Test file is empty

[caufieldjh]

Describe the bug

As of the most recent release (https://github.com/monarch-initiative/phenio/releases/tag/v2024-09-04b), the test artifact contains no terms.

It is created like so:

robot --catalog catalog-v001.xml extract --method MIREOT --input phenio.owl --branch-from-term "UPHENO:0084945" --output phenio-test.owl

The issue is that UPHENO no longer contains a term with the CURIE UPHENO:0084945.

[caufieldjh]

Partially fixed in https://github.com/monarch-initiative/phenio/releases/tag/v2024-11-05 due to Upheno's reintroduction of obsolete terms. Should change the branch term used in test set creation.

The current phenio-test.owl looks like:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
     xml:base="http://www.w3.org/2002/07/owl"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
    <Ontology/>
    


    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Annotation properties
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->

    


    <!-- http://www.w3.org/2000/01/rdf-schema#comment -->

    <AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
    


    <!-- http://www.w3.org/2002/07/owl#deprecated -->

    <AnnotationProperty rdf:about="http://www.w3.org/2002/07/owl#deprecated"/>
    


    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Classes
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->

    


    <!-- http://purl.obolibrary.org/obo/UPHENO_0084945 -->

    <Class rdf:about="http://purl.obolibrary.org/obo/UPHENO_0084945">
        <rdfs:comment>http://purl.obolibrary.org/obo/CL_0000015-abnormalMorphologyOfAnatomicalEntity.tsv</rdfs:comment>
        <deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</deprecated>
    </Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->