tests should now all pass

Author: rmobmina

api/__init__.py

@@ -1,15 +1,52 @@
+import re as _re
+import sqlite3
+import statistics as _statistics
+
 from flask import Flask
 from flask_sqlalchemy import SQLAlchemy
 from flask_restx import Api
 from flask_cors import CORS
 from flask_caching import Cache
 from flask_limiter import Limiter
 from flask_limiter.util import get_remote_address
+from sqlalchemy import event
+from sqlalchemy.engine import Engine
 import os
 from pathlib import Path
 import tempfile
 
 
+@event.listens_for(Engine, "connect")
+def _register_sqlite_functions(dbapi_conn, connection_record):
+    """Register MySQL-compatible functions for SQLite (used in CI and local tests)."""
+    if not isinstance(dbapi_conn, sqlite3.Connection):
+        return
+
+    class _PopStdDev:
+        """Population standard deviation aggregate (equivalent to MySQL STD())."""
+
+        def __init__(self):
+            self._vals = []
+
+        def step(self, value):
+            if value is not None:
+                self._vals.append(float(value))
+
+        def finalize(self):
+            if len(self._vals) < 2:
+                return None
+            return _statistics.pstdev(self._vals)
+
+    dbapi_conn.create_aggregate("std", 1, _PopStdDev)
+
+    def _regexp_replace(string, pattern, replacement):
+        if string is None:
+            return None
+        return _re.sub(pattern, replacement, string)
+
+    dbapi_conn.create_function("regexp_replace", 3, _regexp_replace)
+
+
 def create_app():
     """Initialize the app factory based on the official Flask documentation"""
     bar_app = Flask(__name__)

api/resources/gene_expression.py

@@ -47,11 +47,6 @@
 class GeneExpression(Resource):
     def get(self, database, gene_id):
         """Retrieve expression values for a gene from a given eFP database.
-
-        :param database: Database name (e.g., 'klepikova', 'embryo').
-        :param gene_id: Gene or probeset ID (e.g., 'AT1G01010', '261585_at').
-        :returns: JSON with expression values per sample, or an error message.
-        :rtype: flask.Response
         """
         database = str(escape(database))
         gene_id = str(escape(gene_id))

config/databases/annotations_lookup.sql

@@ -45,7 +45,7 @@ CREATE TABLE `agi_alias` (
 
 LOCK TABLES `agi_alias` WRITE;
 /*!40000 ALTER TABLE `agi_alias` DISABLE KEYS */;
-INSERT INTO `agi_alias` VALUES ('At1g01010','ANAC001','2022-06-30'),('At1g01010','NAC001','2022-06-30'),('At1g01010','NTL10','2022-06-30'),('At1g01020','ARV1','2022-06-30');
+INSERT INTO `agi_alias` VALUES ('AT1G01010','ANAC001','2022-06-30'),('AT1G01010','NAC001','2022-06-30'),('AT1G01010','NTL10','2022-06-30'),('AT1G01020','ARV1','2022-06-30');
 /*!40000 ALTER TABLE `agi_alias` ENABLE KEYS */;
 UNLOCK TABLES;
 
@@ -71,7 +71,7 @@ CREATE TABLE `at_agi_lookup` (
 
 LOCK TABLES `at_agi_lookup` WRITE;
 /*!40000 ALTER TABLE `at_agi_lookup` DISABLE KEYS */;
-INSERT INTO `at_agi_lookup` VALUES ('261568_at','At1g01030','2010-12-20'),('261585_at','At1g01010','2009-07-29'),('261585_at','At1g01010','2010-12-20');
+INSERT INTO `at_agi_lookup` VALUES ('261568_at','AT1G01030','2010-12-20'),('261585_at','AT1G01010','2009-07-29'),('261585_at','AT1G01010','2010-12-20');
 /*!40000 ALTER TABLE `at_agi_lookup` ENABLE KEYS */;
 UNLOCK TABLES;
 /*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;

tests/resources/test_fastpheno.py

@@ -202,19 +202,14 @@ def test_timeseries_tree(self):
     def test_timeseries_genotype_aggregate(self):
         """Tests GET /fastpheno/timeseries/genotype/<tree_site_id>/<band>/aggregate"""
         response = self.app_client.get("/fastpheno/timeseries/genotype/619/398nm/aggregate")
-        expected = {
-            "wasSuccessful": True,
-            "data": [
-                {
-                    "flight_date": "2022-06-10T00:00:00",
-                    "flights_pk": 14,
-                    "avg_value": 0.036833333,
-                    "std_value": 0.0016526006441027672,
-                    "n_trees": 3,
-                },
-            ],
-        }
-        self.assertEqual(response.json, expected)
+        self.assertTrue(response.json["wasSuccessful"])
+        self.assertEqual(len(response.json["data"]), 1)
+        row = response.json["data"][0]
+        self.assertEqual(row["flight_date"], "2022-06-10T00:00:00")
+        self.assertEqual(row["flights_pk"], 14)
+        self.assertEqual(row["n_trees"], 3)
+        self.assertAlmostEqual(row["avg_value"], 0.036833333, places=7)
+        self.assertAlmostEqual(row["std_value"], 0.0016526006441027672, places=12)
 
         # With site filter
         response = self.app_client.get("/fastpheno/timeseries/genotype/619/398nm/aggregate?site=Pintendre")