Add unit test for ensembl.io.genomio.genome_metadata.dump module

src/python/ensembl/io/genomio/genome_metadata/dump.py

@@ -14,7 +14,12 @@
 # limitations under the License.
 """Generates a JSON file representing the genome metadata from a core database."""
 
-__all__ = ["get_genome_metadata", "filter_genome_meta", "check_assembly_version"]
+__all__ = [
+    "get_genome_metadata",
+    "filter_genome_meta",
+    "check_assembly_version",
+    "check_genebuild_version",
+]
 
 import json
 from typing import Any, Dict
@@ -120,58 +125,58 @@ def filter_genome_meta(gmeta: Dict[str, Any]) -> Dict[str, Any]:
     return gmeta_out
 
 
-def check_assembly_version(gmeta_out: Dict[str, Any]) -> None:
-    """Update the assembly version of the genome metadata provided to use an integer.
-    Get the version from the assembly accession as alternative.
+def check_assembly_version(genome_metadata: Dict[str, Any]) -> None:
+    """Updates the assembly version of the genome metadata provided.
+
+    If `version` meta key is not and integer or it is not available, the assembly accession's version
+    will be used instead.
 
     Args:
-        gmeta (Dict[str, Any]): Nested metadata key values from the core metadata table.
+        genome_metadata: Nested metadata key values from the core metadata table.
+
+    Raises:
+        ValueError: If both `version` and the assembly accession's version are not integers or are missing.
     """
-    assembly = gmeta_out["assembly"]
+    assembly = genome_metadata["assembly"]
     version = assembly.get("version")
-
     # Check the version is an integer
     try:
         assembly["version"] = int(version)
     except (ValueError, TypeError) as exc:
         # Get the version from the assembly accession
         accession = assembly["accession"]
-        parts = accession.split(".")
-        if len(parts) == 2 and parts[1].isdigit():
-            version = parts[1]
+        version = accession.partition(".")[2]
+        try:
             assembly["version"] = int(version)
-            logging.info(
-                f'Asm version [v{version}] obtained from: assembly accession ({assembly["accession"]}).'
-            )
-        else:
+        except ValueError:
             raise ValueError(f"Assembly version is not an integer in {assembly}") from exc
+        logging.info(f"Assembly version [v{version}] obtained from assembly accession ({accession}).")
     else:
-        logging.info(f"Located version [v{int(version)}] info from meta data.")
+        logging.info(f'Located version [v{assembly["version"]}] info from meta data.')
 
 
-def check_genebuild_version(metadata: Dict[str, Any]) -> None:
+def check_genebuild_version(genome_metadata: Dict[str, Any]) -> None:
     """Updates the genebuild version (if not present) from the genebuild ID, removing the latter.
 
     Args:
-        metadata: Nested metadata key values from the core metadata table.
+        genome_metadata: Nested metadata key values from the core metadata table.
 
     Raises:
         ValueError: If there is no genebuild version or ID available.
     """
-    genebuild = metadata.get("genebuild")
-    if genebuild is None:
+    try:
+        genebuild = genome_metadata["genebuild"]
+    except KeyError:
         return
-    version = genebuild.get("version")
-
-    # Check there is a version
-    if version is None:
-        gb_id = genebuild.get("id")
-        if gb_id is None:
-            raise ValueError("No genebuild version or id")
-        metadata["genebuild"]["version"] = str(gb_id)
-
-    if "id" in genebuild:
-        del metadata["genebuild"]["id"]
+    if "version" not in genebuild:
+        try:
+            genebuild_id = genebuild["id"]
+        except KeyError:
+            # pylint: disable=raise-missing-from
+            raise ValueError("No genebuild version or ID found")
+        genome_metadata["genebuild"]["version"] = str(genebuild_id)
+    # Drop genebuild ID since there is a genebuild version
+    genome_metadata["genebuild"].pop("id", None)
 
 
 def main() -> None:
@@ -190,7 +195,3 @@ def main() -> None:
         genome_meta = filter_genome_meta(genome_meta)
 
     print(json.dumps(genome_meta, indent=2, sort_keys=True))
-
-
-if __name__ == "__main__":
-    main()

src/python/tests/genome_metadata/test_dump.py

@@ -0,0 +1,115 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Unit testing of `ensembl.io.genomio.genome_metadata.dump` module.
+
+Typical usage example::
+    $ pytest test_dump.py
+
+"""
+
+from contextlib import nullcontext as does_not_raise
+from typing import Any, ContextManager, Dict
+
+from deepdiff import DeepDiff
+import pytest
+from pytest import param
+
+from ensembl.io.genomio.genome_metadata import dump
+
+
+@pytest.mark.dependency(name="test_check_assembly_version")
+@pytest.mark.parametrize(
+    "genome_metadata, output, expectation",
+    [
+        param(
+            {"assembly": {"version": "1"}},
+            {"assembly": {"version": 1}},
+            does_not_raise(),
+            id="Version is '1'",
+        ),
+        param(
+            {"assembly": {"accession": "GCA_00000001.1", "version": "a"}},
+            {"assembly": {"accession": "GCA_00000001.1", "version": 1}},
+            does_not_raise(),
+            id="Version is 'a', accession is '1'",
+        ),
+        param(
+            {"assembly": {"accession": "GCA_00000001.1"}},
+            {"assembly": {"accession": "GCA_00000001.1", "version": 1}},
+            does_not_raise(),
+            id="No version, accession with version",
+        ),
+        param(
+            {"assembly": {"accession": "GCA_00000001"}},
+            {},
+            pytest.raises(ValueError),
+            id="No version, accession without version",
+        ),
+    ],
+)
+def test_check_assembly_version(
+    genome_metadata: Dict[str, Any], output: Dict[str, Any], expectation: ContextManager
+) -> None:
+    """Tests the `dump.check_assembly_version()` method.
+
+    Args:
+        genome_metadata: Nested metadata key values from the core metadata table.
+        output: Expected change in the genome metadata dictionary.
+        expectation: Context manager for the expected exception (if any).
+    """
+    with expectation:
+        dump.check_assembly_version(genome_metadata)
+        assert not DeepDiff(genome_metadata, output)
+
+
+@pytest.mark.dependency(name="test_check_genebuild_version")
+@pytest.mark.parametrize(
+    "genome_metadata, output, expectation",
+    [
+        param({}, {}, does_not_raise(), id="No 'genebuild' entry"),
+        param(
+            {"genebuild": {"version": "v1"}},
+            {"genebuild": {"version": "v1"}},
+            does_not_raise(),
+            id="Version is 'v1', no ID",
+        ),
+        param(
+            {"genebuild": {"version": "v1", "id": "v1"}},
+            {"genebuild": {"version": "v1"}},
+            does_not_raise(),
+            id="Version is 'v1', ID dropped",
+        ),
+        param(
+            {"genebuild": {"id": "v1"}},
+            {"genebuild": {"version": "v1"}},
+            does_not_raise(),
+            id="No version, ID moved to version",
+        ),
+        param({"genebuild": {}}, {}, pytest.raises(ValueError), id="No version or ID"),
+    ],
+)
+def test_check_genebuild_version(
+    genome_metadata: Dict[str, Any], output: Dict[str, Any], expectation: ContextManager
+) -> None:
+    """Tests the `dump.check_genebuild_version()` method.
+
+    Args:
+        genome_metadata: Nested metadata key values from the core metadata table.
+        output: Expected change in the genome metadata dictionary.
+        expectation: Context manager for the expected exception (if any).
+    """
+    with expectation:
+        dump.check_genebuild_version(genome_metadata)
+        assert not DeepDiff(genome_metadata, output)