From 5f4cef3640f84092e5692e16865002a832b7838c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 6 Apr 2026 09:51:26 +0200
Subject: Added a test that creates an ontology

---
 tests/test_network_gemini_ontology.py | 58 +++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 tests/test_network_gemini_ontology.py

(limited to 'tests')

diff --git a/tests/test_network_gemini_ontology.py b/tests/test_network_gemini_ontology.py
new file mode 100644
index 0000000..4a9db34
--- /dev/null
+++ b/tests/test_network_gemini_ontology.py
@@ -0,0 +1,58 @@
+"""Test Gemini API for generating SUD ontology terms.
+
+Requires a Gemini API key in ~/.config/gemini/credentials and internet access.
+
+Run with: python3 -m unittest tests.test_network_gemini_ontology -v
+"""
+
+import os
+import sys
+import time
+import unittest
+
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
+from more_functions import gemini_query
+
+PROMPT = (
+    """
+    Give me a list of terms on substance abuse disorder (SUD) that act
+    as traits and classifiers in scientific literature with a focus on
+    behaviour and brain attributes related to the hippocampus. Avoid
+    aliases and synonyms as well as gene names. Each term should be
+    1-3 words (max).  Give me a list of at least 20, but no more than
+    80, most used terms.  Return only the terms, one per line, no
+    numbering."""
+)
+
+class TestGeminiOntology(unittest.TestCase):
+    def test_1_sud_ontology_terms(self):
+        """Gemini should return 20-50 SUD ontology terms."""
+        t0 = time.time()
+        response = gemini_query(PROMPT)
+        elapsed = time.time() - t0
+        terms = [t.strip() for t in response.strip().split("\n") if t.strip()]
+        print(f"  Got {len(terms)} terms ({elapsed:.2f}s)")
+        for t in terms:
+            print(f"    - {t}")
+        self.assertGreaterEqual(len(terms), 20,
+                                f"Expected at least 20 terms, got {len(terms)}")
+        self.assertLessEqual(len(terms), 80,
+                             f"Expected at most 80 terms, got {len(terms)}")
+        # Each term should be short (1-3 words, allow some slack)
+        long_terms = [t for t in terms if len(t.split()) > 5]
+        self.assertEqual(len(long_terms), 0,
+                         f"Terms too long: {long_terms}")
+
+    def test_2_cached_ontology(self):
+        """Second call should use cache and be fast."""
+        # Ensure cache is populated from test_1
+        gemini_query(PROMPT)
+        t0 = time.time()
+        response = gemini_query(PROMPT)
+        elapsed = time.time() - t0
+        terms = [t.strip() for t in response.strip().split("\n") if t.strip()]
+        print(f"  Cached: {len(terms)} terms ({elapsed:.4f}s)")
+        self.assertLess(elapsed, 0.01, f"Cache lookup too slow: {elapsed:.4f}s")
+
+if __name__ == "__main__":
+    unittest.main()
-- 
cgit 1.4.1


From 5c28db960087ddb282a13e4dd2c3a3dd5c4cc207 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 6 Apr 2026 09:56:19 +0200
Subject: Add aliases

---
 tests/test_network_gemini_ontology.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'tests')

diff --git a/tests/test_network_gemini_ontology.py b/tests/test_network_gemini_ontology.py
index 4a9db34..2a84909 100644
--- a/tests/test_network_gemini_ontology.py
+++ b/tests/test_network_gemini_ontology.py
@@ -21,7 +21,7 @@ PROMPT = (
     aliases and synonyms as well as gene names. Each term should be
     1-3 words (max).  Give me a list of at least 20, but no more than
     80, most used terms.  Return only the terms, one per line, no
-    numbering."""
+    numbering. Add abbreviations and aliases as a list with each term, separated by commas"""
 )
 
 class TestGeminiOntology(unittest.TestCase):
@@ -40,8 +40,6 @@ class TestGeminiOntology(unittest.TestCase):
                              f"Expected at most 80 terms, got {len(terms)}")
         # Each term should be short (1-3 words, allow some slack)
         long_terms = [t for t in terms if len(t.split()) > 5]
-        self.assertEqual(len(long_terms), 0,
-                         f"Terms too long: {long_terms}")
 
     def test_2_cached_ontology(self):
         """Second call should use cache and be fast."""
-- 
cgit 1.4.1