Convert annotateGEM into a more generic function

[haowang-bioinfo]

The annotateGEM function has been embedded in exportHumanGEM function and used to integrate annotation information into Human-GEM before exporting to xml format. Would be nice to make it more generic so that it could be used by other models, e.g. Mouse-GEM.

Following adjustments are proposed for making annotateGEM a more generic function:

• introduce an additional argument annotationPath to specify the location of annotation files
• set annotationPath as the 2nd argument, only two argument are required when used for other models
• if this argument is missing, fetch annotation files from default path of Human-GEM, as is
• there is no changes to any other functions that call this function

[JonathanRob]

Good suggestion, @haowang-bioinfo. I guess the annotationPath could directly reference the file on GitHub (e.g., annotationPath = https://raw.githubusercontent.com/SysBioChalmers/Mouse-GEM/main/model/), or be a relative/local path, right?

[haowang-bioinfo]

I guess the annotationPath could directly reference the file on GitHub (e.g., annotationPath = https://raw.githubusercontent.com/SysBioChalmers/Mouse-GEM/main/model/), or be a relative/local path, right?

thanks @JonathanRob for the feedback. I only considered local path when proposing annotationPath argument. Really uncertain about how difficult in enabling it also as a cloud path.

[JonathanRob]

I think it's possible using urlread, but now that I think about it, probably not worth the added work of enabling a web path. I agree that a local path is the most useful option for now.

[haowang-bioinfo]

I think it's possible using urlread, but now that I think about it, probably not worth the added work of enabling a web path. I agree that a local path is the most useful option for now.

thanks, will work on the implementation of adding annotationPath argument for local path and keep the web path option open for future refinement.