Closed GwennyGit closed 1 year ago
I changed the implementation of how BioCyc identifiers are treated. The newer version makes more sense with the new setup. However, I also found that the 'bug' was not caused by the 'polish' module itself but rather by the fact that in the AGORA 2 models, it was tested on, the BioCyc identifiers contain no indication for the BioCyc sub-database like 'META:' for the MetaCyc database. I think this issue can be coped with in Polish and, thus, before releasing the newer version I will try to cope with missing sub-database prefixes for BioCyc identifiers.
I found another bug within polish
concerning the resulting invalid_curies.tsv
file. For a lot of entities None
values for the database prefix and the corresponding identifier are printed. Before pushing the changes to main and generating a new release I will investigate and fix this bug.
Describe the bug
invalid_curies.tsv
make no sense as they haveNone
as database prefix andNone
as identifier.Expected behavior
polish
needs to handle missing sub-database prefixes for BioCyc URIs/IRIs.None
this invalid curie should not be reported in theinvalid_curies.tsv
.