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update_uns can now handle nested keys #22

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update_uns can now handle nested keys #22

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88 changes: 73 additions & 15 deletions src/cell_type_mapper/utils/anndata_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,21 +74,79 @@ def update_uns(h5ad_path, new_uns, clobber=False):

Otherwise, raise an exception of there are duplicate keys.
"""
uns = read_uns_from_h5ad(h5ad_path)
if not clobber:
new_keys = set(new_uns.keys())
old_keys = set(uns.keys())
duplicates = new_keys.intersection(old_keys)
if len(duplicates) > 0:
duplicates = list(duplicates)
duplicates.sort()
msg = (
"Cannot update uns. The following keys already exist:\n"
f"{duplicates}"
)
raise RuntimeError(msg)
uns.update(new_uns)
write_uns_to_h5ad(h5ad_path, uns_value=uns)
updated_uns = read_uns_from_h5ad(h5ad_path)

for new_key in new_uns:
updated_uns = _update_uns_key(
old_uns=updated_uns,
key=new_key,
new_data=new_uns[new_key],
clobber=clobber
)

write_uns_to_h5ad(h5ad_path, uns_value=updated_uns)


def _update_uns_key(
old_uns,
key,
new_data,
clobber,
key_str=None):
"""
Update one key, value pair in the uns dict.

Parameters
----------
old_uns:
a dict. The uns dict being updated
key:
any. The key in old_uns being updated
new_data:
any. The data that goes with key in the new uns dict
clobber:
a boolean. If True and key already exists in old_uns, overwrite.
If False and key already exists in old_uns, raise an exception.
key_str:
a str. Used to keep track of the chain of nested keys we
are updating for more helpful error messages)

Returns
-------
The updated old_uns dict (note that old_uns is also updated in place)
"""
if key_str is None:
key_str = f'{key}'
else:
key_str = f'{key_str}:{key}'

if key not in old_uns:
old_uns[key] = new_data
else:
if isinstance(new_data, dict):
if not isinstance(old_uns[key], dict):
raise RuntimeError(
f"Cannot update uns. '{key_str}' points to a dict in the "
"new data, but not in the original data"
)
for inner_key in new_data:
old_uns[key] = _update_uns_key(
old_uns=old_uns[key],
key=inner_key,
new_data=new_data[inner_key],
clobber=clobber,
key_str=key_str
)
else:
if not clobber:
msg = (
"Cannot update uns. The following key already exists:\n"
f"{key_str}"
)
raise RuntimeError(msg)
old_uns[key] = new_data

return old_uns


def does_obsm_have_key(h5ad_path, obsm_key):
Expand Down
131 changes: 130 additions & 1 deletion tests/utils/test_anndata_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -279,9 +279,18 @@ def test_update_uns(tmp_dir_fixture, which_test):
assert actual.uns[k] == new_uns[k]

elif which_test == 'error':
with pytest.raises(RuntimeError, match="keys already exist"):
with pytest.raises(RuntimeError, match="key already exists"):
update_uns(h5ad_path, new_uns={'a':2, 'f': 6}, clobber=False)

# make sure uns was unchanged
actual = anndata.read_h5ad(h5ad_path)
assert set(actual.uns.keys()) == set(original_uns.keys())
for k in original_uns:
if isinstance(actual.uns[k], np.ndarray):
np.testing.assert_array_equal(actual.uns[k], original_uns[k])
else:
assert actual.uns[k] == original_uns[k]

elif which_test == 'clobber':
update_uns(h5ad_path, new_uns={'a': 2, 'f': 6}, clobber=True)
actual = anndata.read_h5ad(h5ad_path, backed='r')
Expand All @@ -293,6 +302,126 @@ def test_update_uns(tmp_dir_fixture, which_test):
else:
raise RuntimeError(f"cannot parse which_test = {which_test}")


@pytest.mark.parametrize(
'clobber', [True, ]
)
def test_compound_update_uns(tmp_dir_fixture, clobber):

original_uns = {
'a': 1,
'b': 9,
'c': {
'd': 4,
'other_dict': {
'z': 88,
'u': 14
}
}
}

a_data = anndata.AnnData(
uns=original_uns)
h5ad_path = mkstemp_clean(
dir=tmp_dir_fixture,
prefix='update_uns_',
suffix='.h5ad')
a_data.write_h5ad(h5ad_path)

new_uns = {
'c': {
'e': 2,
'f': 3,
'other_dict': {
'x': 17,
},
'still_another_dict': {
'y': 55
}
}
}

update_uns(h5ad_path, new_uns=new_uns, clobber=False)
roundtrip = anndata.read_h5ad(h5ad_path)
expected = {
'a': 1,
'b': 9,
'c': {
'd': 4,
'e': 2,
'f': 3,
'other_dict': {
'z': 88,
'x': 17,
'u': 14
},
'still_another_dict': {
'y': 55
}
}
}
assert roundtrip.uns == expected

a_data = anndata.AnnData(
uns=original_uns)
h5ad_path = mkstemp_clean(
dir=tmp_dir_fixture,
prefix='update_uns_',
suffix='.h5ad')
a_data.write_h5ad(h5ad_path)

new_uns = {
'c': {
'd': 3,
'e': 4,
'still_another_dict': {
'y': 45
},
'other_dict': {
'x': 66,
'z': 13
}
}
}

if clobber:
update_uns(h5ad_path, new_uns=new_uns, clobber=clobber)
expected = {
'a': 1,
'b': 9,
'c': {
'd': 3,
'e': 4,
'other_dict': {
'z': 13,
'x': 66,
'u': 14
},
'still_another_dict': {
'y': 45
}
}
}
roundtrip = anndata.read_h5ad(h5ad_path)
if roundtrip.uns != expected:
import json
from cell_type_mapper.utils.utils import (
clean_for_json
)
msg = (
f"{json.dumps(clean_for_json(roundtrip.uns), indent=2)}\n"
"=======n"
f"{json.dumps(clean_for_json(expected), indent=2)}\n"
)
raise RuntimeError(msg)
else:
with pytest.raises(RuntimeError, match="key already exists"):
update_uns(h5ad_path, new_uns=new_uns, clobber=clobber)
# make sure uns was unchanged
actual = anndata.read_h5ad(h5ad_path)
assert actual.uns == original_uns


def test_read_empty_uns(tmp_dir_fixture):
"""
Make sure that reading uns from an h5ad file that
Expand Down