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[python] Fix registration path with non-standard obs/var index names #2281

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Mar 18, 2024
Merged

[python] Fix registration path with non-standard obs/var index names #2281

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619caf5
[python] Neaten registration-mapping test code
johnkerl Mar 18, 2024
d1f433c
[python] Fix registration path with non-standard obs/var index names
johnkerl Mar 15, 2024
2599508
Merge branch 'main' into kerl/aov
johnkerl Mar 18, 2024
4fa9f64
lint
johnkerl Mar 18, 2024
afd6d7b
code-review feedback
johnkerl Mar 18, 2024
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4 changes: 4 additions & 0 deletions apis/python/src/tiledbsoma/io/_registration/ambient_label_mappings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -400,6 +400,8 @@ def from_anndata_appends_on_experiment(
registration_data,
measurement_name=measurement_name,
append_obsm_varm=append_obsm_varm,
obs_field_name=obs_field_name,
var_field_name=var_field_name,
)

tiledbsoma.logging.logger.info("Registration: complete.")
Expand Down Expand Up @@ -459,6 +461,8 @@ def from_h5ad_appends_on_experiment(
registration_data,
measurement_name=measurement_name,
append_obsm_varm=append_obsm_varm,
obs_field_name=obs_field_name,
var_field_name=var_field_name,
)

tiledbsoma.logging.logger.info("Registration: complete.")
Expand Down
40 changes: 20 additions & 20 deletions apis/python/tests/test_registration_mappings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,8 +158,8 @@ def anndata_larger():
var_ids=["AKT1", "APOE", "ESR1", "TP53", "VEGFA", "ZZZ3"],
X_value_base=0,
measurement_name="measname",
obs_field_name="obs_id",
var_field_name="var_id",
obs_field_name="cell_id",
var_field_name="gene_id",
)


Expand Down Expand Up @@ -327,8 +327,8 @@ def test_pandas_indexing(args):
assert actual_signature == args["expected_signature"]


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
def test_axis_mappings(obs_field_name, var_field_name):
anndata1 = create_anndata_canned(1, obs_field_name, var_field_name)
mapping = registration.AxisIDMapping.identity(10)
Expand All @@ -352,8 +352,8 @@ def test_axis_mappings(obs_field_name, var_field_name):
assert d.id_mapping_from_values(keys).data == tuple(range(len(keys)))


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
def test_isolated_anndata_mappings(obs_field_name, var_field_name):
anndata1 = create_anndata_canned(1, obs_field_name, var_field_name)
rd = registration.ExperimentAmbientLabelMapping.from_isolated_anndata(
Expand All @@ -370,8 +370,8 @@ def test_isolated_anndata_mappings(obs_field_name, var_field_name):
).data == (6, 3, 4)


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
def test_isolated_h5ad_mappings(obs_field_name, var_field_name):
h5ad1 = create_h5ad_canned(1, obs_field_name, var_field_name)
rd = registration.ExperimentAmbientLabelMapping.from_isolated_h5ad(
Expand All @@ -389,8 +389,8 @@ def test_isolated_h5ad_mappings(obs_field_name, var_field_name):
).data == (6, 3, 4)


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
def test_isolated_soma_experiment_mappings(obs_field_name, var_field_name):
soma1 = create_soma_canned(1, obs_field_name, var_field_name)
rd = registration.ExperimentAmbientLabelMapping.from_isolated_soma_experiment(
Expand All @@ -407,8 +407,8 @@ def test_isolated_soma_experiment_mappings(obs_field_name, var_field_name):
).data == (6, 3, 4)


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
@pytest.mark.parametrize("permutation", [[0, 1, 2, 3], [2, 3, 0, 1], [3, 2, 1, 0]])
@pytest.mark.parametrize("solo_experiment_first", [True, False])
def test_multiples_without_experiment(
Expand Down Expand Up @@ -684,8 +684,8 @@ def test_multiples_without_experiment(
assert X.non_empty_domain() == ((0, 11), (0, 6))


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
def test_multiples_with_experiment(obs_field_name, var_field_name):
soma1 = create_soma_canned(1, obs_field_name, var_field_name)
h5ad2 = create_h5ad_canned(2, obs_field_name, var_field_name)
Expand Down Expand Up @@ -747,8 +747,8 @@ def test_multiples_with_experiment(obs_field_name, var_field_name):
}


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
def test_append_items_with_experiment(obs_field_name, var_field_name):
soma1 = create_soma_canned(1, obs_field_name, var_field_name)
h5ad2 = create_h5ad_canned(2, obs_field_name, var_field_name)
Expand Down Expand Up @@ -861,8 +861,8 @@ def test_append_items_with_experiment(obs_field_name, var_field_name):
assert all(actual_X == expect_X)


@pytest.mark.parametrize("obs_field_name", ["obs_id"])
@pytest.mark.parametrize("var_field_name", ["var_id"])
@pytest.mark.parametrize("obs_field_name", ["obs_id", "cell_id"])
@pytest.mark.parametrize("var_field_name", ["var_id", "gene_id"])
@pytest.mark.parametrize("use_same_cells", [True, False])
def test_append_with_disjoint_measurements(
tmp_path, obs_field_name, var_field_name, use_same_cells
Expand Down Expand Up @@ -1119,8 +1119,8 @@ def test_registration_with_batched_reads(tmp_path, soma_larger, use_small_buffer
rd = registration.ExperimentAmbientLabelMapping.from_isolated_soma_experiment(
soma_larger,
context=context,
obs_field_name="obs_id",
var_field_name="var_id",
obs_field_name="cell_id",
var_field_name="gene_id",
)

assert len(rd.obs_axis.data) == 1000
Expand Down
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