cicd: add DB check script

scripts/check_db.py

@@ -0,0 +1,49 @@
+"""Perform basic checks on database to verify import success."""
+import psycopg
+
+# figures from 2024-11-27 dump
+expected_values = {
+    "gene_claims": 81019,
+    "genes": 12062,
+    "drug_claims": 130616,
+    "drugs": 39581,
+    "interaction_claims": 98920,
+    "interactions": 69907,
+    "sources": 45,
+    "gene_category_claims": 33066,
+    "gene_categorizations": 20137,
+    "drug_approval_ratings": 13332,
+    "publications": 13142
+}
+
+
+def handle_warn(name, actual_value):
+    """Just because a value drops below that of a previous release doesn't mean something's wrong;
+    but it'd be good to know.
+    """
+    if expected_values[name] > actual_value:
+        print(f"WARNING: {name} value is {actual_value}, expected {expected_values[name]}")
+
+
+def check_value(name, query):
+    cur.execute(query)
+    value = cur.fetchone()[0]
+    print(f"# {name}: {value}")
+    handle_warn(name, value)
+
+with psycopg.connect("dbname=dgidb user=postgres") as conn:
+    with conn.cursor() as cur:
+        check_value("gene_claims", "SELECT COUNT(*) FROM gene_claims;")
+        check_value("genes", "SELECT COUNT(*) FROM genes;")
+        check_value("drug_claims", "SELECT COUNT(*) FROM drug_claims;")
+        check_value("drugs", "SELECT COUNT(*) FROM drugs;")
+        check_value("interaction_claims", "SELECT COUNT(*) FROM interaction_claims;")
+        check_value("interactions", "SELECT COUNT(*) FROM interactions;")
+
+        check_value("sources", "SELECT COUNT(*) FROM sources;")
+
+        check_value("gene_category_claims", "SELECT COUNT(*) FROM gene_claim_categories_gene_claims;")
+        check_value("gene_categorizations", "SELECT COUNT(*) FROM gene_categories_genes;")
+
+        check_value("drug_approval_ratings", "SELECT COUNT(*) FROM drug_approval_ratings;")
+        check_value("publications", "SELECT COUNT(*) FROM publications;")

scripts/requirements.txt

@@ -0,0 +1,3 @@
+psycopg==3.2.3
+psycopg-binary==3.2.3
+typing_extensions==4.12.2