add fixtures for concept folders/tables

Author: alistairewj

mimic-iv/tests/conftest.py

@@ -1,5 +1,6 @@
 import os
 from collections import namedtuple
+from pathlib import Path
 
 import pytest
 from google.cloud import bigquery
@@ -33,3 +34,25 @@ def project_id():
     Return the name of the BigQuery project used.
     """
     return 'physionet-data'
+
+@pytest.fixture(scope="session")
+def concept_folders():
+    """
+    Returns the folders containing concepts.
+    """
+    return ['comorbidity', 'demographics', 'measurement', 'medication', 'organfailure', 'treatment', 'score', 'sepsis', 'firstday']
+
+@pytest.fixture(scope="session")
+def concepts(concept_folders):
+    """
+    Returns all concepts which should be generated.
+    """
+    concepts = {}
+    current_dir = Path(__file__).parent
+    concept_dir = current_dir / '../concepts'
+    for folder in concept_folders:
+        files = os.listdir(concept_dir / folder)
+        # add list of the concepts in this folder to the dict
+        concepts[folder] = [f[:-4] for f in files if f.endswith('.sql')]
+
+    return concepts