Allow selecting punned entities in remove and filter command
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Add a `--allow-punning` option to the `remove` and `filter` command. When enabled, if a given IRI to select corresponds to several punned entities, all corresponding entities will be selected (contrary to the default behaviour, which is completely ignore all punned entities).
Mention the `--allow-punning` option in the documentation for the `remove` command. Add two test cases based on the UO ontology, which makes an intensive use of punning.
Add a unit test for the new overloading variant of OntologyHelper#getEntities() method, checking that it can return punned entities or not depending of the third parameter.
matentzn
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Mar 27, 2025
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Clean implementation, backwards compatible, important feature. Thank you!
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docs/have been added/updatedmvn verifysays all tests passmvn sitesays all JavaDocs correctCHANGELOG.mdhas been updatedCurrently, the
removeandfiltercommands completely ignore punned entities. That is, if the ontology contains, for example, both a class and an individual with the same IRIhttp://purl.obolibrary.org/obo/UO_0000039, thenrobot remove --term UO:0000039will fail to remove anything.This is because the
OntologyHelper#getEntities()method, and theOntologyHelper#getEntity()it calls in turn, does not expect any IRI to match more than exactly one entity (OntologyHelper#getEntity()explicitly throws an exception if it finds more than one entity).This PR adds a
--allow-punning(defaulting to false, preserving the default behaviour) to theremoveandfiltercommand. When set to true, whenever a term IRI matches several entities, all matching entities will be selected.This is particularly useful when dealing with the UO ontology, which makes intensive use of punning (most if not all units in that ontology are defined both as a class and as an individual).