BaseX-Talk

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9 participants
5241 discussions

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>

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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.

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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>

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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

1 0

Odd "Access denied" messages in the log
by Eliot Kimber 28 Feb '24

28 Feb '24

I have an application (our Mirabel system) running on a server inside our firewall (so not visible to the open Internet). I’ve recently started seeing messages like this in the log: Access denied: ��. Access denied: PRI * HTTP/2.0 SM . Where the value reported can be quite varied, but is often unrenderable characters or other stuff. (In this case the characters are all \uFFFD). The log messages all report the same IP address. This server does not use named users, so there’s no authentication required to access it. The IP address is not one of my own servers, so I don’t think it’s something generated by my own code. Any idea what this might be? It’s started relatively recently, which makes me think it might be some sort of penetration test. 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 1

Item Separator
by Leo Studer 27 Feb '24

27 Feb '24

Hello I am serialising the following expressions on oxygen/saxonEE12.3 as text (item-separator=“”) and wonder why the differente outputs let $xml:=<xml><element>text1</element><element>text2</element></xml> return $xml/element/text() gives text1text2 And let $xml:=<xml><element>text1</element><element>text2</element></xml> return $xml/element/string() text1 text2 When I set the item-separator =“, “ then I get text1, text2 Or text1, , text2 Any explanations??? Thanks, Leo

3 3

file:write, formatting, and maps in select attributes
by Graydon Saunders 24 Feb '24

24 Feb '24

Hello -- I'm trying to regularize the formatting of some XSLT files by loading them (via doc()) and writing them back out via file:write() I know about the *indent* and *indent-attributes* serialization parameters, and mostly they're doing what I want. What I'd like is to preserve a one-line-per-entry format for a map in a select attribute. For example, I'd like to keep <xsl:variable as="map(xs:integer,xs:string)" name="hexNum" select=" map { 1: '0', 2: '1', 3: '2', 4: '3', 5: '4', 6: '5', 7: '6', 8: '7', 9: '8', 10: '9', 11: 'a', 12: 'b', 13: 'c', 14: 'd', 15: 'e', 16: 'f' }" static="yes" /> instead of <xsl:variable as="map(xs:integer,xs:string)" name="hexNum" select=" map { 1: '0', 2: '1', 3: '2', 4: '3', 5: '4', 6: '5', 7: '6', 8: '7', 9: '8', 10: '9', 11: 'a', 12: 'b', 13: 'c', 14: 'd', 15: 'e', 16: 'f' }" static="yes"/> I don't think there's a way to do this with the serialization parameters, but is there a way to do this? Thanks! Graydon -- Graydon Saunders | graydonish(a)fastmail.com Þæs oferéode, ðisses swá mæg. -- Deor ("That passed, so may this.")

3 3

basex failed to cast large numbers as xs:integer
by mx z 22 Feb '24

22 Feb '24

Hi, I found a bug in basex. Version: 1ce0618 (2024.02.22) Java: openjdk 17.0.9 2023-10-17 LTS OpenJDK Runtime Environment Corretto-17.0.9.8.1 (build 17.0.9+8-LTS) OpenJDK 64-Bit Server VM Corretto-17.0.9.8.1 (build 17.0.9+8-LTS, mixed mode, sharing) OS: Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy input.xml: <a xmlns:C="p"> <C:A id="1">1458820431</C:A>1438466813 </a> query.xq: //*[not(. castable as xs:integer)] Reproduce: java -cp basex-core/target/basex-11.0-SNAPSHOT.jar org.basex.BaseX -i input.xml query.xq It printed out <a xmlns:C="p"> <C:A id="1">1458820431</C:A>1438466813 </a> While basex should return empty, as both 1458820431 and 1438466813 are integers. Max Zhang

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