Wrong base namespaces in merged ontologies

[mereolog]

Some, but not all, merged ontologies got wrong base namespaces.

For example, https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/ gets https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/ as its base namespace:

<?xml version="1.0"?>
<rdf:RDF xmlns="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/"
     xml:base="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     ...
     xmlns:idmp-phdf="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms/"
    ...
>
<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/">
     <owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/idmp-550/latest/ISO/ISO11239-PharmaceuticalDoseForms-Merged/"/>
     ...

Note the original file as well:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE rdf:RDF [
	<!ENTITY cmns-av "https://www.omg.org/spec/Commons/AnnotationVocabulary/">
	<!ENTITY cmns-cds "https://www.omg.org/spec/Commons/CodesAndCodeSets/">
	....
	<!ENTITY idmp-mprd "https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11615-MedicinalProducts/">
	<!ENTITY idmp-phdf "https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms/">
	....
]>
<rdf:RDF xml:base="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms/"
	xmlns:cmns-av="https://www.omg.org/spec/Commons/AnnotationVocabulary/"
	xmlns:cmns-cds="https://www.omg.org/spec/Commons/CodesAndCodeSets/"
	...
>

<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms/">

This issue may be related to #364.

[przemekgradzki]

Some, but not all, merged ontologies got wrong base namespaces.

For example, https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/ gets https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/ as its base namespace:

<?xml version="1.0"?>
<rdf:RDF xmlns="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/"
     xml:base="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11616-PharmaceuticalProducts/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     ...
     xmlns:idmp-phdf="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms/"
    ...
>
<owl:Ontology rdf:about="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/">
     <owl:versionIRI rdf:resource="https://spec.pistoiaalliance.org/idmp/ontology/idmp-550/latest/ISO/ISO11239-PharmaceuticalDoseForms-Merged/"/>

The current ontology https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/ generated on Fri, 30 Jun 2023 13:42:48 GMT (see the output of the curl --head -L https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/ 2>/dev/null | grep 'last-modified' command) contains the correct values ​​- the result of the following command:

curl -q -L https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/ 2>/dev/null | grep -P 'xml(ns|:base)='

is correct:

<rdf:RDF xmlns="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/"
xml:base="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/"

---

The current version of the ontology was generated using the updated version of ontology-publisher (see Last pushed ... for ontology-publisher:stable), but earlier versions of the ontology (before the ontology-publisher update) also contain the correct values ​​- e.g. the command to check xmlns and xml:base against the last merged pr-392 (i.e. identical to the current one):

curl -q -L https://spec.pistoiaalliance.org/idmp/ontology/pr-392/latest/ISO/ISO11239-PharmaceuticalDoseForms-Merged/ 2>/dev/null | grep -P 'xml(ns|:base)='

show valid values

<rdf:RDF xmlns="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/"
xml:base="https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11239-PharmaceuticalDoseForms-Merged/"

---

@mereolog the problem cannot be reproduced