BaseX-Talk

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1 participants
5252 discussions

Selecting nodes in a db by source file name
by Charles Bearden 19 May '22

19 May '22

Let's say I have a database built from 40+ XML documents, each with about 4 million nodes for a total of about 404 million nodes, of which 30k are high-level records of interest. Let's say that a given node of interest (a PubMed record, actually) may occur once in this database for each time it has been updated, and I can identify the most recent version of that record by the PubMed ID and the filename (an ascending sort of the filenames sorts them from least recent to most recent). Is there a way in XQuery I can identify a record in this database not only by its PubMed ID but also limit the result set by source document name? I know that `db:path($elem)` gives me the document name for an element, but I want to use the document name to help pick out the element from among several that may share its PMID. Context: I have 26 such databases, each of which contains 43-44 source files, each of which contains 30000 records. I have built one index database that, for each record, includes PubMed ID, source filename, and database name. For a given PMID I can very quickly retrieve the db name and the file name, but I need to search the db not only by PMID but also by source filename in order to select the most recent version of a record. Thank you & all the best, Chuck Bearden

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Checking run time characteristics according to the handling of customised indexes
by Markus Elfring 17 May '22

17 May '22

Hello, Some indexes are generally supported also by the software “BaseX”. https://docs.basex.org/wiki/Indexes Some data processing approaches would usually depend on indexes for primary and foreign keys. https://en.wikipedia.org/wiki/Primary_key How much do run time characteristics influence data transfers (and conversion of corresponding data structures) for the available indexing technologies? Regards, Markus

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Repeating data based on varying items in an array
by Markus Elfring 16 May '22

16 May '22

Hello, It seems that I am still not familiar enough with the programming language “XQuery” for the quick specification of a bit of code for a general data processing task. Thus I hope that the following use case can be clarified better. A sequence like “(["f" [1 2 3]], ["g" [4, 5]])” might be an interesting test example. It contains two nested arrays. * One part refers to fixed data. * Another part refers to some items with a varying number. I would like to convert the varying items into a data representation like the following. f,1 f,2 f,3 g,4 g,5 Can any customised functions help for the desired transformation? Regards, Markus

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Add a comment to a backup?
by Jonathan Robie 13 May '22

13 May '22

I have been making backups before doing particularly complex things to my treebanks, and I find myself writing down information about what stage of processing a given backup corresponds to. "after replacing subtrees for missing compounds" I wish I could associate these strings with backups in BaseX so I can more easily know which one I would restore if something went wrong. Jonathan

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Developments for address books
by Markus Elfring 12 May '22

12 May '22

Hello, Various data models and corresponding applications can be constructed also with the help of the software “BaseX”. One popular data management tool is the address book (which can be supported by customised hardware and software), isn't it? Would you like to point any development repositories and further information sources out for such an application domain? Regards, Markus

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Oxygen and BaseX Integrations?
by Eliot Kimber 06 May '22

06 May '22

I’m looking at ways to better integrate BaseX with Oxygen, both for XQuery editing and as a way to augment Oxygen’s DITA authoring features (i.e., using BaseX to provide more comprehensive link and search database features). Radu pointed me to Project Argon https://github.com/axxepta/project-argon but it looks like it hasn’t been updated in a few years (last commit was 2017) and my initial attempt to run the gradle build failed on the Java version detection. I’ll reach to the Project Argon team but I’m wondering if anyone else is doing anything with Oxygen integration. I’m looking for a couple of things: * Enable editing XQuery modules in Oxygen with validation, either using Saxon or BaseX, whichever is easier. While the BaseX editor is decent I really miss the Oxygen features I’ve come to know and love, like outline view. My initial attempt to set up an entity resolution catalog to make this work did not succeed, but I didn’t have a lot of time to spend on it. * Embedded BaseX server in an Oxygen add-on. This shouldn’t be too hard and we have a ServiceNow-specific add-on I could do this in, but I’m always looking for solutions I can crib from… 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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Not sure if feature/bug/my mistake!
by Patrick Durusau 06 May '22

06 May '22

Greetings! I have a directory of files that I use to create a database, using the directory as my starting point. On Debian, the files appear in this order: 01-matthew.xml 02-mark.xml 03-luke.xml 04-john.xml If I create an empty database and then add the files one by one, in that order, then //title[@type="main"] returns: ΚΑΤΑ ΜΑΘΘΑΙΟΝ ΚΑΤΑ ΜΑΡΚΟΝ ΚΑΤΑ ΙΩΑΝΗΝ ΚΑΤΑ ΙΩΑΝΗΝ On the other hand, if I start at the directory, add xml files, the database is created and //title[@type="main"] returns: ΚΑΤΑ ΙΩΑΝΗΝ ΠΡΟΣ ΕΦΕΣΙΟΥΣ ΚΑΤΑ ΜΑΘΘΑΙΟΝ ΙΩΑΝΟΥ Α Question (sorry for the long setup): Is the sort order of manually added files an artifact of the manual addition? That is I cannot expect users across systems to experience the same load order as I do? Asking because I'm writing documentation along with example queries for several datasets and documenting random results, isn't likely to be helpful to readers. I am aware I can use db:list(database-name) to obtain and sort on the original file names but that takes me away from the file content. Ah, BaseX 9.7.1 on Debian. You know, the files don't have internal sort attributes. ntorder = "digit" would be enough to sort on that attribute and return the book names in the expected order. I'm sure there are better solutions, suggestions appreciated! Patrick -- Patrick Durusau patrick(a)durusau.net Technical Advisory Board, OASIS (TAB) Editor, OpenDocument Format TC (OASIS), Project Editor ISO/IEC 26300 Co-Editor, ISO/IEC 13250-1, 13250-5 (Topic Maps) Another Word For It (blog): http://tm.durusau.net Homepage: http://www.durusau.net Twitter: patrickDurusau

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Session issue
by Bondeson, Carl 04 May '22

04 May '22

We are seeing the following exception if we run under very heavy multi-thread conditions. ERROR] 2022-05-04 08:49:41.345 [Thread-3012] - General Throwable occurred message: No buffer space available (maximum connections reached?): connect Caused by this // create BaseX session on singleton server mapperSession = new ClientSession(BaseXDictionary.BASEX_HOST, basexdict.baseXPort, basexdict.baseXUser, basexdict.baseXPass); We are using XSLT and invoking Java methods to handle the things not easily managed in XSLT. Should we be closing sessions in Java classes or is this supposed to be handled by the JVM? This is running under Windows Server 2016 , deployed using JBoss 7.3.9, with 16 GB ram, and 4 cores. Thanks 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@01D85F9D.FCF29490][cid:image002.png@01D85F9D.FCF29490]

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Re: [basex-talk] [basex-announce] BaseX 9.7.1: Tweaks, Fixes, Features
by Christian Grün 03 May '22

03 May '22

Confirmed, thanks. A new snapshot is available [1]. If you want to stick with BaseX 9.7.1, you can remove the trailing slash in your URL. [1] https://files.basex.org/releases/latest/ On Tue, May 3, 2022 at 5:13 PM Majewski, Steven Dennis (sdm7g) < sdm7g(a)virginia.edu> wrote: > > I’m also seeing a new error crop up with 9.7.1 > > Could this be connected ? > > ( I’ll try to revert to previous version to make sure that there hasn’t > been a change at the source URL that would cause a change in result. ) > > *WTJU$* basex 'html:doc( "https://www.wtju.net/recent-shows/" )' > Stopped at /Users/sdm7g/Desktop/WTJU/, 1/9: > [FODC0002] URI 'https://www.wtju.net/recent-shows/' points to directory. > *WTJU$* > *WTJU$* curl -I https://www.wtju.net/recent-shows/ > HTTP/2 200 > *server*: nginx/1.10.3 > *date*: Tue, 03 May 2022 15:10:52 GMT > *content-type*: text/html; charset=UTF-8 > *x-pingback*: https://www.wtju.net/xmlrpc.php > *link*: <https://www.wtju.net/wp-json/>; rel="https://api.w.org/" > *link*: <https://www.wtju.net/?p=173>; rel=shortlink > >

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Re: [basex-talk] [basex-announce] BaseX 9.7.1: Tweaks, Fixes, Features
by Majewski, Steven Dennis (sdm7g) 03 May '22

03 May '22

I still had BaseX971-20220411.133348.zip ( 9.7.1 beta) sitting around to try And I don’t get that error using it. > On May 3, 2022, at 11:12 AM, sdm7g <sdm7g(a)virginia.edu> wrote: > > > I’m also seeing a new error crop up with 9.7.1 > > Could this be connected ? > > ( I’ll try to revert to previous version to make sure that there hasn’t been a change at the source URL that would cause a change in result. ) > > WTJU$ basex 'html:doc( "https://www.wtju.net/recent-shows/ <https://www.wtju.net/recent-shows/>" )' > Stopped at /Users/sdm7g/Desktop/WTJU/, 1/9: > [FODC0002] URI 'https://www.wtju.net/recent-shows/ <https://www.wtju.net/recent-shows/>' points to directory. > WTJU$ > WTJU$ curl -I https://www.wtju.net/recent-shows/ <https://www.wtju.net/recent-shows/> > HTTP/2 200 > server: nginx/1.10.3 > date: Tue, 03 May 2022 15:10:52 GMT > content-type: text/html; charset=UTF-8 > x-pingback: https://www.wtju.net/xmlrpc.php <https://www.wtju.net/xmlrpc.php> > link: <https://www.wtju.net/wp-json/ <https://www.wtju.net/wp-json/>>; rel="https://api.w.org/ <https://api.w.org/>" > link: <https://www.wtju.net/?p=173 <https://www.wtju.net/?p=173>>; rel=shortlink >

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