BaseX-Talk

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6 participants
5269 discussions

Re: [basex-talk] BaseX mail archive stopped working
by Christian Grün 13 Jan '25

13 Jan '25

Hi Yitzhak (cc to the list), Thanks for letting us know. I don’t know who maintains the mail archive. What I know is that the administrators of our mailing list (located at University of Konstanz) will upgrade to a new version of Mailman. Maybe that caused the archiver to stop. If we are lucky, it will work again once the upgrade is completed. Until then, you may need to resort to the threaded list of messages (without search function): https://mailman.uni-konstanz.de/pipermail/basex-talk/ Maybe it’s time for us to write our own little indexer. Or maybe someone else wants to tackle that, as a little XQuery Full Text project? ;) Best, Christian On Mon, Jan 13, 2025 at 3:17 PM <ykhabins(a)bellsouth.net> wrote: > Mr. Grun, > > > > It seems that the BaseX mail archive stopped working starting from > 2025-01-03: > > > https://www.mail-archive.com/basex-talk@mailman.uni-konstanz.de/maillist.ht… > > > > Re: [basex-talk] Basex stops with error: 'Index -1 out of bounds for > length 32'. > <https://www.mail-archive.com/basex-talk@mailman.uni-konstanz.de/msg16014.ht…> > was the last thread. > > > > I received few email notifications dated after 2025-01-03. > > So, it is a proof that the BaseX mail archive is not updated. ☹ > > > > > > *Regards,Yitzhak Khabinsky**Skype: ykhabins* > > >

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Error when passing a value via %rest:form-param in combination with a security function
by Jan Meijer 09 Jan '25

09 Jan '25

In BaseX v11.6 an error occurs when passing a value via "%rest:form-param" in combination with a security function. The example below consists of two RESTXQ functions "p:post" and "p:form". After submitting the form with a value for input "resource-id" the following error occurs in function "p:post": Stopped at /usr/local/basex/webapp/ui/problem.xqm, 16/10: [basex:restxq] Value of "resource-id" must be xs:string, supplied: (). Example module problem.xqm: module namespace p = 'problem'; declare %perm:check('/p', '{$perm}') function p:check( $perm as map(*) ) as element(rest:response)? { }; declare %rest:path('/p/post') %rest:POST %rest:form-param("resource-id", "{$resource-id}") %output:method('html') %output:version('5.0') function p:post( $resource-id as xs:string ) { <div> <p>$resource-id={$resource-id}</p> </div> }; declare %rest:path('/p/form') %rest:GET %output:method('html') %output:version('5.0') function p:form() { <div> <form method="post" action="/p/post"> <input type="text" name="resource-id" id="resource-id" required="required"/><br/> <button type="submit">Ok</button> </form> </div> }; The described behavior is caused by the security function "p:check". 1. If you remove the security function "p:check" it works fine. 2. If you replace `%rest:form-param` with `%rest:query-param` it also works fine, but that doesn't seem right to me. Is this a bug or do I something wrong? Kind regards, Jan Meijer

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Basex stops with error: 'Index -1 out of bounds for length 32'.
by Rob Stapper 03 Jan '25

03 Jan '25

Hi Christian, First of all best wishes for the next year, may it be an interesting one. Having said that, I encountered this 'interesting' issue. I vagely think to remember something lijke this is adressed before but I'm not sure. I hereby send you a self containing application: 'nastyIssueTest2.xq', that triggers the error. I've made the code as small as possible, but since the occurrence of the error very much depends on the context, some context code is necessary. ( I don't think the context code triggers the error but more suppresses it, adding a trace somewhere could make the error just disappear) I suspect that the first function in the app: 'local:for-each-component#4', is the culprit, but I can't really tell. I've also added a workaround in the app: 'local:for-each-component2#2', which seems a stable solution. The issue looks like something like 'https://github.com/BaseXdb/basex/issues/909' of march 2014. Btw. I used version 11.3. Updating to version 11.6 triggers a different error when code of function: 'local:folderDialog.new#2', is activated. When deactivated it triggers the above mentioned error. I hope this helps. mvgr. Rob Stapper

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No create permission error in BaseX fiddle on HTTP(S) request
by Martin Honnen 03 Jan '25

03 Jan '25

Hi folks, today when trying HTTP(S) requests in the BaseX fiddle like e.g. json-doc('https://martin-honnen.github.io/xslt/2024/sample1.json') I get an error No create permission: json-doc("https://martin-honnen.github.io/xslt/2024/sample1.json") Is that some intended restriction/limitation of the fiddle or some bug/quirk that has slipped in?

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Re: [basex-talk] XSD validation: cache invalidation stopped working
by ykhabins＠bellsouth.net 30 Dec '24

30 Dec '24

Hello, >> Note that the GUI runs in an independent JVM; it does not influence HTTP calls. The explanation was very helpful. I ended up with a CURL command to invalidate XSD that is cached behind HTTP listener calls (different JVM). curl -i -u <username>:<password> -X POST -H "Content-Type: application/xml" -d "<query xmlns='http://basex.org/rest'><text>validate:xsd-init()</text></query>" "http://<host>:8080/rest" It emits the following: HTTP/1.1 200 OK Date: Mon, 30 Dec 2024 14:44:03 GMT Content-Type: application/xml; charset=UTF-8 Content-Length: 0 Server: Jetty(11.0.24) And everything is working as expected. Thanks a lot. Regards, Yitzhak Khabinsky

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Re: [basex-talk] XSD validation: cache invalidation stopped working
by ykhabins＠bellsouth.net 30 Dec '24

30 Dec '24

Here is a full repro. Initial setup, four files: 1) XML: e:\Temp\XSD_CACHE\input.xml 2) XSD: e:\Temp\XSD_CACHE\state.xsd 3) XQuery: c:\Program Files (x86)\BaseX\webapp\XSD11_Validation_RECEIPT_2.xq 4) c# file making BaseX REST HTTP call XML file: e:\Temp\XSD_CACHE\input.xml ====================================== <?xml version="1.0"?> <root> <state>FL</state> <state>TX</state> </root> XSD file: e:\Temp\XSD_CACHE\state.xsd ========================================= <?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" version="1.0.0"> <xs:element name="root"> <xs:complexType> <xs:sequence> <xs:element maxOccurs="unbounded" ref="state"/> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="state" type="state_type"/> <xs:simpleType name="state_type"> <xs:restriction base="xs:string"> <xs:length value="2"/> <xs:enumeration value="FL"/>  </xs:restriction> </xs:simpleType> </xs:schema> XQuery file: XSD11_Validation_RECEIPT_2.xq ========================================== declare variable $xml as xs:string external; declare variable $xsd as xs:string external; try { let $timezone := timezone-from-dateTime(current-dateTime()) let $before_datetime := adjust-dateTime-to-timezone(convert:integer-to-dateTime(prof:current-ms()), xs:dayTimeDuration($timezone)) (: current-dateTime() :) let $result := validate:xsd-report($xml, $xsd, map { 'http://apache.org/xml/features/validation/cta-full-xpath-checking': true(), 'cache': true() }) let $after_datetime := adjust-dateTime-to-timezone(convert:integer-to-dateTime(prof:current-ms()), xs:dayTimeDuration($timezone)) (: current-dateTime() :) return <root><metadata> <result>{data($result/status)}</result> <errors>{count($result/message[@level="Error"])}</errors> <warnings>{count($result/message[@level="Warning"])}</warnings> <startTime>{$before_datetime}</startTime> <endTime>{$after_datetime}</endTime> <xmlFile>{$xml}</xmlFile> <xsdFile>{$xsd}</xsdFile> <xsdProcessor>BaseX {data(db:system()//version)}, Java {proc:property('java.vendor')} v.{proc:property('java.runtime.version')}, {validate:xsd-processor()} 2.12.2</xsdProcessor> <xsdVersion>{data(doc($xsd)/*:schema/@version)}</xsdVersion> </metadata> <messages>{ $result/message transform with { delete node @url } }</messages> </root> } catch * { <error> <errorCode>{$err:code}</errorCode> <errorDescription>{$err:description}</errorDescription> </error> } c# REST HTTP call: ================== void Main() { const string HOST = "HostName"; const int PORT = 8080; const string USERNAME = "username"; const string PASSWORD = "password"; System.Net.ServicePointManager.SecurityProtocol = SecurityProtocolType.Tls12 | SecurityProtocolType.Tls11 | SecurityProtocolType.Tls; const string XQUERY = "XSD11_Validation_RECEIPT_2.xq"; string xmlFile = @"e:\Temp\XSD_CACHE\input.xml"; string xsdFile = @"e:\Temp\XSD_CACHE\state.xsd"; string REQUESTURL = $"http://{HOST}:{PORT}/rest?run={XQUERY}&$xml={xmlFile}&$xsd={xsdFile}"; try { using (HttpClientHandler handler = new HttpClientHandler() {UseDefaultCredentials = true}) // for mdpd proxy //{UseDefaultCredentials = true, UseProxy = true, DefaultProxyCredentials = CredentialCache.DefaultNetworkCredentials}) using (HttpClient client = new HttpClient(handler)) { // Encode username and password pair with a base64 implementation. String encoded = Convert.ToBase64String(Encoding.UTF8.GetBytes(USERNAME + ":" + PASSWORD)); client.DefaultRequestHeaders.Add("Authorization", "Basic " + encoded); client.DefaultRequestHeaders.Accept.Add(new MediaTypeWithQualityHeaderValue("application/xml")); var response = client.GetAsync(REQUESTURL).Result; System.Net.Http.HttpContent content = response.Content; var contentString = content.ReadAsStringAsync().Result; // get the actual content string if (response.StatusCode == HttpStatusCode.OK) // 200 //IsSuccessStatusCode == True { XDocument xdoc2 = XDocument.Parse(contentString); Console.WriteLine(xdoc2); string fileRECEIPT = $@"{Path.Combine(Path.GetDirectoryName(xmlFile), Path.GetFileNameWithoutExtension(xmlFile))}_RECEIPT_{DateTime.Now.ToString(" yyyy-MM-ddTHH-mm-ss")}.xml"; xdoc2.Save(fileRECEIPT, SaveOptions.None); } else { string fileErrorResponse = $@"{Path.Combine(Path.GetDirectoryName(xmlFile), Path.GetFileNameWithoutExtension(xmlFile))}_ErrorResponse_{DateTime.Now.ToSt ring("yyyy-MM-ddTHH-mm-ss")}.xml"; File.WriteAllText(fileErrorResponse, contentString); } } } catch (Exception ex) { ex.Message.Dump(); } } In BaseX GUI: SET BINDINGS xml=e:\Temp\XSD_CACHE\input.xml,xsd=e:\Temp\XSD_CACHE\state.xsd Start BaseX HTTP listener via launching c:\Program Files (x86)\BaseX\bin\basexhttp.bat First execution emits the following correct result in both BaseX GUI as well as c# REST HTTP: ============================================================================ ================= <root> <metadata> <result>invalid</result> <errors>2</errors> <warnings>0</warnings> <startTime>2024-12-29T21:00:55.659-05:00</startTime> <endTime>2024-12-29T21:00:55.729-05:00</endTime> <xmlFile>e:\Temp\XSD_CACHE\input.xml</xmlFile> <xsdFile>e:\Temp\XSD_CACHE\state.xsd</xsdFile> <xsdProcessor>BaseX 11.6, Java Eclipse Adoptium v.22.0.2+9, Xerces 2.12.2</xsdProcessor> <xsdVersion>1.0.0</xsdVersion> </metadata> <messages> <message level="Error" line="4" column="19">cvc-enumeration-valid: Value 'TX' is not facet-valid with respect to enumeration '[FL]'. It must be a value from the enumeration.</message> <message level="Error" line="4" column="19">cvc-type.3.1.3: The value 'TX' of element 'state' is not valid.</message> </messages> </root> Modified XSD file: xsd=e:\Temp\XSD_CACHE\state.xsd 1) attribute version="1.0.1" 2) uncommented <xs:enumeration value="TX"/> to make XML file valid ========================================================== <?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" version="1.0.1"> <xs:element name="root"> <xs:complexType> <xs:sequence> <xs:element maxOccurs="unbounded" ref="state"/> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="state" type="state_type"/> <xs:simpleType name="state_type"> <xs:restriction base="xs:string"> <xs:length value="2"/> <xs:enumeration value="FL"/> <xs:enumeration value="TX"/> </xs:restriction> </xs:simpleType> </xs:schema> Execute in BaseX GUI: validate:xsd-init() Re-run c# REST HTTP CALL emits incorrect result. It shows correct xsdVersion: 1.0.1, but result is invalid with the same error ============================================================================ = <root> <metadata> <result>invalid</result> <errors>2</errors> <warnings>0</warnings> <startTime>2024-12-29T21:20:07.457-05:00</startTime> <endTime>2024-12-29T21:20:07.459-05:00</endTime> <xmlFile>e:\Temp\XSD_CACHE\input.xml</xmlFile> <xsdFile>e:\Temp\XSD_CACHE\state.xsd</xsdFile> <xsdProcessor>BaseX 11.6, Java Eclipse Adoptium v.22.0.2+9, Xerces 2.12.2</xsdProcessor> <xsdVersion>1.0.1</xsdVersion> </metadata> <messages> <message level="Error" line="4" column="19">cvc-enumeration-valid: Value 'TX' is not facet-valid with respect to enumeration '[FL]'. It must be a value from the enumeration.</message> <message level="Error" line="4" column="19">cvc-type.3.1.3: The value 'TX' of element 'state' is not valid.</message> </messages> </root> Though executing XSD11_Validation_RECEIPT_2.xq directly in the BaseX GUI emits the correct result: <root> <metadata> <result>valid</result> <errors>0</errors> <warnings>0</warnings> <startTime>2024-12-29T21:23:51.738-05:00</startTime> <endTime>2024-12-29T21:23:51.739-05:00</endTime> <xmlFile>e:\Temp\XSD_CACHE\input.xml</xmlFile> <xsdFile>e:\Temp\XSD_CACHE\state.xsd</xsdFile> <xsdProcessor>BaseX 11.6, Java Eclipse Adoptium v.22.0.2+9, Xerces 2.12.2</xsdProcessor> <xsdVersion>1.0.1</xsdVersion> </metadata> <messages/> </root> Just restart of the BaseX HTTP listener resolves the issue with the BaseX REST HTTP call. Regards, Yitzhak Khabinsky

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XSD validation: cache invalidation stopped working
by ykhabins＠bellsouth.net 29 Dec '24

29 Dec '24

Hello, My environment has BaseX 11.6 installed. The XQuery is called in c# via REST HTTP call: string REQUESTURL = $"http://{HOST}:{PORT}/rest?run={XQUERY}&$xml={xmlFile}&$xsd={xsdFile}"; XQuery is using XSD validation with caching, along the following: let $result := validate:xsd-report($xml, $xsd, map { 'http://apache.org/xml/features/validation/cta-full-xpath-checking': true(), 'cache': true() }) It seems that the cache invalidation call stopped working ?! It is not picking up the latest XSD. I launch it from the BaseX GUI as follows: validate:xsd-init() Just restart of the HTTP listener picks up the latest/modified XSD. Please advise. Regards, Yitzhak Khabinsky

2 1

serialization order of map in fiddle
by Martin Honnen 29 Dec '24

29 Dec '24

After some recent announcement of ordered maps in the BaseX fiddle I played around with some JSON serialization, to my surprise the result is different whether I use the serialize function directly on a single map <https://fiddle.basex.org/?share=%28%27query%21%27%2803.*2%2C%5Cn%28.30*24%2…>: {'foo' : 'bar', 'data' : array { 1 to 5 }} => serialize({'method' : 'json', 'indent' : true() }), {'data' : array { 1 to 5 }, 'foo' : 'bar'} => serialize({'method' : 'json', 'indent' : true() }) gives { "foo": "bar", "data": [ 1, 2, 3, 4, 5 ] } { "data": [ 1, 2, 3, 4, 5 ], "foo": "bar" } or in a for .. return <https://fiddle.basex.org/?share=%28%27query%21%27for+%24map+in+%7B%280.-%29…>: for $map in ({'foo' : 'bar', 'data' : array { 1 to 5 }}, {'data' : array { 1 to 5 }, 'foo' : 'bar'}) return serialize($map, {'method' : 'json', 'indent' : true() }) gives { "foo": "bar", "data": [ 1, 2, 3, 4, 5 ] } { "foo": "bar", "data": [ 1, 2, 3, 4, 5 ] } Should the JSON serialization reflect the map as created or is that still random/arbitrary order for the properties?

2 1

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

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