unit testing [skip ci]

apis/python/tests/test_basic_anndata_io.py

@@ -7,6 +7,7 @@
 import anndata
 import numpy as np
 import pandas as pd
+import pyarrow as pa
 import pytest
 import scipy
 import somacore
@@ -1349,20 +1350,103 @@ def test_nan_append(conftest_pbmc_small, dtype, nans, new_obs_ids):
     )
 
 
-# TODO:
-# * Make adata_under with nobs < tiledbsoma/io/conversions.STRING_DECAT_THRESHOLD
-# * Make adata_over  with nobs > tiledbsoma/io/conversions.STRING_DECAT_THRESHOLD
-# * Ingest adata_under solo
-#   o Assert is-enum in the AnnData obs
-#   o Assert is-enum in the soma obs
-# * Ingest adata_over solo
-#   o Assert is-enum in the AnnData obs
-#   o Assert not-enum in the soma obs
-# * Ingest under then append over
-#   o Assert is-enum in the soma obs
-#   o Check levels and data
-# * Ingest over then append under
-#   o Assert is-string in the soma obs
-#   o Check data
+## TODO:
+## * Make adata_under with nobs < tiledbsoma/io/conversions.STRING_DECAT_THRESHOLD
+## * Make adata_over  with nobs > tiledbsoma/io/conversions.STRING_DECAT_THRESHOLD
+## * Ingest adata_under solo
+##   o Assert is-enum in the AnnData obs
+##   o Assert is-enum in the soma obs
+## * Ingest adata_over solo
+##   o Assert is-enum in the AnnData obs
+##   o Assert not-enum in the soma obs
+## * Ingest under then append over
+##   o Assert is-enum in the soma obs
+##   o Check levels and data
+## * Ingest over then append under
+##   o Assert is-string in the soma obs
+##   o Check data
 def test_decat_append(tmp_path):
-    pass
+    nobs_under = tiledbsoma.io.conversions.STRING_DECAT_THRESHOLD - 2
+    nobs_over = tiledbsoma.io.conversions.STRING_DECAT_THRESHOLD + 2
+    nvar = 100
+
+    obs_ids_under = [f"under_{e:08}" for e in range(nobs_under)]
+    obs_ids_over = [f"over_{e:08}" for e in range(nobs_over)]
+    var_ids = [f"gene_{e:08}" for e in range(nvar)]
+
+    enum_values_under = [f"enum_u_{e:06}" for e in range(nobs_under)]
+    enum_values_over  = [f"enum_o_{e:06}" for e in range(nobs_over)]
+
+    obs_under = pd.DataFrame(
+        data={
+            "obs_id": np.asarray(obs_ids_under),
+            "is_primary_data": np.asarray([True] * nobs_under),
+             "myenum": pd.Series(np.asarray(enum_values_under), dtype="category"),
+        }
+    )
+    obs_under.set_index("obs_id", inplace=True)
+
+    obs_over = pd.DataFrame(
+        data={
+            "obs_id": np.asarray(obs_ids_over),
+            "is_primary_data": np.asarray([True] * nobs_over),
+            "myenum": pd.Series(np.asarray(enum_values_over), dtype="category"),
+        }
+    )
+    obs_over.set_index("obs_id", inplace=True)
+
+    var = pd.DataFrame(
+        data={
+            "var_id": np.asarray(var_ids),
+            "mybool": np.asarray([True] * nvar),
+        }
+    )
+    var.set_index("var_id", inplace=True)
+
+    X_under = scipy.sparse.random(
+        nobs_under, nvar, density=0.1, dtype=np.float64
+    ).tocsr()
+    X_over = scipy.sparse.random(nobs_over, nvar, density=0.1, dtype=np.float64).tocsr()
+
+    adata_under = anndata.AnnData(
+        X=X_under, obs=obs_under, var=var, dtype=X_under.dtype
+    )
+    adata_over = anndata.AnnData(X=X_over, obs=obs_over, var=var, dtype=X_over.dtype)
+
+    path_under = (tmp_path / "under").as_posix()
+    path_over = (tmp_path / "over").as_posix()
+
+    tiledbsoma.io.from_anndata(path_under, adata_under, "RNA")
+    tiledbsoma.io.from_anndata(path_over, adata_over, "RNA")
+
+    with tiledbsoma.Experiment.open(path_under) as exp_under:
+        assert pa.types.is_dictionary(exp_under.obs.schema.field("myenum").type)
+        obs_table = exp_under.obs.read().concat()
+        assert obs_table.column("myenum").to_pylist() == enum_values_under
+
+    with tiledbsoma.Experiment.open(path_over) as exp_over:
+        assert not pa.types.is_dictionary(exp_over.obs.schema.field("myenum").type)
+        obs_table = exp_over.obs.read().concat()
+        assert obs_table.column("myenum").to_pylist() == enum_values_over
+
+    rd_under_over = tiledbsoma.io.register_anndatas(
+        experiment_uri=path_under,
+        adatas=[adata_over],
+        measurement_name="RNA",
+        obs_field_name="obs_id",
+        var_field_name="var_id",
+    )
+
+    rd_over_under = tiledbsoma.io.register_anndatas(
+        experiment_uri=path_over,
+        adatas=[adata_under],
+        measurement_name="RNA",
+        obs_field_name="obs_id",
+        var_field_name="var_id",
+    )
+
+    # XXX OVER THEN UNDER
+    # XXX PRE-ASSERTS AND POST-ASSERTS
+
+    # XXX UNDER THEN OVER
+    # XXX PRE-ASSERTS AND POST-ASSERTS