BaseX-Talk

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8 participants
5255 discussions

Out of Main Memory
by Murray, Gregory 15 Mar '24

15 Mar '24

Hello, I’m working with a database that has a full-text index. I have found that if I iteratively add XML documents, then optimize, add more documents, optimize again, and so on, eventually the “optimize” command will fail with “Out of Main Memory.” I edited the basex startup script to change the memory allocation from -Xmx2g to -Xmx12g. My computer has 16 GB of memory, but of course the OS uses up some of it. I have found that if I exit memory-hungry programs (web browser, Oxygen), start basex, and then run the “optimize” command, I still get “Out of Main Memory.” I’m wondering if there are any known workarounds or strategies for this situation. If I understand the documentation about indexes correctly, index data is periodically written to disk during optimization. Does this mean that running optimize again will pick up where the previous attempt left off, such that running optimize repeatedly will eventually succeed? Thanks, Greg Gregory Murray Director of Digital Initiatives Wright Library Princeton Theological Seminary

4 8

validate:xsd() questions
by Murray, Gregory 11 Mar '24

11 Mar '24

Hello, What is the default value of the “cache” option for the validate:xsd() function? The default doesn’t seem to be indicated in the documentation for that function. Also, the following code raises an error message saying “Item expected, empty sequence found” but that seems odd since the second argument to validate:xsd() is supposed to be optional, thereby telling the validation process to fall back to using the schema indicated in the document itself. let $options := map {'cache' : true()} for $doc in collection() return validate:xsd($doc, (), $options) Is this a bug or have I misunderstood something? Thanks, Greg Gregory Murray Director of Digital Initiatives Wright Library Princeton Theological Seminary

2 1

xslt:transform-report result
by Andy Bunce 11 Mar '24

11 Mar '24

Hi, Using BaseX 9.7.1 and saxon9he-9.9.1.jar The documentation suggests the ?result from xslt:transform-report should be *a* document-node where possible [1] This seems not quite to be the case when there are processing instructions or comments at the top level. In these cases a sequence of document-nodes is returned. /Andy [1] https://docs.basex.org/wiki/XSLT_Module#xslt:transform-report let $xslt:=<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="3.0"> <xsl:mode on-no-match="shallow-copy"/> </xsl:stylesheet> let $xml:=document{ <?something type="compact"?>, <foo/>} return xslt:transform-report($xml,$xslt) Returns map { "messages": (), "result": (<?something type="compact"?>, <foo/>) }

3 7

Troubles with ft:mark
by Jack Steyn 07 Mar '24

07 Mar '24

Hi BaseXers, Consider the following query run on a database 'factbook' containing factbook.xml with full-text indexing: declare function local:search( $database as xs:string, $query as xs:string ) { let $country-search := ft:search($database, $query)/ancestor::country let $city-search := ft:search($database, $query)/ancestor::city/ancestor::country let $other-search := ft:search($database, $query)/parent::*[name() = ('ethnicgroups', 'languages')]/ancestor::country let $country-mark := $country-search[.//name[text() contains text { $query }]] => ft:mark() let $city-mark := $city-search[.//city[text() contains text { $query }]] => ft:mark() let $other-mark := $other-search[.//*[name() = ('ethnicgroups', 'languages')][text() contains text { $query }]] => ft:mark() return ( $country-mark, $city-mark, $other-mark ) }; local:search('factbook', 'German') The first result of this query is the entry for Austria. I would expect both of the instances of the word 'German' in that entry to be surrounded by <mark> tags. However only the first instance is. Some changes that produce the correct result for the Austria entry: - replacing $database with 'factbook' in the definition of $other-search, or - deleting either $country-mark or $city-mark in the sequence returned. If you make either of the above changes, but additionally change the predicate [text() contains text { $query }] to [ft:contains(text(), $query)], the incorrect result returns. Any idea what might be causing this? I'm running BaseX 10.7. Cheers, Jack

2 5

Inconsistent behavior for root context in BaseX GUI
by Thompson, Timothy 06 Mar '24

06 Mar '24

I’ve been noticing an inconsistent behavior in the GUI with BaseX 11 beta (build 17d8426). I have a simple query on a database created from a CSV file. Sometimes it works, but sometimes the root context is evaluated as an empty sequence: - rewrite context value: . -> () - rewrite util:root(nodes): util:root(()) -> () I notice this when I open the database as context and try to execute the query. After the query fails, if I try to click on the “home” icon in the result panel, it also returns an empty sequence, even though the database is open. If I reopen the database and run the query, it works again. Sample data: <csv> <record> <entry>http://id.loc.gov/authorities/names/n00000121</entry<http://id.loc.gov/authorities/names/n00000121%3c/entry>> <entry>http://id.loc.gov/rwo/agents/n00000121</entry<http://id.loc.gov/rwo/agents/n00000121%3c/entry>> <entry>0.11861849</entry> </record> <record> <entry>http://id.loc.gov/authorities/names/n00000122</entry<http://id.loc.gov/authorities/names/n00000122%3c/entry>> <entry>http://id.loc.gov/rwo/agents/n00000122</entry<http://id.loc.gov/rwo/agents/n00000122%3c/entry>> <entry>0.11699477</entry> </record> <record> <entry>http://id.loc.gov/authorities/names/n00000267</entry<http://id.loc.gov/authorities/names/n00000267%3c/entry>> <entry>http://id.loc.gov/rwo/agents/n00000267</entry<http://id.loc.gov/rwo/agents/n00000267%3c/entry>> <entry>0.10811427</entry> </record> </csv> Query (with DB open as context): count(distinct-values( for $rec in /csv/record where contains($rec/entry[1], "id.loc.gov") return $rec/entry[1] )) Thanks in advance, Tim -- Tim A. Thompson (he, him) Librarian for Applied Metadata Research Yale University Library www.linkedin.com/in/timathompson<http://www.linkedin.com/in/timathompson>

2 3

DBA Editor behavior in v11 not as expected
by Eliot Kimber 04 Mar '24

04 Mar '24

Using the 27-02-2024 build of v11, if I create a query in the Editor panel and then save it, the Run button is disabled, which is unexpected. If I then open the file, the Run button remains disabled. If I cut the contents of the editing panel, select “close” to clear the panel, then paste back into the panel, the Run button is enabled. I think this behavior is incorrect—as long as there is some content in the editor the Run button should be enabled. Cheers, 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>

2 5

Inconsistency in base-uri()
by Eliot Kimber 04 Mar '24

04 Mar '24

Using BaseX 11 (but I think the code is the same in BaseX 10). I’m trying to understand how base-uri() behaves relative to how it should behave when the database path of a document is not a valid URI, i.e., it has a space in it. First I have this test: let $doc as document-node() := document { <root><child xml:base="temp/child-uri%20with%20space.xml">child</child></root> } return $doc/*/child ! base-uri(.) Which produces: file:///data/basex/data/.dba/temp/child-uri%20with%20space.xml Which is the correct result: it’s the value of @xml:base and the escaped spaces make it a valid URI. Replacing %20 with “ “ in the @xml:base value results in this error: Invalid URI: Illegal character in path at index 14: temp/child-uri with space.xml. Also correct as the spaces have to be escaped. This verifies that base-uri() applied to nodes with explicit @xml:base attributes work per the spec. But this test does not involve database paths. To try to test things with database paths I then created this pair of test scripts: Script to put docs in a database: let $db := 'temp' let $filename as xs:string := 'with space.xml' let $doc1 as document-node() := document {<root><child>No xml:base</child></root>} let $doc2 as document-node() := document { <root><child xml:base="{'/temp/xmlbase/doc2_' || $filename}">With xml:base unescaped</child></root> } let $doc3 as document-node() := document { <root><child xml:base="{iri-to-uri( '/temp/xmlbase/doc3_' || $filename)}">With xml:base escaped</child></root> } return (() ,db:put($db, $doc1, 'doc1_' || $filename) ,db:put($db, $doc2, 'doc2_' || $filename) ,db:put($db, $doc3, 'doc3_' || $filename) ) Script to report on them: let $db := 'temp' let $filenameBase as xs:string := 'with space.xml' return for $i in 1 to 3 let $filename := 'doc' || $i || '_' || $filenameBase let $doc := db:get($db, $filename) let $child as element() := $doc/*/child let $dbPath := db:path($doc) let $baseUriDoc := base-uri($doc) let $baseUriChild := try { base-uri($child) } catch * { $err:description } return (() ,``[ Doc "`{$dbPath}`":]`` ,$doc ,``[xml:base att: "`{$child/@xml:base}`"]`` ,``[base URI of doc: "`{$baseUriDoc}`"]`` ,``[base URI of child: "`{$baseUriChild}`"]`` ) Which returns this result: Doc "doc1_with space.xml": <root> <child>No xml:base</child> </root> xml:base att: "" base URI of doc: "/temp/doc1_with space.xml" base URI of child: "/temp/doc1_with space.xml" Doc "doc2_with space.xml": <root> <child xml:base="/temp/xmlbase/doc2_with space.xml">With xml:base unescaped</child> </root> xml:base att: "/temp/xmlbase/doc2_with space.xml" base URI of doc: "/temp/doc2_with space.xml" base URI of child: "Invalid URI: Illegal character in path at index 23: /temp/xmlbase/doc2_with space.xml." Doc "doc3_with space.xml": <root> <child xml:base="/temp/xmlbase/doc3_with%20space.xml">With xml:base escaped</child> </root> xml:base att: "/temp/xmlbase/doc3_with%20space.xml" base URI of doc: "/temp/doc3_with space.xml" base URI of child: "Invalid URI: Illegal character in path at index 15: /temp/doc3_with space.xml." Note the result for doc3: It’s reporting the base URI of the document (/temp/doc3_with space.xml), not the base URI of the child (/temp/xmlbase/doc_with%20space.xml). Why? I think the answer is that under the covers it’s doing resolve-uri(), which also checks the validity of both the base and relative parts. One observation is that base-uri() is treating the db-provided base URI differently from an xml:base-provided base URI, but only when there is no @xml:base attribute. In doc 1, the database path has a space but base-uri() does not fail when returning it even though it’s not a valid URI. Why not? In doc 2, the xml:base-supplied base URI is correctly reported as invalid, but the database-supplied base URI of the root is not reported as invalid. My expectation would be that the behavior is consistent: Either all URIs must be valid, including those coming from database paths or all are automatically escaped (as though iri-to-uri() had been applied). Finally, why do I get the result for doc 3, where it’s reporting the database path as the base URI of the child rather than the @xml:base-defined base URI (which is correctly escaped). In my code, which depends on the use of @xml:base to do DITA link resolution for “resolved” DITA maps, I’ve adjusted my code to escape URIs in @xml:base values and as far as I can tell everything works as it should. But I’m still concerned about the inconsistency in the behavior of base-uri(). I tried to trace through the code that handles base-uri() but it’s pretty twisty and does different things for files and nodes. It would obviously be very disruptive to have base-uri() start failing on database paths with spaces—I think the current behavior dates back to the very start of BaseX, but it’s still an inconsistency that can lead to trouble with the unawares. For example, consider this code: let $topicref := db:get('maps', 'map with space.ditamap')/*/topicref[@href][1] let $target as element()? := local:resolve-href($topicref) let $baseUri as xs:string := base-uri($target) ! string(.) let $newElem as element := <submap xml:base="{$baseURI}"/> return base-uri($newElem) The value of $baseUri will be “map with space.ditamap”, not “map%20with%20space.ditamap”, making the value of @xml:base on $newElem: xml:base=”map with space.ditamap”, meaning that base-uri($newElem) will throw an invalid URI exception. My expectation would be either that base-uri($target) also throws an exception or, more usefully, that it returns the iri-to-uri() result, ensuring that the values will always be treated as valid URIs, consistent with how the database paths are treated. Cheers, E.

2 2

Possible lingering issues with database optimization in v11
by Eliot Kimber 04 Mar '24

04 Mar '24

I’m continuing to test my process for loading data which depends on optimizing databases, some of which are pretty large (100+MB with 100s of 1000s of elements). I’m testing on both macOS and linux using the 27 Feb build on macOS and the 29 build on linux (just a matter of when I downloaded them). What I’m seeing is that when I test with a relatively small content set the optimization completes reliably and everything works as it should. When I test with a realistically large data set, the optimization either takes a very long time (as much as an hour to complete) or never completes with the server at 100% CPU utilization. It seems to be worse on macOS but it’s difficult to verify, partly because a test takes several hours to run. I have the BaseX source code available locally, although I’m unable to compile with maven due to internal maven issues (we have a pretty locked down maven proxy and I don’t know maven well enough to know how I might configure around that). Is there anything I can do to diagnose this issue to at least confirm or deny that there are still deadlock issues with the optimization? I assume that it should not take 10s of minutes to optimize even a large database. Here's the details for a typical database that has failed to optimize on macOS: [cid:image001.png@01DA6D49.2FC41230] 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>

2 2

Optimize database never returns, leaves database in "opened by another process" state
by Eliot Kimber 04 Mar '24

04 Mar '24

Using Basex 10.7 on Linux. I’m running a sequence of jobs to update and optimize a set of databases following loading a number of documents created dynamically (as opposed to being read from disk). I’m seeing a new behavior, which is that the optimization step never completes but also doesn’t show any error in the log. The database shows no items and is in the locked by another process state if I try to drop it. This behavior seems to be consistently repeatable with my current code base (I’m working on some code updates, so it’s possible I’ve introduced something that would cause this behavior but I haven’t changed the code that leads up to the failing optimize). The server has plenty of disk space, etc. Optimization code is: try { if (db:exists($database)) then ( util:logToConsole('dbadmin:optimizeDatabase', ``[Optimizing database `{$database}`]``), db:optimize($database, true(), $dbadmin:dbOptimizeOptions) ) else util:logToConsole('dbadmin:optimizeDatabase', ``[Database '`{$database}`' does not exist. Nothing to optimize.]``) } catch * { util:logToConsole( 'dbadmin:optimizeDatabase', ``[Exception optimizing database '`{$database}`': `{$err:code}` - `{$err:description}`]``, 'error') } And the optimization options are: declare variable $dbadmin:dbOptimizeOptions as map(*) := (: Turn on all the indexes :) map { 'attrindex' : true(), 'tokenindex' : true(), 'textindex' : true(), 'ftindex' : true() }; This code has been working fine for a long time and I’ve been running 10.7 for a least a couple of months, so I’m wondering: A) Would would cause this behavior? B) How can I diagnose it short of debugging the Java code (which I can do but it’s non-trivial for me to set up). 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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Re: [basex-talk] Item Separator
by Leo Studer 29 Feb '24

29 Feb '24

Dear Martin Thank you for investigating. > The "text1, , text2" I only see if oXygen shows the result as a sequence in its result viewer; I would suggest to ask the oXygen support why you get that result for that case, it seems like some quirk in their result viewer (it shows two xs:string items but for reasons I can't investigate serializes the two items for the result viewer as "text1, , text2"). > This is incredible news. I will get to Oxygen about that. Really troubling … Blessings, Leo

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