Merge pull request #204 from biocommons/185-sqlite-database-connection-left-open-on-exit-during-testing

Closes #185: resolve sqlite database connections left open during tes…

Author: reece

src/biocommons/eutils/_internal/queryservice.py

@@ -144,6 +144,15 @@ def __init__(
             cache_path = False
         self._cache = SQLiteCache(cache_path) if cache_path else None
 
+    def close(self):
+        """Close the cache connection."""
+        if self._cache is not None:
+            self._cache.close()
+
+    def __del__(self):
+        """Ensure cache connection is closed on object destruction."""
+        self.close()
+
     def efetch(self, args):
         """
         execute a cached, throttled efetch query

src/biocommons/eutils/_internal/sqlitecache.py

@@ -1,7 +1,4 @@
-"""simple key-value cache with transparent payload compression and expiration
-
-Taken from http://bitbucket.org/reece/rcore/
-"""
+"""simple key-value cache with transparent payload compression and expiration"""
 
 import logging
 import pickle
@@ -35,6 +32,26 @@ def __init__(self, db_path, compress_values=True):
         self._logger = logging.getLogger(__name__)
         self._connect(db_path)
 
+    def close(self):
+        """Close the database connection."""
+        if self._con is not None:
+            self._con.close()
+            self._logger.info("closed %s", self._db_path)
+            self._con = None
+
+    def __enter__(self):
+        """Context manager entry."""
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """Context manager exit."""
+        self.close()
+        return False
+
+    def __del__(self):
+        """Ensure connection is closed on object destruction."""
+        self.close()
+
     def expire(self, age):
         cur = self._execute("DELETE FROM cache WHERE strftime('%s','now') - created > ?", [age])
         return cur.rowcount

tests/test_rcore_sqllitecache.py

@@ -15,6 +15,9 @@ def setUp(self):
 
         self.cache = SQLiteCache(self._fn)
 
+    def tearDown(self):
+        self.cache.close()
+
 
 class Test_SQLiteCache_AttrLookup(Test_SQLiteCacheBase):
     def test_str_str(self):