3 files changed, 103 insertions, 0 deletions
diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/gn3/db/__init__.py
diff --git a/gn3/db/calls.py b/gn3/db/calls.py
new file mode 100644
index 0000000..547bccf
--- /dev/null
+++ b/gn3/db/calls.py
@@ -0,0 +1,51 @@
+"""module contains calls method for db"""
+import json
+import urllib
+from flask import g
+from gn3.utility.logger import getLogger
+logger = getLogger(__name__)
+# should probably put this is env
+USE_GN_SERVER = False
+LOG_SQL = False
+
+GN_SERVER_URL = None
+
+
+def fetch1(query, path=None, func=None):
+    """fetch1 method"""
+    if USE_GN_SERVER and path:
+        result = gn_server(path)
+        if func is not None:
+            res2 = func(result)
+
+        else:
+            res2 = result
+
+        if LOG_SQL:
+            pass
+            # should probably and logger
+            # logger.debug("Replaced SQL call", query)
+
+        # logger.debug(path,res2)
+        return res2
+
+    return fetchone(query)
+
+
+def gn_server(path):
+    """Return JSON record by calling GN_SERVER
+
+    """
+    res = urllib.request.urlopen(GN_SERVER_URL+path)
+    rest = res.read()
+    res2 = json.loads(rest)
+    return res2
+
+
+def fetchone(query):
+    """method to fetchone item from  db"""
+    def helper(query):
+        res = g.db.execute(query)
+        return res.fetchone()
+
+    return logger.sql(query, helper)
diff --git a/gn3/db/webqtlDatabaseFunction.py b/gn3/db/webqtlDatabaseFunction.py
new file mode 100644
index 0000000..9e9982b
--- /dev/null
+++ b/gn3/db/webqtlDatabaseFunction.py
@@ -0,0 +1,52 @@
+"""
+# 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