Merge pull request #1192 from kunal-10-cloud/fix/replace-assert-isinstance-with-explicit-validation

fix: replace assert isinstance with explicit type validation

Author: jonbrenas

malariagen_data/anoph/cnv_frq.py

@@ -90,7 +90,11 @@ def _gene_cnv(
         inline_array,
     ):
         # Sanity check.
-        assert isinstance(region, Region)
+        if not isinstance(region, Region):
+            raise TypeError(
+                f"Expected region to be a Region object, "
+                f"got {type(region).__name__}: {region!r}"
+            )
 
         # Access genes within the region of interest.
         df_genome_features = self.genome_features(region=region)
@@ -260,7 +264,11 @@ def _gene_cnv_frequencies(
         debug = self._log.debug
 
         debug("sanity check - this function is one region at a time")
-        assert isinstance(region, Region)
+        if not isinstance(region, Region):
+            raise TypeError(
+                f"Expected region to be a Region object, "
+                f"got {type(region).__name__}: {region!r}"
+            )
 
         debug("get gene copy number data")
         ds_cnv = self.gene_cnv(
@@ -504,7 +512,11 @@ def _gene_cnv_frequencies_advanced(
         debug = self._log.debug
 
         debug("sanity check - here we deal with one region only")
-        assert isinstance(region, Region)
+        if not isinstance(region, Region):
+            raise TypeError(
+                f"Expected region to be a Region object, "
+                f"got {type(region).__name__}: {region!r}"
+            )
 
         debug("access gene CNV calls")
         ds_cnv = self.gene_cnv(

malariagen_data/anoph/frq_base.py

@@ -341,7 +341,11 @@ def plot_frequencies_heatmap(
             for j in range(1, idx_vals.shape[1]):
                 index_col = index_col + ", " + idx_vals[:, j]
         else:
-            assert isinstance(index, str)
+            if not isinstance(index, str):
+                raise TypeError(
+                    f"Expected index to be str or list, "
+                    f"got {type(index).__name__}: {index!r}"
+                )
             index_col = df[index].astype(str)
 
         # Check that index is unique.
@@ -588,7 +592,11 @@ def plot_frequencies_map_markers(
             ds_variant = ds.isel(variants=variant)
             variant_label = ds["variant_label"].values[variant]
         else:
-            assert isinstance(variant, str)
+            if not isinstance(variant, str):
+                raise TypeError(
+                    f"Expected variant to be int or str, "
+                    f"got {type(variant).__name__}: {variant!r}"
+                )
             ds_variant = ds.set_index(variants="variant_label").sel(variants=variant)
             variant_label = variant
 

malariagen_data/anoph/sample_metadata.py

@@ -1235,7 +1235,11 @@ def lookup_sample(
         if isinstance(sample, str):
             sample_rec = df_samples.loc[sample]
         else:
-            assert isinstance(sample, int)
+            if not isinstance(sample, int):
+                raise TypeError(
+                    f"Expected sample to be str or int, "
+                    f"got {type(sample).__name__}: {sample!r}"
+                )
             sample_rec = df_samples.iloc[sample]
         return sample_rec
 
@@ -1348,7 +1352,11 @@ def _setup_sample_symbol(
 
         else:
             # Custom grouping using queries.
-            assert isinstance(symbol, Mapping)
+            if not isinstance(symbol, Mapping):
+                raise TypeError(
+                    f"Expected symbol to be str or Mapping, "
+                    f"got {type(symbol).__name__}: {symbol!r}"
+                )
             data["symbol"] = ""
             for key, value in symbol.items():
                 data.loc[data.query(value).index, "symbol"] = key
@@ -1397,7 +1405,11 @@ def _setup_sample_colors_plotly(
 
         else:
             # Custom grouping using queries.
-            assert isinstance(color, Mapping)
+            if not isinstance(color, Mapping):
+                raise TypeError(
+                    f"Expected color to be str or Mapping, "
+                    f"got {type(color).__name__}: {color!r}"
+                )
             data["color"] = ""
             for key, value in color.items():
                 data.loc[data.query(value).index, "color"] = key
@@ -1493,13 +1505,17 @@ def _setup_cohort_queries(
         """Convenience function to normalise the `cohorts` parameter to a
         dictionary mapping cohort labels to sample metadata queries."""
 
-        if isinstance(cohorts, dict):
+        if isinstance(cohorts, Mapping):
             # User has supplied a custom dictionary mapping cohort identifiers
             # to pandas queries.
             cohort_queries = cohorts
 
         else:
-            assert isinstance(cohorts, str)
+            if not isinstance(cohorts, str):
+                raise TypeError(
+                    f"Expected cohorts to be Mapping or str, "
+                    f"got {type(cohorts).__name__}: {cohorts!r}"
+                )
             # User has supplied a column in the sample metadata.
             df_samples = self.sample_metadata(
                 sample_sets=sample_sets,
@@ -1855,7 +1871,11 @@ def _locate_cohorts(*, cohorts, data, min_cohort_size):
             coh_dict[coh] = loc_coh
 
     else:
-        assert isinstance(cohorts, str)
+        if not isinstance(cohorts, str):
+            raise TypeError(
+                f"Expected cohorts to be Mapping or str, "
+                f"got {type(cohorts).__name__}: {cohorts!r}"
+            )
         # User has supplied the name of a sample metadata column.
 
         # Convenience to allow things like "admin1_year" instead of "cohort_admin1_year".

malariagen_data/util.py

@@ -311,7 +311,11 @@ def _dask_compress_dataset(ds, indexer, dim):
         # the underlying data
         indexer_computed = indexer.compute()
     else:
-        assert isinstance(indexer, np.ndarray)
+        if not isinstance(indexer, np.ndarray):
+            raise TypeError(
+                f"Expected indexer to be a dask.array.Array or numpy.ndarray, "
+                f"got {type(indexer).__name__}"
+            )
         indexer_computed = indexer
 
     coords = dict()
@@ -375,7 +379,11 @@ def _da_compress(
 
     # Load the indexer temporarily for chunk size computations.
     if indexer_computed is None:
-        assert isinstance(indexer, da.Array)
+        if not isinstance(indexer, da.Array):
+            raise TypeError(
+                f"Expected indexer to be a dask.array.Array, "
+                f"got {type(indexer).__name__}"
+            )
         indexer_computed = indexer.compute()
 
     # Ensure indexer and data are chunked in the same way.
@@ -665,7 +673,11 @@ def _parse_single_region(resource, region: single_region_param_type) -> Region:
             end=region.get("end"),
         )
 
-    assert isinstance(region, str)
+    if not isinstance(region, str):
+        raise TypeError(
+            f"Expected region to be a mapping or str, "
+            f"got {type(region).__name__}: {region!r}"
+        )
 
     # check if region is a whole contig
     if region in _valid_contigs(resource):
@@ -1495,8 +1507,14 @@ def _apply_allele_mapping(x, mapping, max_allele):
 
 
 def _dask_apply_allele_mapping(v, mapping, max_allele):
-    assert isinstance(v, da.Array)
-    assert isinstance(mapping, np.ndarray)
+    if not isinstance(v, da.Array):
+        raise TypeError(
+            f"Expected v to be a dask.array.Array, " f"got {type(v).__name__}"
+        )
+    if not isinstance(mapping, np.ndarray):
+        raise TypeError(
+            f"Expected mapping to be a numpy.ndarray, " f"got {type(mapping).__name__}"
+        )
     assert v.ndim == 2
     assert mapping.ndim == 2
     assert v.shape[0] == mapping.shape[0]
@@ -1516,8 +1534,14 @@ def _genotype_array_map_alleles(gt, mapping):
     # Transform genotype calls via an allele mapping.
     # N.B., scikit-allel does not handle empty blocks well, so we
     # include some extra logic to handle that better.
-    assert isinstance(gt, np.ndarray)
-    assert isinstance(mapping, np.ndarray)
+    if not isinstance(gt, np.ndarray):
+        raise TypeError(
+            f"Expected gt to be a numpy.ndarray, " f"got {type(gt).__name__}"
+        )
+    if not isinstance(mapping, np.ndarray):
+        raise TypeError(
+            f"Expected mapping to be a numpy.ndarray, " f"got {type(mapping).__name__}"
+        )
     assert gt.ndim == 3
     assert mapping.ndim == 3
     assert gt.shape[0] == mapping.shape[0]
@@ -1536,8 +1560,14 @@ def _genotype_array_map_alleles(gt, mapping):
 
 
 def _dask_genotype_array_map_alleles(gt, mapping):
-    assert isinstance(gt, da.Array)
-    assert isinstance(mapping, np.ndarray)
+    if not isinstance(gt, da.Array):
+        raise TypeError(
+            f"Expected gt to be a dask.array.Array, " f"got {type(gt).__name__}"
+        )
+    if not isinstance(mapping, np.ndarray):
+        raise TypeError(
+            f"Expected mapping to be a numpy.ndarray, " f"got {type(mapping).__name__}"
+        )
     assert gt.ndim == 3
     assert mapping.ndim == 2
     assert gt.shape[0] == mapping.shape[0]