Make sure there is no hard dependency on AnnotateDB

draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

MIT License

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Make sure there is no hard dependency on AnnotateDB #79

Closed mephenor closed 4 years ago

mephenor commented 4 years ago

The parameter combination --annotate-with-bigg=true --add-adb-annotations=false was reported to currently throw edu.ucsd.sbrg.bigg.AnnotateDB getAnnotations --- WARNING: The connection attempt failed. Additionally models don't seem to get much annotation. This needs to be investigated and code touching AnnotateDB needs to be revisited.

mephenor commented 4 years ago

Should be fixed in the refactoring branch and already merged into master, if I am not mistaken. Need to check possible input parameter combinations for null pointer issues, however.

Schmoho commented 2 years ago

This issue is closed and at least the parameter combination seems to work fine for me. I'm closing the issue for the November 2019 and forward project.