Committer: root <root@alexandria.uthsc.edu>

On branch master

2 files changed, 61 insertions, 2 deletions

diff --git a/wqflask/maintenance/dataset/load_phenotypes.py b/wqflask/maintenance/dataset/load_phenotypes.py
index e5a85b32..6e7f049b 100644
--- a/wqflask/maintenance/dataset/load_phenotypes.py
+++ b/wqflask/maintenance/dataset/load_phenotypes.py
@@ -9,8 +9,9 @@ def main(argv):
     print "config:"
     for item in config.items('config'):
         print "\t%s" % (str(item))
-    #
+    # var
     inbredsetid = config.get('config', 'inbredsetid')
+    cursor = utilities.get_cursor()
     print "inbredsetid: %s" % inbredsetid
     # datafile
     datafile = open(config.get('config', 'datafile'), 'r')
@@ -22,7 +23,41 @@ def main(argv):
     phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
     phenotypemeta_head = phenotypemeta.next()
     print "phenotypemeta head:\n\t%s" % phenotypemeta_head
-    #
+    # load
+    for metarow in phenotypemeta:
+        #
+        datarow_value = phenotypedata.next()
+        datarow_se = phenotypedata.next()
+        datarow_n = phenotypedata.next()
+        # Phenotype
+        sql = """
+            INSERT INTO Phenotype
+            SET
+            Phenotype.`Pre_publication_description`=%s,
+            Phenotype.`Post_publication_description`=%s,
+            Phenotype.`Original_description`=%s,
+            Phenotype.`Pre_publication_abbreviation`=%s,
+            Phenotype.`Post_publication_abbreviation`=%s,
+            Phenotype.`Lab_code`=%s,
+            Phenotype.`Submitter`=%s,
+            Phenotype.`Owner`=%s,
+            Phenotype.`Authorized_Users`=%s,
+            Phenotype.`Units`=%s
+            """
+        cursor.execute(sql, (
+            metarow[1],
+            metarow[2],
+            metarow[3],
+            metarow[4],
+            metarow[5],
+            metarow[6],
+            metarow[7],
+            metarow[8],
+            metarow[9],
+            metarow[18]
+            ))
+        re = cursor.rowcount
+        print "INSERT INTO Phenotype: %d record" % re
         
 if __name__ == "__main__":
     print "command line arguments:\n\t%s" % sys.argv
diff --git a/wqflask/maintenance/dataset/utilities.py b/wqflask/maintenance/dataset/utilities.py
index 63a3e84d..e542cb43 100644
--- a/wqflask/maintenance/dataset/utilities.py
+++ b/wqflask/maintenance/dataset/utilities.py
@@ -41,6 +41,30 @@ def overlap(dic1, dic2):
                 values2.append(value2)
     return keys, values1, values2
 
+def to_db_string_null(s):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return None
+        elif s == 'x':
+            return None
+        else:
+            return s
+    else:
+        return None
+
+def to_db_string_empty(s):
+    if s:
+        s = s.strip()
+        if len(s) == 0:
+            return ''
+        elif s == 'x':
+            return ''
+        else:
+            return s
+    else:
+        return ''
+
 def get_config(configfile):
     config = ConfigParser.ConfigParser()
     config.read(configfile)