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

Incompatibility with Tomcat 10
by Marc Balston 06 Apr '22

06 Apr '22

Hello, I've been successfully running BaseX on Amazon AWS using Tomcat 8.5, but I've been looking to upgrade my server to Tomcat 10.0.2.However, I've run into an issue: BaseX does not startup and from the logs the cause appears to be a missing class: java.lang.NoClassDefFoundError: javax/servlet/http/HttpSessionListener I believe this is because there was a change between Tomcat 9.x and Tomcat 10 which led to a renaming of the javax.* package to jakata.* (related to a change in the servlet API version) see here for a discussion: https://stackoverflow.com/questions/66711660/tomcat-10-x-throws-java-lang-n… Is my understanding correct and is this a known issue?If it is a genuine incompatibility, it would be useful to mention this in the documentation (Web Application - BaseX Documentation) ThanksMarc Marc Balston

2 5

Support for performing queries on query results
by Markus Elfring 05 Apr '22

05 Apr '22

Hello, XQuery scripts can be used also to compute values from selected XML data structures. Query results can be exported then into other file formats. But I would like to reuse query results for further queries directly. The SQL standard is providing named views for this purpose. How will the support evolve for such data processing requirements with XML tools? Regards, Markus

6 18

copy-paste, can't copy in BaseX and then paste into Emacs (Debian)
by Patrick Durusau 04 Apr '22

04 Apr '22

Hello, I tried to copy a string out of results with the copy command on the drop down but don't seem to be able to paste into Emacs. Trying to be good and document my steps but if I can't copy-paste, that's going to be tedious. Suggestions? Thanks! 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

3 8

Typo in basexgui.bat? since 9.6.4? Also in 9.7
by Patrick Durusau 04 Apr '22

04 Apr '22

Greetings! Friday afternoon is a bad time to open a Windows VM for anything but while pursuing a question about BaseX 9.7 and Windows 10,... basexgui fails with: "Windows cannot find 'javaw.' Make sure you typed the name correctly, then try again." basexgui.bat reports: "start javaw -cp "%CP%" ..." All the other .bat file report "start java ...." BTW, Windows is very cranky about running "unknown publisher" software. Hope everyone has already started a great weekend and will tend to this next Monday. Patrick PS: I'm still running 9.4.6 on Debian and report the same from the files there. 9.7 was on Windows 10. -- 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

2 3

keeping relative paths in the document-uri?
by Graydon Saunders 31 Mar '22

31 Mar '22

Hello -- An approach that uses db:create and file:descendant doesn't seem to work; the file paths have all been truncated to the name part of the path in the document-uri property of the individual documents in the DB. I'm using 9.6.4 with Oracle Java 1.8.0_211 on a Windows 10 machine. (I have no control over any of the environment.) Is there a way to keep the full path (relative or absolute) in the document uri property? I'm trying to inspect files with identical names in different directories, so I need the directory name to tell the files apart. Thanks! Graydon

3 2

Simple delete bug
by Jonathan Robie 30 Mar '22

30 Mar '22

Expressions like this fail silently without raising an error in BaseXGUI: delete //m/@n Of course, it should be: delete nodes //m/@n But there should be an error to remind me ;-> Jonathan

2 2

Serialization ... one attribute per line ...
by Jonathan Robie 29 Mar '22

29 Mar '22

I have a set of syntax trees that I would like to serialize with one attribute per line, like this: https://github.com/biblicalhumanities/greek-new-testament/blob/master/synta… The current serialization looks more like this: https://github.com/biblicalhumanities/greek-new-testament/blob/master/synta… Is there a way to get there using just serialization parameters, or do I need to do something fancier? Jonathan

1 0

fn:count() performance
by Josselin Morvan 29 Mar '22

29 Mar '22

Hi everyone, We are experimenting a small issue with the count() function, and I wanted to know if you have any idea to reduce the response time of the server : We have a database containing almost 5.000 descriptions of expert reports from the 18th century. As a report can take place over several years, we want to list all the years mentioned in the reports and then count for each year how many reports we have. Our goal with this query is to produce a filter by year for our web application. But, if the first part of the query is quite fast, it is not the case for the second part… here is a simplified sample of our code : xquery version "3.1"; declare default element namespace "xpr" ; (: to create the xprDB ;) db:create('xpr', 'https://raw.githubusercontent.com/anrExperts/data/master/db/xpr.xml') :) let $years := fn:distinct-values(db:open('xpr')/xpr/expertises/expertise/description/sessions/date[@when castable as xs:date]/fn:year-from-date(@when)) for $year in $years return $year || ' : ' (:this first part of the query is quite fast 0.09sec on my old computer:) || fn:count(db:open('xpr')/xpr/expertises/expertise[description/sessions/date[fn:matches(@when, xs:string($year))]]) (:it takes 5sec to execute the second part of the query:) Do you see anything we are doing wrong or we can improve to reduce the server response time ? We thank you in advance! Best, Josselin

2 2

(no subject)
by Charles Bearden 29 Mar '22

29 Mar '22

I have loaded all the Pubmed baseline XML records into a series of 20 BaseX databases, 55 or 56 of the baseline files per database, each of which is about 12GB in size and has between 520 and 530 million nodes in 55 or 56 documents. Text, Token, and Attribute indices are enabled, but with 6GB RAM allocated to the Java VM it would not create a full text index. Each of the 55 or 56 documents has 30000 article records in it under a root PubmedArticleSet element. I typically use basexgui for interactive work and basex for scripted loads & queries, and I allocate 6G to the Java VM in each case: BASEX_JVM="-Xmx6g $BASEX_JVM" I'm exploring ways to search the data in a moderately performant way, starting with the realtively simple lookup by PubMed ID: /PubmedArticleSet/PubmedArticle[MedlineCitation/PMID[text()=$pmid]] I generated a seriers of five index XML files that pair PubMed IDs with database names, like so: <index> <entry> <dbname>pmed_baseline_a</dbname> <pmid>579614</pmid> </entry> … </index> Each file contains entries for four of the 20 BaseX databases. I loaded the five files into a single database. My hope was that I could quickly lookup the name of the database that contained a record by that record's PMID, and that I could then open that collection and quickly obtain that record, but it isn't working the way I had hoped. If I query the index database by PMID, I get the answer in 156ms: let $pmid := '22345065' let $icoll := collection('idx_pmed_baseline') let $pmid_lookup := $icoll/index/entry/pmid let $entry := $pmid_lookup[text()=$pmid] let $dbname := $entry/parent::entry/dbname/text() return $dbname (: returns 'pmed_baseline_s' :) If I open and query that collection by XPath for that PMID, also get the answer quickly, in about 420ms: let $coll := collection('pmed_baseline_s') let $pmid := '22345065' let $wanted := $coll/PubmedArticleSet/PubmedArticle[MedlineCitation/PMID/text()=$pmid] return $wanted (: returns desired XML record :) But if I combine the code to run in a single execution, it takes about 40s: let $pmid := '22345065' let $icoll := collection('idx_pmed_baseline') let $pmid_lookup := $icoll/index/entry/pmid let $entry := $pmid_lookup[text()=$pmid] let $dbname := $entry/parent::entry/dbname/text() let $coll := collection($dbname) let $wanted := $coll/PubmedArticleSet/PubmedArticle[MedlineCitation/PMID/text()=$pmid] return $wanted I feel like I must be doing some simple thing wrong, but the only difference I see in my code between the two separate steps and the single execution version is that I'm passing the db name in a variable instead of as a string literal to the collection() function, and I'm running the whole thing in a single execution. Note that before each execution of an XQuery, I exited basexgui and restarted it to avoid any caching effect in memory at least. The VM I'm running on is modest (spinning drives in RAID 1, four modest AMD CPU cores, dynamic memory growth up to 32GB). But these factors would not explain the difference in speed between the two steps in separate executions and both steps in a single execution. Can anyone point out what I'm doing wrong? And is there a better way to go about this? Many thanks & all the best, Chuck

2 5

attribute-range()
by Johannes Bauer 29 Mar '22

29 Mar '22

Hello, when I use the db:attribute-range function with the attribute name filter I always get all attributes: db:attribute-range("db", "1", "1000", "id") I would expect that it only returns the "id" attributes. It seems the attribute name does not matter at all. The results are always the same even for a bogus attribute name. Regards Johannes

2 1