Add .get_entities() method to BIDSLayout

[effigies]

Currently, you can get valid entities by running BIDSLayout(bids_root).entities and a little parsing. It would be nice to have a helper function such as bids.layout.list_entities():

def list_entities(domains=('bids',)):
    res = []
    for domain in domains:
        res.extend(...)  # Parse the entities from the JSON files
    return res

The reason this comes up is that, currently, nipype.interfaces.io.BIDSDataGrabber manually parses the JSON files, found in a path relative to bids.__file__. This isn't great.

[tyarkoni]

Grabbit's Layout has a .get_domain_entities() method that may do what you want. The name reflects the fact that it takes an optional domains argument (so, e.g., you can get all and only derivatives entities), but we could easily add an alias in pybids if you think it's worth it.

[effigies]

If this is a classmethod, then that works just fine. The main thing is we need access to this information without necessarily populating a layout.

[tyarkoni]

It's an instance method at the moment, but in the interest of preserving the API and not adding new methods, we can make it a static method and pull the entities directly from the JSON. Unfortunately this isn't entirely straightforward because of the way Domains are currently initialized (through the Layout, for reasons not worth getting into). So it'll require a bit of refactoring. But it's probably worth doing anyway, because the resulting code will be a bit cleaner in other places too.

[tyarkoni]

Following up on this, in 0.8, you can do Config.load('bids') to get back a Config object that has a dictionary of entities only valid for that config. This doesn't require populating a layout, but it only works for a single config at a time. So at this point it would be very straightforward to add a static method in BIDSLayout that takes a list of config names and returns the union of available entities across all resulting Config objects.

[tyarkoni]

0.9 adds a get_entities() method that accepts scope and is_metadata arguments, where the former controls where to look for entities, and the latter allows you to restrict to only metadata or non-metadata entities if desired.