Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

2 files changed, 45 insertions, 0 deletions

diff --git a/gn2/db/__init__.py b/gn2/db/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/db/__init__.py
diff --git a/gn2/db/webqtlDatabaseFunction.py b/gn2/db/webqtlDatabaseFunction.py
new file mode 100644
index 00000000..9438c474
--- /dev/null
+++ b/gn2/db/webqtlDatabaseFunction.py
@@ -0,0 +1,45 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from gn2.wqflask.database import database_connection
+
+from gn2.utility.tools import get_setting
+
+
+def retrieve_species(group):
+    """Get the species of a group (e.g. returns string "mouse" on "BXD"
+
+    """
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute(
+            "SELECT Species.Name FROM Species, InbredSet WHERE InbredSet.Name = %s AND InbredSet.SpeciesId = Species.Id",
+            (group,))
+        results = cursor.fetchone()
+        if results and results[0]:
+            return results[0]
+
+
+def retrieve_species_id(group):
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        cursor.execute("SELECT SpeciesId FROM InbredSet WHERE Name = %s",
+                       (group,))
+        return cursor.fetchone()[0]