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

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

Unable to paste into external variable dialogue box in the GUI-Basex 11.4
by brian＠kennison.name 25 Oct '24

25 Oct '24

Hello Everyone, Not a big deal but can’t paste into the external variable dialog box. I have a script that has several external variables (urls) which are long so I paste them in the dialog box in the GUI (Basex-11.4). Anybody else experiencing this? Thanks for your time —Brian

6 9

Write files in parallel?
by Thompson, Timothy 17 Oct '24

17 Oct '24

Hello, Is it possible to call file:write-text-lines in parallel inside a fork-join operation? I have multiple databases that I would like to run a query over, in parallel, and write the results as JSON Lines to a file per database. When I try this, it doesn’t seem to parallelize. Thanks in advance, Tim -- Tim A. Thompson (he, him) Librarian for Applied Metadata Research Interim Manager, Metadata Services Unit Yale University Library www.linkedin.com/in/timathompson<http://www.linkedin.com/in/timathompson>

3 7

How to recognize a byte-order-mark?
by Hans-Juergen Rennau 11 Oct '24

11 Oct '24

Dear BaseX people, there is a serializatioin parameter for adding a byte-order-mark when serializing. Such a document cannot be parsed using fn:doc() - error message: [FODC0002] "C:/projects/ofx-works/work/test-bom.xml" (Line 1): Content ist nicht zulässig in Prolog. This message is rather unspecific. My question: is there a way how to determine if a byte-order-mark is used in a given file? Kind regards,Hans-Jürgen

2 2

Re: [basex-talk] Setting multiple CSV EXPORTER options is not documented on docs.basex.org
by Christian Grün 03 Oct '24

03 Oct '24

Hi Navel, > BaseX Xquery CSV module is for dealing with CSV files which we don't have. With this module, you can serialize XML data as CSV (and parse CSV back to XML). But that’s certainly just one way to do it. Hi Owen, > However, I wonder how BaseX might deal with more than a million records. Feel free to get back to us once you encounter any limits. Best, Christian Naval Sarda <nsarda(a)epicomm.net> schrieb am Do., 3. Okt. 2024, 14:45: > Hi Owen, Christian, > > We are working on Stratml files which are in XML format. BaseX Xquery CSV > module is for dealing with CSV files which we don't have. > > We can scale up BaseX by adding more servers and splitting the data > between more servers if the record counts goes high. > > Naval > > > On 02/10/24 10:54 pm, Owen Ambur wrote: > > Naval, can you answer Christian's question? > > My sense is that a lot of features have been built into BaseX that we > could use but I don't have the knowledge or expertise to understand how > best to do so. At least, I hope we're not reinventing capabilities that > are already available to address our technical objectives > <https://aboutthem.info/SQS.xml> as well as our broader conceptual > objectives <https://aboutthem.info/ATI.xml>. > > Christian, this morning we had a very encouraging Zoom meeting with folks > at GSA who are finally getting around to figuring out how to help Uncle > Sam's agencies comply with section 10 > <https://www.linkedin.com/pulse/trustworthy-institutions-owen-ambur/> of > the GPRA Modernization Act. I encouraged them not to reinvent the StratML > schemas and it would be great if the BaseX community could help us > demonstrate the benefits of using them, not only by U.S. federal agencies > but agencies at all levels of government, worldwide, as well as tax-favored > organizations and others whose plans and reports should be matters of > public record. > > There are >5.8K plans in the StratML collection > <https://stratml.us/drybridge/index.htm> and indexed in the query > service. Their URLs are listed in sitemap format at > https://stratml.us/docs/sitemap.xml > > I am contemplating whether to hire someone to convert the relevant > elements of the IRS Form 990 database > <https://www.irs.gov/charities-non-profits/tax-exempt-organization-search-bu…> > to StratML format, using the templates at > https://stratml.us/drybridge/index.htm#MPR4CO However, I wonder how > BaseX might deal with more than a million records. > > Owen Ambur > https://www.linkedin.com/in/owenambur/ > > > On Wednesday, October 2, 2024 at 12:18:16 PM EDT, Christian Grün > <christian.gruen(a)gmail.com> <christian.gruen(a)gmail.com> wrote: > > > Hi Owen, > > Is it based on the BaseX XQuery CSV Module? > > Best, > Christian > > > > > Owen Ambur <owen.ambur(a)verizon.net> schrieb am Mi., 2. Okt. 2024, 18:12: > > I'm not sure how this exchange might relate but my developer has provided > CSV export capabilities for query results listings at StratML > <https://search.aboutthem.info/> > > > StratML <https://search.aboutthem.info/> > > > > Any comments or suggestions on how we might enhance the functionality of > our StratML-enabled query service would be most welcome. > > Owen Ambur > https://www.linkedin.com/in/owenambur/ > > > On Tuesday, October 1, 2024 at 04:42:12 AM EDT, Christian Grün < > christian.gruen(a)gmail.com> wrote: > > > Hi Omar, > > Thanks for the observation. For the SERIALIZER option, there was a > corresponding note which I have added to the EXPORTER option, along with > a little example for exporting CSV [1]. > > Best, > Christian > > [1] https://docs.basex.org/main/Options#exporter > > > > On Mon, Sep 30, 2024 at 4:04 PM Omar Siam <Omar.Siam(a)oeaw.ac.at> wrote: > > Hi, > > I just tried after some time to script a CSV export with a BXS file. I > forgot how to set multiple options for the csv serialization. In the end > this worked: > <set > option="EXPORTER">method=csv,csv=header=true,,lax=false,,quotes=true</set> > I can not find it on docs.basex.org. Perhaps this should be added and > explained. > > 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 > >

1 0

Setting multiple CSV EXPORTER options is not documented on docs.basex.org
by Omar Siam 02 Oct '24

02 Oct '24

Hi, I just tried after some time to script a CSV export with a BXS file. I forgot how to set multiple options for the csv serialization. In the end this worked: <set option="EXPORTER">method=csv,csv=header=true,,lax=false,,quotes=true</set> I can not find it on docs.basex.org. Perhaps this should be added and explained. 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

3 4