SPLIT fails with owl:NamedIndividual

[hkir-dev]

In ROBOT version 1.8.1, I have a very simple template:

ID,Entity Type,Synonyms
ID,TYPE,A oboInOwl:hasExactSynonym SPLIT=|
ex:indv_2,owl:NamedIndividual,Sncg_4|Alpha7 cell

robot template --template ./template_fail2.csv --output ./output.owl

output is:

<NamedIndividual rdf:about="ex:indv_2">
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sncg_4|Alpha7 cell</oboInOwl:hasExactSynonym>
</NamedIndividual>

if I change owl:NamedIndividual to owl:Class, owl:DataProperty etc. or completely delete the column, SPLIT works as expected:

<Class rdf:about="ex:indv_2">
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alpha7 cell</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Sncg_4</oboInOwl:hasExactSynonym>
</Class>

[hkir-dev]

Seems SPLIT is removed from template while processing individuals:

robot/robot-core/src/main/java/org/obolibrary/robot/Template.java

Line 1868 in dd5641e

template = template.substring(0, template.indexOf("SPLIT=")).trim();

So TemplateHelper.getAnnotations works like there is no SPLIT.

Do you have any suggestions for a workaround or quick fix?

[matentzn]

We are planning a new release relatively soon. If you can provide a pull request with a fix, you can in the meantime use the DEV version of ROBOT, but we will get it in production asap as well.

[hkir-dev]

I am using robot as part of ODK. Do you know if there will be a new ODK release also?

[matentzn]

As soon as we have a new ROBOT version, we will update ODK - 1,2 days later.

[matentzn]

(just for yourself, I can show you how you can quickly compile the ODK with a ROBOT development version, so you don't have to wait)

[hkir-dev]

This seem like a good opportunity to contribute the robot tool. If OK for you, I can implement the fix and make a pull request next week.

[jamesaoverton]

@hkir-dev Thanks for reporting the issue. I can replicate the problem, and I think you're correct about the cause. A PR would be very much appreciated! If you don't have time, or have trouble with it, just let us know.

[jamesaoverton]

Should be fixed by #924