Fix load_phenotypes to run with GN2 latest

1 files changed, 89 insertions, 0 deletions

diff --git a/scripts/maintenance/utilities.py b/scripts/maintenance/utilities.py
new file mode 100644
index 00000000..886410c2
--- /dev/null
+++ b/scripts/maintenance/utilities.py
@@ -0,0 +1,89 @@
+import MySQLdb
+import re
+import configparser
+
+def get_cursor():
+    host = 'tux.uthsc.edu'
+    user = 'webqtlout'
+    passwd = 'webqtlout'
+    db = 'db_webqtl'
+    con = MySQLdb.Connect(db=db, host=host, user=user, passwd=passwd)
+    cursor = con.cursor()
+    return cursor, con
+
+def clearspaces(s, default=None):
+    if s:
+        s = re.sub('\s+', ' ', s)
+        s = s.strip()
+        return s
+    else:
+        return default
+        
+def to_dic(keys, values):
+    dic = {}
+    for i in range(len(keys)):
+        key = keys[i]
+        value = values[i]
+        dic[key] = value
+    return dic
+
+def overlap(dic1, dic2):
+    keys = []
+    values1 = []
+    values2 = []
+    for key in dic1.keys():
+        if key in dic2:
+            value1 = dic1[key]
+            value2 = dic2[key]
+            if value1 and value2:
+                keys.append(key)
+                values1.append(value1)
+                values2.append(value2)
+    return keys, values1, values2
+
+def to_db_string(s, default):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return default
+        elif s == 'x':
+            return default
+        else:
+            return s
+    else:
+        return default
+
+def to_db_float(s, default):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return default
+        elif s == 'x':
+            return default
+        else:
+            try:
+                return float(s)
+            except:
+                return default
+    else:
+        return default
+        
+def to_db_int(s, default):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return default
+        elif s == 'x':
+            return default
+        else:
+            try:
+                return int(s)
+            except:
+                return default
+    else:
+        return default
+
+def get_config(configfile):
+    config = configparser.ConfigParser()
+    config.read(configfile)
+    return config