exemple 3, Results : <div> <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quis nisl ultrices, viverra erat id, volutpat magna. Mauris cursus tellus non nisi commodo faucibus. Pellentesque <persName>condimentum</persName>feugiat sem quis interdum. <placeName>Vestibulum</placeName>tempus lectus a augue viverra molestie. Ut <persName>condimentum</persName>vehicula nisi, vel tincidunt mauris accumsan malesuada. Aliquam quis facilisis justo. Proin convallis eget enim vel eleifend. Nullam faucibus ultricies diam, iaculis feugiat odio <persName>condimentum</persName>non. <persName>Cras</persName>vitae dignissim lectus, in pellentesque est. Vivamus pharetra semper magna, sed sodales dui porttitor in. Pellentesque eget sodales quam, et dignissim velit. Aliquam vulputate pulvinar cursus. Phasellus commodo nibh a diam imperdiet cursus. Maecenas dui orci, aliquet quis porttitor non, auctor fringilla leo.</p> <p><placeName>Vestibulum</placeName>venenatis velit in imperdiet iaculis. Vivamus consectetur mollis augue, ac efficitur nisl ultrices eu.<persName>Cras</persName>commodo eleifend mi a luctus. Vivamus sed odio maximus, laoreet mauris quis, tincidunt lorem. Duis non elementum tortor. Nam hendrerit dolor ac interdum <persName>condimentum</persName>. <placeName>Vestibulum</placeName>ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia curae; Aenean vitae massa commodo, <persName>condimentum</persName>quam in, malesuada massa. Maecenas finibus convallis erat at aliquet. Aliquam erat volutpat. Praesent ligula nisi, tempus id arcu id, scelerisque <persName>condimentum</persName>dolor. Sed quis tincidunt sem. Nulla ac ex hendrerit, ullamcorper leo et, sodales nulla.</p> </div>

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Clarification on registering a job service
by Zimmel, Daniel 06 May '21

06 May '21

Hi, can someone clarify on the following behaviour? The docs say: "Job services can be updated: If a new job is registered, and if there is already a job with the same id, the old entry will be replaced." https://docs.basex.org/wiki/Jobs_Module#Services So when I try to update an existing job service with the following query, I get an unexpected error "Job id already exists: myquery.": jobs:eval( xs:anyURI('myquery.xq'), (), map { 'id':'myquery', 'start':'19:00:00', 'interval':'P1D', 'service': true() } ) Am I reading the documentation wrong? Thanks Daniel

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Re: [basex-talk] feature request: EXI support
by Christian Grün 06 May '21

06 May '21

Hi Mikhail (cc to the list), If your queries generate hundreds of Megabytes, you could check if the full result is actually required. If yes, you may need to check which step is responsible for letting you wait: Is it the pure transmission over the network, is it the evaluation time or is it the client that processes the query result? If it’s the data traffic, and if you use Jetty as BaseX web server, you could enable GZIP compression [1]. If you use another web server, or if your architecture is more complex, you could install a proxy in between that takes care of compressing the transferred data. Best, Christian [1] https://docs.basex.org/wiki/Options#GZIP On Wed, May 5, 2021 at 7:17 AM Mikhail Kuznetsov <mikekuznetsov(a)mail.ru> wrote: > > Hi, Christian. > > I am trying to build a central server for processing multiple QXuery tasks. In some cases the output will be used by a BI system for visualization. For example: > > the BaseX server will accumulate a lot of "raw" xml files collected from multiple entities, say their tax returns > this is great that I can have the flexibility to write new queries and adapt existing ones without modifying the underlying data (which would be the case if I had chosen an SQL database for storage) > a Power BI server gets connected to BaseX through RESTful API and retrieves two kinds of data: individual by entity and benchmark based on the average. > > Some queries may result in hundreds of Mb of xml data. My BaseX server is hosted in AWS, while the Power BI server is located internally. The communication takes too much time, which is a show stopper for me. I am looking for ways to optimize the data transfer. The BaseX server itself is perfect, many thanks for the great job. > > Regards, > Mikhail > > > Среда, 5 мая 2021, 2:45 +03:00 от Christian Grün <christian.gruen(a)gmail.com>: > > Hi Mikhail, > > > Hi there. I have recently been looking at ways to improve the efficiency of my XQuery server and have come across Efficient XML Interchange (EXI) Format. Is there a way that BaseX could support encoding/ decoding for this format? > > The internal storage of XML documents in BaseX differs quite a lot > from the original and verbose textual representation (for which EXI > provides improvements). > > What kind of performance penalties did you encounter so far? > > Best, > Christian > > > On Tue, May 4, 2021 at 10:34 PM Mikhail Kuznetsov <mikekuznetsov(a)mail.ru> wrote: > > > > > > Thanks. > > Mikhail > > > > -- > Mikhail Kuznetsov >

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feature request: EXI support
by Mikhail Kuznetsov 05 May '21

05 May '21

Hi there. I have recently been looking at ways to improve the efficiency of my XQuery server and have come across Efficient XML Interchange (EXI) Format. Is there a way that BaseX could support encoding/ decoding for this format? Thanks. Mikhail

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Re: [basex-talk] Make use of external Identity Management for BaseX
by Adam Law 04 May '21

04 May '21

If Rob isn't interested, I certain am... Yes please share >>We have also a RestXQ module that in combination with basex:perm annotations protects access to a GUI implementing the Oauth2 Code-grant flow. If Rob is interested we could share. Many thanks for sharing https://code-repo.d4science.org/gCubeSystem/d4science-keycloak-themes/src/b… This is a bit forward of me, but would you consider changing the license away from European Union Public Licence which appears to be 'copyleft' to say BSD 3-Clause, MIT, ... Adam On Fri, Apr 30, 2021 at 6:00 PM <basex-talk-request(a)mailman.uni-konstanz.de> wrote: > 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. Make use of external Identity Management for BaseX (Rob) > 2. Re: Reloading jars on a running http server. (Reece Dunn) > 3. Getting profile information in server responses. (Reece Dunn) > 4. Re: Make use of external Identity Management for BaseX > (Christian Gr?n) > 5. Re: Reloading jars on a running http server. (Christian Gr?n) > 6. Re: Getting profile information in server responses. > (Christian Gr?n) > 7. Re: Reloading jars on a running http server. (Reece Dunn) > 8. Re: Reloading jars on a running http server. (Christian Gr?n) > 9. Re: Make use of external Identity Management for BaseX > (Marco Lettere) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 29 Apr 2021 15:54:08 +0200 > From: Rob <private(a)tjalma.com> > To: BaseX <basex-talk(a)mailman.uni-konstanz.de> > Subject: [basex-talk] Make use of external Identity Management for > BaseX > Message-ID: <39036EF3-E67D-470D-B2F4-E6FBFFDF40E6(a)tjalma.com> > Content-Type: text/plain; charset=utf-8 > > Hi, > > I have a question. > Can BaseX make use of an Identity Management application like Keycloak for > Users? > > I can?t find anything about it :) > > With kind regards, > Rob Tjalma > > ------------------------------ > > Message: 2 > Date: Thu, 29 Apr 2021 20:48:09 +0100 > From: Reece Dunn <msclrhd(a)googlemail.com> > To: Christian Gr?n <christian.gruen(a)gmail.com> > Cc: BaseX <basex-talk(a)mailman.uni-konstanz.de> > Subject: Re: [basex-talk] Reloading jars on a running http server. > Message-ID: > <CAGdtn24Qdgbe3= > nebYA1je4hCrZVAgi_sercCRxsTxmZcWcAxQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Christian, > > Thanks for the response. Unfortunately, I've not been able to get the > reloading working. > > Kind regards, > Reece > > On Wed, 21 Apr 2021 at 18:49, Christian Gr?n <christian.gruen(a)gmail.com> > wrote: > > > Hi Reece, > > > > If you install your Java code as JAR file in the repository [1], the > > code will be loaded and unloaded every time when your query is > > executed. If you get an error message? > > > > java.lang.reflect.InaccessibleObjectException: Unable to make field > > private final jdk.internal.loader.URLClassPath > > java.net.URLClassLoader.ucp accessible: module java.base does not > > "opens java.net" to unnamed module @79e2c065 > > > > ?unloading fails [2], as you?re probably using a more recent version > > of the JDK, which restricts reflective access to internal variables. > > You can get around this by adding Java flags at startup time: > > > > --add-opens java.base/java.net=ALL-UNNAMED > > --add-opens java.base/jdk.internal.loader=ALL-UNNAMED > > > > Maybe there are better solutions to unload JAR files today. > > Suggestions are welcome! > > > > Hope this helps, > > Christian > > > > [1] https://docs.basex.org/wiki/Repository#Java > > [2] > > > https://github.com/BaseXdb/basex/blob/master/basex-core/src/main/java/org/b… > > > > > > > > On Tue, Apr 20, 2021 at 6:44 PM Reece Dunn <msclrhd(a)googlemail.com> > wrote: > > > > > > Hi all, > > > > > > I'm working on a Java class that I'm importing into an XQuery, so I can > > do additional processing on the data that isn't easily expressible in > > XQuery (or XSLT). In order to get BaseX to pick up a modified version of > > the jar file I'm building, I'm restarting the BaseX http server. > > > > > > This makes it slower to turn around testing the changes. Is there a > > better way of doing this? > > > > > > Kind regards, > > > Reece > > >

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Re: [basex-talk] BaseX-Talk Digest, Vol 137, Issue 3
by Adam Law 03 May '21

03 May '21

Thanks Marco, I understand. As an aside for others, a GO edge router with BaseX is another option - say https://github.com/thomseddon/traefik-forward-auth. OIDC, ACME and SSL are all built in. BaseX can trust / check the forwarded cookie as part of BaseX permissions checking. https://docs.basex.org/wiki/Permissions Adam On Mon, May 3, 2021 at 6:00 PM <basex-talk-request(a)mailman.uni-konstanz.de> wrote: > 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. Re: Make use of external Identity Management for BaseX > (Marco Lettere) > 2. Re: Make use of external Identity Management for BaseX > (Marco Lettere) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 May 2021 09:20:45 +0200 > From: Marco Lettere <m.lettere(a)gmail.com> > To: basex-talk(a)mailman.uni-konstanz.de > Subject: Re: [basex-talk] Make use of external Identity Management for > BaseX > Message-ID: <0978b86f-a884-052c-dd2c-0eb18291f7f5(a)gmail.com> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi Adam, > sorry but licensing terms are out of our choice. > We've developed that code in the framework of EU H2020 funded projects > [1,2] thus we have to adhere to the policies of the Institution we > cooperate with (Italian Council of Research). > > Anyway as I told this code is more a proof of concept for administrative > activities related to batch creation of clients ... Feel free to use and > adapt the code as you prefer. > > Regards, > Marco. > > [1] https://www.blue-cloud.org/ > [2] http://project.sobigdata.eu/ > > On 01/05/21 05:29, Adam Law wrote: > > If Rob isn't interested, I certain am... Yes please share > > > > >>We have also a RestXQ module that in combination with basex:perm > > annotations protects access to a GUI implementing the Oauth2 Code-grant > > flow. If Rob is interested we could share. > > > > Many thanks for sharing > > > https://code-repo.d4science.org/gCubeSystem/d4science-keycloak-themes/src/b… > > < > https://code-repo.d4science.org/gCubeSystem/d4science-keycloak-themes/src/b… > > > > > > This is a bit forward of me, but would you consider changing?the > > license away from European Union Public Licence which appears to be > > 'copyleft' to say BSD 3-Clause, MIT, ... > > > > Adam > > > > On Fri, Apr 30, 2021 at 6:00 PM > > <basex-talk-request(a)mailman.uni-konstanz.de > > <mailto:basex-talk-request@mailman.uni-konstanz.de>> wrote: > > > > Send BaseX-Talk mailing list submissions to > > basex-talk(a)mailman.uni-konstanz.de > > <mailto:basex-talk@mailman.uni-konstanz.de> > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mailman.uni-konstanz.de/mailman/listinfo/basex-talk > > <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 > > <mailto:basex-talk-request@mailman.uni-konstanz.de> > > > > You can reach the person managing the list at > > basex-talk-owner(a)mailman.uni-konstanz.de > > <mailto:basex-talk-owner@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. Make use of external Identity Management for BaseX (Rob) > > ? ?2. Re: Reloading jars on a running http server. (Reece Dunn) > > ? ?3. Getting profile information in server responses. (Reece Dunn) > > ? ?4. Re: Make use of external Identity Management for BaseX > > ? ? ? (Christian Gr?n) > > ? ?5. Re: Reloading jars on a running http server. (Christian Gr?n) > > ? ?6. Re: Getting profile information in server responses. > > ? ? ? (Christian Gr?n) > > ? ?7. Re: Reloading jars on a running http server. (Reece Dunn) > > ? ?8. Re: Reloading jars on a running http server. (Christian Gr?n) > > ? ?9. Re: Make use of external Identity Management for BaseX > > ? ? ? (Marco Lettere) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 29 Apr 2021 15:54:08 +0200 > > From: Rob <private(a)tjalma.com <mailto:private@tjalma.com>> > > To: BaseX <basex-talk(a)mailman.uni-konstanz.de > > <mailto:basex-talk@mailman.uni-konstanz.de>> > > Subject: [basex-talk] Make use of external Identity Management for > > ? ? ? ? BaseX > > Message-ID: <39036EF3-E67D-470D-B2F4-E6FBFFDF40E6(a)tjalma.com > > <mailto:39036EF3-E67D-470D-B2F4-E6FBFFDF40E6@tjalma.com>> > > Content-Type: text/plain;? ? ? ?charset=utf-8 > > > > Hi, > > > > I have a question. > > Can BaseX make use of an Identity Management application like > > Keycloak for Users? > > > > I can?t find anything about it :) > > > > With kind regards, > > Rob Tjalma > > > > ------------------------------ > > > > Message: 2 > > Date: Thu, 29 Apr 2021 20:48:09 +0100 > > From: Reece Dunn <msclrhd(a)googlemail.com > > <mailto:msclrhd@googlemail.com>> > > To: Christian Gr?n <christian.gruen(a)gmail.com > > <mailto:christian.gruen@gmail.com>> > > Cc: BaseX <basex-talk(a)mailman.uni-konstanz.de > > <mailto:basex-talk@mailman.uni-konstanz.de>> > > Subject: Re: [basex-talk] Reloading jars on a running http server. > > Message-ID: > > ? ? ? ? > > <CAGdtn24Qdgbe3=nebYA1je4hCrZVAgi_sercCRxsTxmZcWcAxQ(a)mail.gmail.com > > <mailto:nebYA1je4hCrZVAgi_sercCRxsTxmZcWcAxQ@mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Christian, > > > > Thanks for the response. Unfortunately, I've not been able to get the > > reloading working. > > > > Kind regards, > > Reece > > > > On Wed, 21 Apr 2021 at 18:49, Christian Gr?n > > <christian.gruen(a)gmail.com <mailto:christian.gruen@gmail.com>> > > wrote: > > > > > Hi Reece, > > > > > > If you install your Java code as JAR file in the repository [1], > the > > > code will be loaded and unloaded every time when your query is > > > executed. If you get an error message? > > > > > >? ?java.lang.reflect.InaccessibleObjectException: Unable to make > > field > > > private final jdk.internal.loader.URLClassPath > > > java.net.URLClassLoader.ucp accessible: module java.base does not > > > "opens java.net <http://java.net>" to unnamed module @79e2c065 > > > > > > ?unloading fails [2], as you?re probably using a more recent > version > > > of the JDK, which restricts reflective access to internal > variables. > > > You can get around this by adding Java flags at startup time: > > > > > >? --add-opens java.base/java.net <http://java.net>=ALL-UNNAMED > > >? --add-opens java.base/jdk.internal.loader=ALL-UNNAMED > > > > > > Maybe there are better solutions to unload JAR files today. > > > Suggestions are welcome! > > > > > > Hope this helps, > > > Christian > > > > > > [1] https://docs.basex.org/wiki/Repository#Java > > <https://docs.basex.org/wiki/Repository#Java> > > > [2] > > > > > > https://github.com/BaseXdb/basex/blob/master/basex-core/src/main/java/org/b… > > < > https://github.com/BaseXdb/basex/blob/master/basex-core/src/main/java/org/b… > > > > > > > > > > > > > > On Tue, Apr 20, 2021 at 6:44 PM Reece Dunn > > <msclrhd(a)googlemail.com <mailto:msclrhd@googlemail.com>> wrote: > > > > > > > > Hi all, > > > > > > > > I'm working on a Java class that I'm importing into an XQuery, > > so I can > > > do additional processing on the data that isn't easily > > expressible in > > > XQuery (or XSLT). In order to get BaseX to pick up a modified > > version of > > > the jar file I'm building, I'm restarting the BaseX http server. > > > > > > > > This makes it slower to turn around testing the changes. Is > > there a > > > better way of doing this? > > > > > > > > Kind regards, > > > > Reece > > > > >

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Make use of external Identity Management for BaseX
by Rob 30 Apr '21

30 Apr '21

Hi, I have a question. Can BaseX make use of an Identity Management application like Keycloak for Users? I can’t find anything about it :) With kind regards, Rob Tjalma

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Reloading jars on a running http server.
by Reece Dunn 30 Apr '21

30 Apr '21

Hi all, I'm working on a Java class that I'm importing into an XQuery, so I can do additional processing on the data that isn't easily expressible in XQuery (or XSLT). In order to get BaseX to pick up a modified version of the jar file I'm building, I'm restarting the BaseX http server. This makes it slower to turn around testing the changes. Is there a better way of doing this? Kind regards, Reece

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7.9 to 9.4 upgrade
by Bondeson, Carl 28 Apr '21

28 Apr '21

We have been using BaseX for about 10 years. We were stuck at 7.9 because the performance of 8 was too restrictive. We tried 9.4 as a last ditch effort to correct some issues and the performance was just as good as 7.9. You made mention that many tcp/ip issues were resolved. We are using BaseX in a multithreaded client server configuration. I have architected a singleton as the server, allowing synchronized clients access to it. Everything is fine until we are under heavy load. We get the following error. IO exception Software caused connection abort: socket write error in mapperProcess query: declare option output:item-separator ""; distinct-values(for $h in //Concept[@NameSpace='Pilotfish.MergeLevel'] for $d in //Concept[@NameSpace=$h/AssociatedConcept/@NameSpace and .=$h/AssociatedConcept/@Concept] where $h/@Value='ByProductCodeDaily' return $d/@Value) retries: 9 We try 8 times, with a 100 msec wait between each attempt, and then generate an exception on the 9th. We have added tcp/ip registry fixes (MaxUserPort, TcpTimedWaitDelay) to the Windows server as a recommended fix for these types of errors. Do you have any other suggestions? Thanks for a great product! Carl R Bondeson IT Analyst 3 Department of Public Health Operation & Support Services Information Technology Phone: 860-509-7434 Carl.Bondeson(a)ct.gov<mailto:Carl.Bondeson@ct.gov> [cid:image001.jpg@01D73B38.801C1390][cid:image002.png@01D73B38.801C1390]

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BaseX and Oxygen scenario
by Zimmel, Daniel 22 Apr '21

22 Apr '21

Hi, am I right in assuming that in order to use the XQJ interface as described here (https://docs.basex.org/wiki/Integrating_oXygen) , you will always need a running local database instance of BaseX? I am not able to use the BaseX.jar standalone in a transformation scenario as I would for example do in a custom ant scenario where I can use BaseX as a standalone transformer (using it as a commandline process). Thanks, Daniel

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