'--annotate-with-source true' does not work with extract --method subset #1157
Description
(Apologies if I have named this ticket incorrectly, please update as required).
I'm trying to add --annotate-with-source true to my ODK build procedure and I'm testing the run with this robot command:
java -jar ~/Programs/robot.jar --catalog catalog-v001.xml query -i mirror/po.owl --update ../sparql/preprocess-module.ru extract -T imports/po_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --annotate-with-source true --method subset --output test-po.owl
The above is a modified version of the command that is generated by the ODK's Makefile, and I'll put it in my own makefile if I can get it working. However, this command does not add any rdfs:isDefinedBy annotations at all.
My terms to extract only has one class (http://purl.obolibrary.org/obo/PO_0025131) and it looks great EXCEPT for the lack of an rdfs:isDefinedBy property as outlined in the ROBOT command:
<owl:Class rdf:about="http://purl.obolibrary.org/obo/PO_0025131">
<obo:IAO_0000115>An anatomical entity that is or was part of a plant.</obo:IAO_0000115>
<oboInOwl:created_by>rwalls</oboInOwl:created_by>
<oboInOwl:creation_date>2010-11-15T11:41:38Z</oboInOwl:creation_date>
<oboInOwl:hasDbXref>PO_GIT:224</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>entidad anat&#243mica vegetal (Spanish, exact)</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>植物 解剖学（形態）的実体 (Japanese, exact)</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace>plant_anatomy</oboInOwl:hasOBONamespace>
<oboInOwl:id>PO:0025131</oboInOwl:id>
<rdfs:comment>Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.</rdfs:comment>
<rdfs:label>plant anatomical entity</rdfs:label>
</owl:Class>
@jamesaoverton suggests on Slack that it may just be a missing bit of code from subset and would like this ticket created.
Thank you!
(Source)