Simplify AnnDataWrapper class by using zarr-based AnnData about vitessce-python HOT 5 CLOSED

We probably need to refactor the data wrapper classes so that many view config file definitions can be created while only a single file / directory is served

from vitessce-python.

@keller-mark Could you make that a bit clearer? I made a "multi-file" config in #32 but feel like I don't know quite know what I am doing. If you want to review there to make your ideas clear that's ok.

from vitessce-python.

That looks fine, I am referring more specifically to this loop https://github.com/vitessce/vitessce-python/blob/07a2721/vitessce/routes.py#L20 over data types: the loop assumes that for a specific data wrapper object obj, the obj._get_data function for a particular data type such as cells will return both:

• dt_obj_file_defs like

     [
           {
                 "url": "http://localhost:4000/my-anndata.zarr",
                 "fileType": "anndata-cells.zarr",
                 "type": "cells"
           }
      ]

• dt_obj_routes which is a list of starlette Routes like

    [
          Mount(self._get_route(dataset_uid, obj_i, "cells"),
                  app=StaticFiles(directory=os.path.dirname(zarr_filepath), html=False, check_dir=False)),
     ]

but for the AnnData data types, we can get multiple data types out of the same anndata Zarr store ("cells", "expression-matrix", "cell-sets"), so if the loop iteration gets to "cell-sets" the route will return different dt_obj_file_defs but will try to mount the same Zarr directory again. I am not actually sure if serving the same zarr store twice on two different routes will cause any issues but I figured there is a possibility

from vitessce-python.

@keller-mark That makes sense ok. Thanks for explaining.

from vitessce-python.

Done in #39

from vitessce-python.