Revised the class MondoCommand to reflect the changes from phenol

TheJacksonLaboratory / HPOworkbench

Human Phenotype Ontology Workbench

http://hpo-workbench.readthedocs.io/en/latest/

BSD 3-Clause "New" or "Revised" License

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Revised the class MondoCommand to reflect the changes from phenol #29

Closed yy20716 closed 6 years ago

yy20716 commented 6 years ago

I made a small change in the class MondoCommand to reflex the change in phenol, i.e. the removal of duplicated DbXref class.
I also confirmed that errors from missing curie_map.yaml were resolved when I ran HPOworkbench with the refactored phenol. However, I saw the error that mondo.obo is missing - I guess this happened because I didn't feed that file as input, but please let me know if you found any other errors. Thank you.

pnrobinson commented 6 years ago

This is now working but I am not able to access the cross references

GenericTerm gt = // get a generic term object
List<Dbxref> xrefs = gt.getXrefs();

Here, getXrefs() always appears to be returning null. I think it would also be better if we implemented that to return an empty Immutable list, something like return ImmutableList.of(), I think.