January 2022 - BaseX-Talk - mailman.uni-konstanz.de

Response from proc:execute() for git Command Not Coming Through as Expected
by Eliot Kimber 22 Jan '22

22 Jan '22

[BaseX 9.6.4 on Mac through BaseX GUI] I’m trying to automate syncing a database with content from a git repo that is locally cloned. My approach is to use proc:exec() to pull the repo and then use git diff-tree to see what files changed: let $pullResult := proc:execute($gitCmd,('pull', '-v'), map{'dir' : $repoPath}) let $changeList := proc:execute($gitCmd, ('diff-tree', '--no-commit-id', '--name-status', 'HEAD'), map{'dir' : $repoPath}) However, the result returned for “diff-tree” appears to get truncated. Here’s a typical result, where I’m echoing out the $pullResult and $changeList values created above: Pull result: <result> <output>Already up to date. </output> <error>From code.devsnc.com:doc/dita-now = [up to date] master -> origin/master = [up to date] dita-now -> origin/dita-now = [up to date] rtprn -> origin/rtprn = [up to date] sanfransokyo -> origin/sanfransokyo = [up to date] scodefreeze -> origin/scodefreeze = [up to date] scratc/table_issues_fix -> origin/scratc/table_issues_fix = [up to date] scratch/fix_canvas_issue -> origin/scratch/fix_canvas_issue = [up to date] scratch/newDitavals2022 -> origin/scratch/newDitavals2022 = [up to date] scratch/simplifyDitavals -> origin/scratch/simplifyDitavals = [up to date] scratch/table_name_issue -> origin/scratch/table_name_issue </error> <code>0</code> </result> Change list: <result> <output>M doc </output> <code>0</code> </result> Note that the pull response looks as expected but the change list response is just “M\tdoc” where “doc” is the first directory in what should be a path to a file. Here’s the same result from the command line: dita-now % git diff-tree --no-commit-id --name-status -r HEAD M doc/source/product/rpa-studio/task/use-datareader-queryexcel.dita M doc/source/product/rpa-studio/task/use-datetime-add.dita M doc/source/product/rpa-studio/task/use-datetime-compare.dita … I can’t see anything I’m doing wrong or options to the execute() or system() functions that would affect the result. Any idea what might be causing this or how I could work around it? 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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Outdated milton-api version
by Matthew Dziuban 21 Jan '22

21 Jan '22

Hi all, While auditing the library dependencies of an application, I found that org.basex:basex-api [1] depends on a very old version of com.ettrema:milton-api -- v1.8.1.4 released in 2014 [2]. The package seems to have been migrated to the io.milton namespace and have a recently (December 2021) released v3.1.0.301 [3]. This stood out to me because my application is using the latest version of Apache commons-io, v2.11.0, while the old version of milton-api depends on Apache commons-io v1.4, released in 2008. Would it be feasible to migrate BaseX to a newer version of the milton-api library? Thanks in advance! Matt [1] https://mvnrepository.com/artifact/org.basex/basex-api/9.6.4 [2] https://mvnrepository.com/artifact/com.ettrema/milton-api/1.8.1.4 [3] https://mvnrepository.com/artifact/io.milton/milton-api/3.1.0.301

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Where-Used: Performance Improvement Strategies?
by Eliot Kimber 18 Jan '22

18 Jan '22

In the context of my 40K topic DITA corpus, I’m trying to build a “where used” report that finds, for each topic, the other topics that directly refer to the topic. I can do this by looking for the target topic’s filename in the values of @href attributes in other topics (I’m taking advantage of a local rule we have where all topic filenames should be unique). My current naive approach is simply: $topics//*[tokenize(@href, '/') = $filename] Where $topics is the 40K topics. Based on profiling, the use of tokenize() is slightly faster than either matches() or contains(), but all forms take about 0.5 seconds per target topic, which is way too slow to make this practical in practice. So I’m trying to work out what my performance optimization strategies are in BaseX. In MarkLogic I would set up an index so I could do fast lookup of tokens in @href values or something similar (it’s been long enough since I had to optimize MarkLogic queries that I don’t remember the details but basically indexes for everything). I know I could do a one-time construction of the where-used table and then use that for quick lookup for subsequent queries but I’m trying to find a solution that is more appropriate for my current “create a new database with the latest files from git and run some queries quickly to get a report” mode. I suspect that using full-text indexing may be a solution here but wondering what other performance optimization options I have for this kind of look up. Thinking about it now I definitely need to see if building the where-used table would actually be slower. That is, find every @href, resolve it and construct a map of topics to href elements that point to that topic. Hmm. Anyway, any guidance on this challenge would be appreciated. Cheers, 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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Questions about the performance of bulk string matching
by Zimmel, Daniel 18 Jan '22

18 Jan '22

Hi, recently I ran into serious (as in SERIOUS) performance trouble regarding expensive regexes, and no wonder why. Here is my scenario: * XML text documents with a total of 1m text nodes * A regex search string, including a huge string dictionary list of 50.000 strings (some of them containing 50 words each) * a match must be wrapped in an element (= create a link) I could drink many cups of tea while waiting for the regex to complete... hours... I ran out of tea! Then I found the 2021 Balisage paper from Mary Holstege titled "Fast Bulk String Matching" [1] in which she explores the Aho-Corasick algorithm, implementing it with XQuery - marvellous! Following this, while I can build a data structure which gives me fast results, building the same structure is still very slow due to the amount of text to build from. So this was not fast enough for my use case - or I may simply not be smart enough to apply it correctly :-| So, I tried tinkering with maps which turned out to give me extraordinary performance gains: * build a map from the string dictionary * walk through all text nodes one by one * for each text node, put any combination of words in the text node in word order (I need to find strings, not words) into another map * strip punctuation (for word boundaries) and do some normalization of whitespaces in both maps * compare the keys of both maps * give the new reduced string dictionary to the regular regex search While comparing the maps, I do not know where in the text my strings are, but at least I know if they are in there - to find out where exactly (and how do they fit my other regex context) I can then use a massively reduced regular regex search. Fast! I am quite happy BUT I still cannot understand why this is so much faster for my sample data: * plain method : 51323.72ms * maps method: 597.94ms(!) Is this due to any optimizations done by BaseX or have I simply discovered the power of maps? How would you do it? Is there still room for improvement? Why does Aho-Corasick not help much with this scenario? Is it because the list of strings is simply too massive? Why is this so much faster with text-splitting-to-map? See below for the query examples to better understand what I am trying to do (bulk data not included) [2],[3] There is no normalization of punctuation in the examples but that is only necessary for completeness. Best, Daniel [1] http://www.balisage.net/Proceedings/vol26/print/Holstege01/BalisageVol26-Ho… [2] plain method let $textnodes := fetch:xml(file:base-dir()||file:dir-separator()||'example.xml')//text() let $strings := file:read-text(file:base-dir()||file:dir-separator()||'strings.txt') let $regex := $strings for $textnode in $textnodes where matches($textnode,$regex) = true() return $textnode [3] maps method (:~ : Create map from string : Tokenization : : @param $strings : @return Map :) declare function local:createMapFromString ( $string as xs:string ) as map(*) { let $map_words := map:merge( for $string in tokenize($string,'\|') let $key := $string let $val := $string return map:entry($key,$val), map { 'duplicates': 'use-first' }) return $map_words }; (:~ : Create map from text nodes : Write any combination of words in document order to the map : : @param $textnodes : @return Map :) declare function local:createMapFromTextnodes ( $textnodes as xs:string+ ) as map(*) { map:merge( for $node in $textnodes let $text := normalize-space($node) let $tokens := tokenize($text,' ') let $map_nodes := map:merge( for $start in 1 to fn:count($tokens) for $length in 1 to fn:count($tokens) - $start + 1 return map:entry(fn:string-join(fn:subsequence($tokens, $start, $length), ' '),'x') ) return $map_nodes) }; (:~ : Compare two maps : : @param $map1 : @param $map2 : @return xs:string* :) declare function local:reduceMaps ( $map1 as map(*), $map2 as map(*) ) as xs:string* { for $key in map:keys($map1) where map:contains($map2,$key) let $value := map:get($map1,$key) return $value }; let $textnodes := fetch:xml(file:base-dir()||file:dir-separator()||'example.xml')//text() let $strings := file:read-text(file:base-dir()||file:dir-separator()||'strings.txt') let $map_words := local:createMapFromString($strings) let $map_textnodes := local:createMapFromTextnodes($textnodes) let $matches := local:reduceMaps($map_words,$map_textnodes) let $regex := string-join(for $match in $matches group by $match return $match,'|') for $textnode in $textnodes where matches($textnode,$regex) = true() return $textnode

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Configuration Option for Files to Parse in Create Database Dialog?
by Eliot Kimber 14 Jan '22

14 Jan '22

I’m using the BaseX GUI in a very informal way where I create new databases as needed to do ad-hoc queries over content that comes from various git repos. I’m trying to setup my local configuration settings to be what I need for this database creation tasks. I’ve found and successfully configured the options for skipping corrupt and parsing archives but I don’t see an option that will populate the Input file or directory field, which I need to be “*.xml, *.dita,*.ditamap”. I found the option that sets the pattern used in the main file selector field but that doesn’t apply to this dialog. I’m not seeing anything for this in the docs. This is for BaseX 9.6.3 Thanks, E. _____________________________________________ 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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9.6
by Bondeson, Carl 12 Jan '22

12 Jan '22

We have been using BaseX since 7.0 in a multi-threaded environment. Our configuration utilizes an architecture where child threads query a singleton BaseX server, running as a service using YAJSW. We were unable to update past 8.0, due to issues with our licensed Java tier. We recently upgraded to a RedHat version of the open JDK.11, and were able to upgrade BaseX to 9.6. The performance is much improved. We also saw better memory management by running BaseX in its own container (YAJSW). This implementation is handling the processing of Corona, and 75 other reportable diseases from over 3,000 sources (labs, hospitals, doctor's offices, etc., etc.). This platform utilizes 6 databases, which work as rule engines, to drive the processing of data as it moves through the system. Thanks again for an outstanding 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@01D8078F.B6177CE0][cid:image002.png@01D8078F.B6177CE0]

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9.6 on Docker Hub
by Johannes Bauer 10 Jan '22

10 Jan '22

Hi, I cannot find the latest BaseX release on Docker Hub (only the 9.5 branch). Is this still planned? Thank you. Best Regards Johannes

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RESTXQ design pattern question
by Hans-Juergen Rennau 07 Jan '22

07 Jan '22

Hello, I have a question concerning RESTXQ design patterns. Imagine you have a page P1 displaying an input field, and you want to provide a button enabling the user to pick the terms from a list, rather than entering them. So after pressing the button, another page P2 appears, listing the terms and enabling a selection. After selection, P1 should again appear, looking as before, except for the selected terms appearing in the field. A common pattern, isn't it. How to implement it? One approach would be P2 calling P1 (via form/@action), passing the selection to P1 as form or query parameters. But then the input of P1 must include everything required to restore the previous appearance, including the values of input fields from forms not yet submitted. There is certainly a simpler way? I suppose a standard approach handles this completely with JavaScript, updating the page. I wonder if RESTXQ and supporting modules enable some alternative? Thank you, with kind regards -Hans-Jürgen

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webapp/static
by Hans-Juergen Rennau 07 Jan '22

07 Jan '22

Hello, dear BaseX team, one question concerning folder $BASEX/webapp/static. Given an HTML page created by a query via REST or RESTXQ execution. It seems to me that referenced resources (e.g. link/@href or img/@src) must be located in that folder or a subfolder of it, and the reference must be "../static/foo.css" or "../static/path/to/subfolder/foo.css", examples: <link rel="stylesheet" type="text/css" href="../static/foo.css"/><link rel="stylesheet" type="text/css" href="../static/foo/foo.css"/> At least I did not succeed with any other locations, specified by full path or by relative path, assuming different context paths (e.g. the folder containing the query producing the HTML, or $BASEX/bin, or $BASEX). My QUESTION: is that correct, if not - what are the rules? Many thanks,Hans-Jürgen PS: Apologies if this is documented, but I failed to find it, and the complete PDF contains a single occurrence of string "/static" which does not apply.

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RESTXQ generated HTML - unexpected behaviour
by Hans-Juergen Rennau 07 Jan '22

07 Jan '22

Hello, I face a problem with RESTXQ of a fairly general character, as it seems to me. When the XQuery functions of a RESTXQ application construct HTML pages, I expect these pages to behave exactly as a static page with the same content would behave. But sometimes this is not the case. As an attachment I send an example. The "webapp" folder contains an XQuery module with a RESTXQ function [2], and the "html" folder contains an HTML page [3] which is identical to the page generated by the RESTXQ function [4]. This page has been copied from [1], and it demonstrates auto completion in an input field. However, auto completion works only when calling the HTML file; it does not work when calling the RESTXQ application. In both cases, the HTML page references a JS file as well as a CSS file, located in a sibling folder "static". An alert box as well as the appearance of the page prove that JS and CSS are found and used in both cases. And yet the behaviour is different ... ~~~ This problem appears to me important, as the trust in RESTXQ would be damaged if the generated HTML "may or may not" behave as it should. On the other hand, if the reason of the problem is understood and a workaround is available, all would be well. Kind regards,Hans-Jürgen [1] https://www.w3schools.com/howto/howto_js_autocomplete.asp [2] $demo-autocomplete/webapp/autocomplete/demo-autocomplete.xq [3] $demo-autocomplete/html/demo-autocomplete.html [4] The contents of the HTML file have been created by (1) entering into a browser the URL of the RESTXQ application (localhost:8984/demo-autocomplete), (2) selecting from the context menu "Show source code", (3) copying the source code into the empty HTML file, (4) replacing <script .../> with <script...></script>. [5] How to reproduce the problem:a. Unzip the archiveb. Call $demo-autocomplete/html/demo-autocomplete.html - after acknowledging the alert box which shows that the imported JS function has been called, enter into the input field letter "a" - a list of completions appears.c. Install the RESTXQ application: copy folder $demo-autocomplete/webapp/autocomplete into the webapp folder of a BaseX instance, and copy the files $demo-autocomplete/webapp/static/* into $BASEX/webapp/static.d. Enter in a browser "localhost:8984/demo-autocomplete" - after acknowledging the alert box, enter into the input field letter "a" - no list of completions appears.

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