embeddings functions do not support same values for organisms as main API

[ivirshup]

Describe the bug

While functions like get_anndata can accept values for the organism argument like "Homo sapiens" or "homo_sapiens", functions in the embedding API only accept snake-case values like "homo_sapiens".

To Reproduce

import cellxgene_census, cellxgene_census.experimental

CENSUS_VERSION = "2023-12-15"
census = cellxgene_census.open_soma(census_version=CENSUS_VERSION)

Both of these work:

cellxgene_census.get_obs(census, "homo_sapiens", coords=[1, 2, 3])
cellxgene_census.get_obs(census, "Homo sapiens", coords=[1, 2, 3])

For the embeddings, this works:

cellxgene_census.experimental.get_embedding_metadata_by_name(
	census_version=CENSUS_VERSION,
	organism="homo_sapiens",
	embedding_name="scvi",
)

But this doesn't:

cellxgene_census.experimental.get_embedding_metadata_by_name(
	census_version=CENSUS_VERSION,
	organism="Homo sapiens",
	embedding_name="scvi",
)

File ~/github/cellxgene-census/api/python/cellxgene_census/src/cellxgene_census/experimental/_embedding.py:207, in get_embedding_metadata_by_name(embedding_name, organism, census_version, embedding_type)
    204         embeddings.append(obj)
    206 if len(embeddings) == 0:
--> 207     raise ValueError(f"No embeddings found for {embedding_name}, {organism}, {resolved_census_version}, {embedding_type}")
    209 return sorted(embeddings, key=lambda x: x["submission_date"])[-1]

ValueError: No embeddings found for scvi, Homo sapiens, 2023-12-15, obs_embedding

Expected behavior

The accepted values and behavior of the organism argument to be consistent across functions.

Environment

Provide a description of your system and the software versions.

-----
IPython             8.24.0
anndata             0.10.7
cellxgene_census    1.14.2.dev4+gcfca649.d20240612
pandas              2.2.2
session_info        1.0.0
tiledbsoma          1.12.0
-----
aiobotocore         2.13.0
aiohttp             3.9.5
aioitertools        0.11.0
aiosignal           1.3.1
asttokens           NA
attr                23.2.0
attrs               23.2.0
botocore            1.34.106
certifi             2024.02.02
cffi                1.16.0
charset_normalizer  3.3.2
cloudpickle         2.2.1
cython_runtime      NA
dask                2024.5.2
dateutil            2.9.0.post0
decorator           5.1.1
dill                0.3.8
executing           2.0.1
frozenlist          1.4.1
fsspec              2024.3.1
h5py                3.11.0
idna                3.7
importlib_metadata  NA
jedi                0.19.1
jinja2              3.1.4
jmespath            1.0.1
llvmlite            0.42.0
markupsafe          2.1.5
multidict           6.0.5
natsort             8.4.0
numba               0.59.1
numpy               1.26.4
packaging           24.0
parso               0.8.4
prompt_toolkit      3.0.45
psutil              5.9.8
pure_eval           0.2.2
pyarrow             15.0.2
pyarrow_hotfix      NA
pycparser           2.22
pygments            2.18.0
pytz                2024.1
requests            2.32.2
s3fs                2024.3.1
scipy               1.13.1
six                 1.16.0
somacore            1.0.11
sparse              0.15.4
stack_data          0.6.3
tblib               1.7.0
tiledb              0.30.0
tlz                 0.12.1
toolz               0.12.1
torch               2.2.2+cu121
torchgen            NA
tqdm                4.66.4
traitlets           5.14.3
typing_extensions   NA
urllib3             2.2.1
wcwidth             0.2.13
wrapt               1.16.0
xxhash              NA
yaml                6.0.1
yarl                1.9.4
zipp                NA
-----
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
Linux-6.8.0-1009-aws-x86_64-with-glibc2.39
-----
Session information updated at 2024-06-24 23:50

Additional context

Some previous discussion:

• Argument organism of cellxgene_census._get_experiment/cellxgene.census::get_experiment should allow computer readable strings: "homo_sapiens" and "mus_musculus" #646