Add xapian database connection context manager.

* gn3/settings.py (XAPIAN_DB_PATH): New variable.
* gn3/db_utils.py: Import xapian and XAPIAN_DB_PATH from gn3.settings.
(xapian_database): New function.

2 files changed, 16 insertions, 1 deletions

diff --git a/gn3/db_utils.py b/gn3/db_utils.py
index 69e88a5..ead0c5b 100644
--- a/gn3/db_utils.py
+++ b/gn3/db_utils.py
@@ -3,7 +3,8 @@ import contextlib
 from typing import Any, Iterator, Protocol, Tuple
 from urllib.parse import urlparse
 import MySQLdb as mdb
-from gn3.settings import SQL_URI
+import xapian
+from gn3.settings import SQL_URI, XAPIAN_DB_PATH
 
 
 def parse_db_url() -> Tuple:
@@ -42,3 +43,14 @@ def database_connection() -> Iterator[Connection]:
         yield connection
     finally:
         connection.close()
+
+
+@contextlib.contextmanager
+def xapian_database():
+    """Open xapian database read-only."""
+    # pylint: disable-next=invalid-name
+    db = xapian.Database(XAPIAN_DB_PATH)
+    try:
+        yield db
+    finally:
+        db.close()
diff --git a/gn3/settings.py b/gn3/settings.py
index 5bb5f17..86bdd95 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -37,6 +37,9 @@ CORRELATION_COMMAND = f"{os.environ.get('GN2_PROFILE')}/bin/correlation_rust"
 GENOTYPE_FILES = os.environ.get(
     "GENOTYPE_FILES", f"{os.environ.get('HOME')}/genotype_files/genotype")
 
+# Xapian index
+XAPIAN_DB_PATH = "xapian"
+
 # CROSS-ORIGIN SETUP
 def parse_env_cors(default):
     """Parse comma-separated configuration into list of strings."""