1 files changed, 52 insertions, 0 deletions
diff --git a/gn3/db/webqtlDatabaseFunction.py b/gn3/db/webqtlDatabaseFunction.py
new file mode 100644
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+++ b/gn3/db/webqtlDatabaseFunction.py
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+"""
+# 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 gn3.db.calls import fetch1
+
+from gn3.utility.logger import getLogger
+logger = getLogger(__name__)
+
+###########################################################################
+# output: cursor instance
+# function: connect to database and return cursor instance
+###########################################################################
+
+
+def retrieve_species(group):
+    """Get the species of a group (e.g. returns string "mouse" on "BXD"
+
+    """
+    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (
+        group), "/cross/"+group+".json", lambda r: (r["species"],))[0]
+    # logger.debug("retrieve_species result:", result)
+    return result
+
+
+def retrieve_species_id(group):
+    """retrieve species id method"""
+
+    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
+        group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0]
+    logger.debug("retrieve_species_id result:", result)
+    return result