Thomas/feature/8 - Githubissues

Porthmeus / MeMoMe

Metabolic Model Merging - a semiautomated way to merge genome scale metabolic models

Apache License 2.0

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Thomas/feature/8 #105

Closed Unaimend closed 1 month ago

Unaimend commented 3 months ago

handles several cases related to missing internet connection as well as some cases where just a subset of DB's could be downloaded.

Please discuss how I handle the cases i.e. returning empty AnnotationResults or should we abort? Further, there were two cases where I was not sure what to return. Those are marked in the code by NotImplemented errors.

This PR also breaks several test cases that I did not fix because we did not decide how to handle missing DBs in final

Unaimend commented 3 months ago

Still broken

Unaimend commented 3 months ago

Still broken Fixed by 3df8a33a390c8df1b1b5779954ee22f10f292985

Unaimend commented 3 months ago

We discussed adding a feature flag: The behavior should be that by default we crash if we cannot find a database, otherwise if the flag is specified we do continue wit the available databases

https://github.com/Porthmeus/MeMoMe/issues/123

Unaimend commented 3 months ago

@Porthmeus Please also fix and merge https://github.com/Porthmeus/MeMoMe/issues/103 then we can merge this branch after the command line parameter has been implemented

Unaimend commented 3 months ago

Also fixes #103