BaseX-Talk

basex-talk@mailman.uni-konstanz.de

9 participants
5241 discussions

Help with recursion
by Chuck Bearden 27 Dec '24

27 Dec '24

I'm trying to ingest a sequence of 6293 strings, each 8 characters long, and create a map in which each key is an integer from 1 to 63, and each value is a subsequence of the 6293 strings, from ($key+1) * 100) to that starting value + 99. I wrote a function to do this recursively (so I thought), but it runs and runs (I've given it over 5 minutes), and so I can see I borked something. I wrote a function to output the starting and ending sequence indices for each execution of the function, but it (as the only change to the first function) quickly causes a stack overflow: *Error:* Stack Overflow: Try tail recursion? Since the recursive call was the last expression in the function, I thought I was doing tail recursion. I'm running 11.6.0. The code with explanatory comments follows. I'd be grateful for any corrections and insights. declare function local:write_results($elems as element()*, $count as xs:integer) { let $dir_path := '/home/cfbearden/projects/mesh_for_pure/20241220/data/' let $count_as_str := xs:string($count) let $content_out := <PubmedArticleSet>{$elems}</PubmedArticleSet> let $path := $dir_path || 'pmed2022_' || $count_as_str || '.xml' let $params := { 'method' : 'xml', 'indent' : 'yes' } return file:write($path, $elems, $params) }; declare function local:by_hundreds($pmids as xs:string*, $pmid_map as map(*)) as map(*) { let $key_count := count(map:keys($pmid_map)) return (: base case: each value except the last should have 100 items in it; the last should have <= 100; in this case we return the map goal is to build a map with 63 keys, with each value a sequence of 100 or 93 (in the last case) strings :) if ((($key_count + 1) * 100) >= count($pmids)) then $pmid_map else (: starting index for subsequence() :) let $start := 1 + ($key_count * 100) (: ending index for subsequence() :) let $end := $start + 99 (: value of the map key for this 100 items :) let $key := $key_count + 1 (: attempt to log all recurrent executions to files let $foo := local:write_results(<res><start>{$start}</start><end>{$end}</end></res>, $key_count) :) (: create a map with $key as key and the subsequence from n to n + 99 of $pmids and merge it with input accumulator map to make a new map :) let $pmid_map_new := map:merge($pmid_map, map { $key : subsequence($pmids, $start, $end) }) (: recur; the number of keys in $pmid_map_new will enable the next execution to determine which items from $pmids to use :) return local:by_hundreds($pmids, $pmid_map_new) }; (: The data format is simple: <DATA_RECORDS> <DATA_RECORD> <pub_uuid>0008980a-f1f3-40bf-8c13-cb0b79dfa81e</pub_uuid> <pmid>35732127</pmid> </DATA_RECORD> ... </DATA_RECORDS> :) let $pure_2022_db := collection('pure_2022') (: yields a sequence of 6293 strings, all 8 characters long :) let $pmids := ( for $drec in $pure_2022_db/DATA_RECORDS/DATA_RECORD let $pmid := $drec/pmid/text() return $pmid ) let $result := local:by_hundreds($pmids, {}) return $result All the best, Chuck Bearden

2 4

Upgrading BaseX by several major versions
by Rémy Delanaux 18 Dec '24

18 Dec '24

Hello, I manage a project I've worked on from 2020 to 2022 and have recently come back to (no one has really worked on since then). The project currently runs BaseX 9.4, and we obviously would like to catch up on versions of BaseX. But I'm wondering what is the best way to process here. I don't remember upgrading major versions of BaseX during my time on project (we changed servers so for BaseX 9 we did a fresh install and backup restore) What is the correct way to do this? Should I straight up install the latest version (probably BaseX at the time of writing) and find all blocking migration changes, or gradually install major version after major version (10 then 11 then 12 when available) and ook for smaller migration processes? I wasn't able to find migration guides except for upgrading from 9 to 10 (although there are individual changelogs for each individual module). Thanks! Best, Remy Delanaux

6 10

parse-json() function reorder keys in the resulting map{}
by Oleksandr Shpak 16 Dec '24

16 Dec '24

Hi team, Found one "issue" with key ordering in the resulting map. Need to clarify, is it normal behavior or a bug. json:parse('{"b":1, "a":3}', { 'format': 'xquery' }) returns {"a":3.0e0,"b":1.0e0} but json:parse('{"b":1, "a":3}') <json type="object"><b type="number">1</b><a type="number">3</a></json> As you see, the standard function returns keys not in the order as it was set in the original JSON string. I didn't find any requirement in xQuery spec that the resulting map entries should be sorted by the key name. Is it a bug or a feature? If a feature I would be really happy to see one additional param to preserve key ordering. Thanks! -- s0rr0w

3 7

BaseX freeze
by Jerome Chauveau 16 Dec '24

16 Dec '24

hi, my basex server (11.5) stops responding when too many clients request my rxq application. I've published a little demo to reproduce the bug here : [ https://git.unicaen.fr/chauveau/basex-freeze-app | https://git.unicaen.fr/chauveau/basex-freeze-app ] I don't know if the problem comes from BaseX, Jetty or the Saxon XSLT processor. Thanks for your help Jérôme

2 3

Runtime failure in DBA optimize database panel
by Eliot Kimber 16 Dec '24

16 Dec '24

Using 11.6, the DBA app’s “optimize” panel gives this runtime error: ``` Stopped at /data1/basex/webapp/dba/databases/db-optimize.xqm, 104/10: [basex:restxq] Value of "name" must be xs:string, supplied: (). ``` Must be a simple code bug but I couldn’t find the source in github. Where is the source for the DBA app? Cheers, E. _____________________________________________ Eliot Kimber Sr. Staff Content Engineer O: 512 554 9368 servicenow servicenow.com<https://www.servicenow.com> LinkedIn<https://www.linkedin.com/company/servicenow> | X<https://twitter.com/servicenow> | YouTube<https://www.youtube.com/user/servicenowinc> | Instagram<https://www.instagram.com/servicenow>

2 1

How best to manage link data collection and storage?
by Eliot Kimber 10 Dec '24

10 Dec '24

Over the last couple of years I’ve developed the Mirabel system that provides DITA link management and query features over large volumes of content (the ServiceNow product documentation source). In particular it knows what links to what and enables viewing the content with all link information available. For a given version of the product docs we have about 60K DITA topics and 100 root maps that organize those topics into publications. The primary job of Mirabel is to capture all the hyperlink details as defined by the DITA source and enable queries about the element-to-element and document-to-document relationships established by those links. My implementation approach for loading the link knowledge uses a multi-step process: 1. Load the entire source content into a database 2. Create a “key space” database that reflects the DITA key-to-resource mappings defined by each root DITA map. The key spaces are XQuery maps that map from key names to resources identified by their database node IDs (essentially, each use of a topic from a map has an associated unique key by which that use of the topic can be referenced). The key spaces are a prerequisite for resolving cross references to keys from one topic to other topics in the context of some root map (the same root map or a different one). 3. Create a “link record keeping” database that contains the “where used” index for the content. The where-used index maps element node IDs to a record of every reference to that node (cross references, content references, topic references from maps). The where-used index is the core data used to know where a given map or topic is used, which is used to answer questions like “what publications use this topic?” or “is this topic used at all?”. The where-used table is constructed as an XQuery map that is then turned into XML for storage (I implemented this before BaseX added direct storage of maps but given the size I think it still makes sense to store it as XML, but I could be wrong). * Process all map-to-map and map-to-topic references and create the initial map entries, one for each map and topic. * For topics referenced from maps, process all topic-to-topic references and update the records for each target topic to reflect the references to it. The map context of a given topic determines the targets of key references from that topic, so it is necessary to process the topics in the context of the root maps that use them (in DITA, root maps determine the key-to-resource bindings to which key references resolve). * For topics not referenced from any maps, add entries for them to the where-used table and process any topic-to-topic references (key references cannot be resolved but direct URI references can be). Convert the XQuery map to a single XML document and store in the link record keeping database. The resulting database takes about 150MB of storage. This third step can take two-to-three hours: 60K topics times 0.2 seconds for each topic is 3.3 hours. 0.1 seconds is about as fast as the link processing can go based on my testing. This is all done using temporary databases so as not to disturb the working databases used by the running Mirabel web application. The work is performed by a BaseX “worker” server, not the main server that serves the web site. I essentially have one BaseX http server for each core on my server and allocate work to them based on load, so queries coming from the web app will not be allocated to a worker currently doing a content update process. Once all the new link data is loaded, the temporary databases are swapped into production by renaming the production databases, renaming the temp databases to their production names, then dropping the old databases. (Saying this just now I’m realizing that I don’t know how to pause or wait for active queries against the in-production databases to finish so I can swap the databases.) Because all the index entries use node IDs, the content database and record-keeping databases have to be put into production at the same time, otherwise the content node IDs will be out of sync with the indexed record IDs. I’m working on the assumption that renaming databases is essentially instantaneous and so I can use that to swap the temp databases into production reliably. I use my job orchestration module (https://github.com/ekimbernow/basex-orchestration) to manage the sequence of operations, where each job calls the next job in the sequence once it has finished. This process works reliably for smaller volumes of content—for example, a content set with only a couple of thousand topics and four or five root maps. But at full scale I’m consistently seeing that the link record keeping database, which only has two large XML documents in it, never completes optimization: The database page shows the database with two things in it, but when you open the database’s page, they do not show up and the job that performs the optimization never completes, leaving the database in a locked state. This means the new where-used index can’t be put into production. I feel like I’m going about this the wrong way to make best use of BaseX and avoid this problem with very large databases but I don’t see any obvious alternative approaches. But it feels like I’m missing something fundamental or making a silly error that I can’t see. So my question: How would you solve this problem? In particular, how would you go about constructing the where-used index in a way that works best with BaseX? Or maybe the question is “should I be updating the in-production database with the new data and doing the swapping into the production within the database itself?” (i.e., by renaming the where used index document rather than the database itself.) I am currently using 11.6 and can move to 12 once it is released. Thanks, Eliot _____________________________________________ Eliot Kimber Sr. Staff Content Engineer O: 512 554 9368 servicenow servicenow.com<https://www.servicenow.com> LinkedIn<https://www.linkedin.com/company/servicenow> | X<https://twitter.com/servicenow> | YouTube<https://www.youtube.com/user/servicenowinc> | Instagram<https://www.instagram.com/servicenow>

1 0

How to unlock a locked database?
by Eliot Kimber 10 Dec '24

10 Dec '24

BaseX 11.6 on Redhat Linux. I have long-running update processes that are failing at some point, leaving databases in a locked state that is not cleared by restarting the server. Short of manually deleting the database from the file system, how can I clear these locks or determine what process has the lock? I do not have FAIRLOCK turned on. This is in the context of my Mirabel system, which loads content into one database and then creates secondary link data databases, which requires lots of data processing and may take several hours to complete. Thanks, Eliot _____________________________________________ Eliot Kimber Sr. Staff Content Engineer O: 512 554 9368 servicenow servicenow.com<https://www.servicenow.com> LinkedIn<https://www.linkedin.com/company/servicenow> | X<https://twitter.com/servicenow> | YouTube<https://www.youtube.com/user/servicenowinc> | Instagram<https://www.instagram.com/servicenow>

1 0

BaseX GUI dark theme
by ykhabins＠bellsouth.net 10 Dec '24

10 Dec '24

Hello, I am using BaseX 11.6 on Windows OS 10 and 11 machines. I followed the following post https://basex-talk.mailman.uni-konstanz.narkive.com/w8VctrkD/editor-backgrou nd-color And downloaded latest JTattoo-1.6.13.jar, and copied it to the c:\Program Files (x86)\BaseX\lib\custom directory. All new themes show up in the Visualization tab dropdown upon BaseX GUI restart. If I select Noire or HiFi themes, i.e. dark themes, BaseX GUI changes menus, toolbars, dropdowns, except Editor, Result, Info, etc. panes background. Please advise. Regards, Yitzhak Khabinsky

2 1

Content is not allowed in prolog.
by Ben Engbers 06 Dec '24

06 Dec '24

Hi, I have been working very hard on my BasexCpp client project for the last few months. The most effort has been to convert the code that worked flawlessly in Eclipse to a library that meets all the requirements (see also https://medium.com/@pananton/modern-cmake-tutorial-for-c-library-developers…, Modern CMake tutorial for C++ library developers). During that work, there turned out to be imperfections anyway. Fixing a memory-leak took the most effort. I now have 2 versions of the code. The first version is based on CMake and builds a shared library that has to be installed. The second version does not use CMake. This version has to be compiled manually. Both versions use the same code for the library. As soon as I fix the last,following problem, I will publish both new versions. The last problem is in the test program. That program contains the following line: Session.Add(“Add_XML_2”, “/home/bengbers/Git/Private/Raw/libBasexCpp/src/extdata/Articles.xml”); This line calls the "Add command" from the server protocol. The above line is executed without errors. However, the problem is that when I change the path to "./Raw/libBasexCpp/src/extdata/Articles.xml" I get the following error message: "Content is not allowed in prolog.". And since the same testprogram is used to test the different versions, the path has to be relative. My question is how I can use a relative path in the Add-command. -- Ben Engbers Grietjeshof 77 6721 VH Bennekom +31 6 23634840

3 2

Limit on Parallelism
by celano＠informatik.uni-leipzig.de 06 Dec '24

06 Dec '24

Is there a way to specify how many parallel processes Basex 11 is allowed to spawn (I am not using the database)? In combination with GNU parallel, it becomes difficult to have control on parallelism. Best, Giuseppe

4 5

← Newer
1
...
8
9
10
11
12
13
14
...
525
Older →

Jump to page:

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

BaseX-Talk