alias feature is not motivated or documented

[nsheff]

There's a parallel yacman object in alias.py, which is said to be "A class that extends YacAttMap to provide alias feature."

@stolarczyk Can you provide any additional context or information about what this is? it is not mentioned anywhere else

[stolarczyk]

There's no docs page for this package so alias usage is documented here: https://github.com/databio/yacman/blob/master/docs/usage.md#key-aliases-in-aliasedyacattmap

[nsheff]

perfect, thanks for the pointer

[nsheff]

@stolarczyk can you tell me where we made use of the AliasedYacAttMap object?

I thought it was refgenconf but I see that is not the case.

[nsheff]

One thing I'm wondering about is: how does this handle nested aliases? All the examples are providing aliases for top-level items in the dict. How do you accommodate aliases for second-level (or lower) items in a nested dict? It seems this isn't implemented to work like that, so can this functionality arise from the recursive nature of attmap?

Follow-up question: is this important for our use case?

I'm asking because in my rewrite of yacman, I'm simplifying things and so I think we'd lose the ability to specify nested aliases like this and I want to know if that is important.

[stolarczyk]

@stolarczyk can you tell me where we made use of the AliasedYacAttMap object?

I thought it was refgenconf but I see that is not the case.

It does use it; search for "AliasedYacAttMap" in refgenconf.py file.

I didn't intend to make the key aliases feature recursive. It is meant to be used for the top level keys only.
It is actually explicitly stated in the document I linked above:

AliasedYacAttMap is a child class of YacAttMap that supports top-level key aliases

[nsheff]

Makes perfect sense, thanks!

I was misled because I noticed the primary RefGenConf object is just a YacAttMap, it didn't cross my mind that it may be used as a separate object as an attribute of that object, but I see now that's how it does. And I'm glad to hear it only requires top-level attributes, that makes my job easier!