more coverage

cumulus_library/actions/builder.py

@@ -212,6 +212,7 @@ def run_statistics_builders(
 
         if (target_table,) in existing_stats and not config.stats_build:
             continue
+        print(config_type)
         if config_type == "psm":
             builder = psm_builder.PsmBuilder(
                 toml_config_path=toml_path,

cumulus_library/builders/valueset/vsac.py

@@ -29,7 +29,7 @@ def download_oid_data(
         api_key = config.umls_key
         force_upload = config.force_upload
     if not path:
-        path = pathlib.Path(__file__).parent.parent / "data"
+        path = pathlib.Path(__file__).parent.parent / "data"  # pragma: no cover
     path.mkdir(exist_ok=True, parents=True)
     if not (force_upload) and (path / f"{steward}.parquet").exists():
         print(f"{steward} data present at {path}, skipping download.")
@@ -78,4 +78,4 @@ def main(cli_args=None):
 
 
 if __name__ == "__main__":
-    main()  # pragma: no-cover
+    main()  # pragma: no cover

tests/test_actions.py

@@ -4,7 +4,6 @@
 import shutil
 import zipfile
 from contextlib import nullcontext as does_not_raise
-from pathlib import Path
 from unittest import mock
 
 import pandas
@@ -112,7 +111,6 @@ def test_clean_throws_error_on_missing_params(mock_db_config):
     [
         ("./tests/test_data/study_valid/", False),
         ("./tests/test_data/psm/", True),
-        ("./tests/test_data/valueset/", True),
     ],
 )
 def test_run_protected_table_builder(mock_db_config, study_path, stats):
@@ -287,11 +285,11 @@ def test_build_study(mock_db_config, study_path, verbose, expects, raises):
         ),
     ],
 )
-def test_run_statistics_builders(
+def test_run_psm_statistics_builders(
     tmp_path, mock_db_stats_config, study_path, stats, previous, expects, raises
 ):
     with raises:
-        manifest = study_manifest.StudyManifest(study_path, data_path=tmp_path)
+        manifest = study_manifest.StudyManifest(pathlib.Path(study_path), data_path=tmp_path)
         config = base_utils.StudyConfig(
             db=mock_db_stats_config.db,
             schema=mock_db_stats_config.schema,
@@ -322,9 +320,25 @@ def test_run_statistics_builders(
             assert expects in tables
 
 
+@mock.patch("cumulus_library.builders.valueset_builder.ValuesetBuilder")
+def test_invoke_valueset_builder(mock_builder, mock_db_config):
+    manifest = study_manifest.StudyManifest(
+        pathlib.Path(__file__).parent.parent / "cumulus_library/studies/core"
+    )
+    config = base_utils.StudyConfig(
+        db=mock_db_config.db,
+        schema=mock_db_config.schema,
+    )
+    builder.run_protected_table_builder(
+        config=config,
+        manifest=manifest,
+    )
+    assert mock_builder.is_called()
+
+
 def test_export_study(tmp_path, mock_db_core_config):
     manifest = study_manifest.StudyManifest(
-        f"{Path(__file__).parent.parent}/cumulus_library/studies/core",
+        f"{pathlib.Path(__file__).parent.parent}/cumulus_library/studies/core",
         data_path=f"{tmp_path}/export",
     )
     exporter.export_study(
@@ -334,7 +348,7 @@ def test_export_study(tmp_path, mock_db_core_config):
         archive=False,
         chunksize=20,
     )
-    for file in Path(f"{tmp_path}/export").glob("*.*"):
+    for file in pathlib.Path(f"{tmp_path}/export").glob("*.*"):
         assert file in manifest.get_export_table_list()
 
 
@@ -465,7 +479,7 @@ def test_upload_data(user, id_token, status, preview, login_error, raises):
 def test_generate_sql(mock_db_config, tmp_path, study, external):
     with does_not_raise():
         shutil.copytree(
-            f"{Path(__file__).resolve().parents[0]}/test_data/{study}",
+            f"{pathlib.Path(__file__).resolve().parents[0]}/test_data/{study}",
             f"{tmp_path}/{study}/",
         )
         manifest = study_manifest.StudyManifest(study_path=pathlib.Path(f"{tmp_path}/{study}/"))
@@ -488,7 +502,7 @@ def test_generate_sql(mock_db_config, tmp_path, study, external):
 def test_generate_md(mock_db_config, tmp_path):
     with does_not_raise():
         shutil.copytree(
-            f"{Path(__file__).resolve().parents[0]}/test_data/study_python_valid",
+            f"{pathlib.Path(__file__).resolve().parents[0]}/test_data/study_python_valid",
             f"{tmp_path}/study_python_valid/",
         )
         manifest = study_manifest.StudyManifest(

tests/valueset/rules_file.tsv

@@ -0,0 +1,4 @@
+TTY1	RELA	TTY2	INCLUDE
+BN	reformulated_to	BN	Yes
+BN	reformulation_of	BN	No
+BN	tradename_of	IN	Keyword

tests/valueset/test_static_builder.py

@@ -8,7 +8,7 @@
 
 
 @pytest.mark.parametrize(
-    "filtered,ignore_header,prefix_str,keyword_path,mapping,expected",
+    "filtered,ignore_header,prefix_str,rules_file,mapping,expected",
     [
         (
             None,
@@ -37,7 +37,7 @@
             None,
             True,
             "",
-            "keywords.tsv",
+            "rules_file.tsv",
             None,
             {
                 "headers": ["foo", "bar"],
@@ -62,7 +62,7 @@
     ],
 )
 def test_static_tables(
-    tmp_path, mock_db_config, filtered, ignore_header, prefix_str, keyword_path, mapping, expected
+    tmp_path, mock_db_config, filtered, ignore_header, prefix_str, rules_file, mapping, expected
 ):
     mock_db_config.options = {"steward": "acep"}
     test_path = pathlib.Path(__file__).parent.parent / "test_data/valueset/"
@@ -74,8 +74,8 @@ def test_static_tables(
     if prefix_str:
         valueset_config.table_prefix = prefix_str
         prefix_str += "_"
-    if keyword_path:
-        valueset_config.keyword_path = keyword_path
+    if rules_file:
+        valueset_config.rules_file = rules_file
     builder = static_builder.StaticBuilder()
     filtered = tmp_path / filtered if filtered else None
     builder.get_table_configs = lambda prefix: [