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

On branch master

2 files changed, 30 insertions, 9 deletions

diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py
index ce588c78..b2af5777 100644
--- a/wqflask/maintenance/dataset/datastructure.py
+++ b/wqflask/maintenance/dataset/datastructure.py
@@ -1,7 +1,7 @@
 import utilities
 
 def get_probesetfreezes(inbredsetid):
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
         FROM ProbeSetFreeze, ProbeFreeze
@@ -12,7 +12,7 @@ def get_probesetfreezes(inbredsetid):
     return cursor.fetchall()
 
 def get_probesetfreeze(probesetfreezeid):
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
         FROM ProbeSetFreeze
@@ -22,7 +22,7 @@ def get_probesetfreeze(probesetfreezeid):
     return cursor.fetchone()
     
 def get_strains(inbredsetid):
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         SELECT Strain.`Id`, Strain.`Name`
         FROM StrainXRef, Strain
@@ -34,7 +34,7 @@ def get_strains(inbredsetid):
     return cursor.fetchall()
 
 def get_inbredset(probesetfreezeid):
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         SELECT InbredSet.`Id`, InbredSet.`Name`, InbredSet.`FullName`
         FROM InbredSet, ProbeFreeze, ProbeSetFreeze
@@ -44,9 +44,20 @@ def get_inbredset(probesetfreezeid):
         """
     cursor.execute(sql, (probesetfreezeid))
     return cursor.fetchone()
+    
+def get_species(inbredsetid):
+    cursor, con = utilities.get_cursor()
+    sql = """
+        SELECT Species.`Id`, Species.`Name`, Species.`MenuName`, Species.`FullName`
+        FROM InbredSet, Species
+        WHERE InbredSet.`Id`=%s
+        AND InbredSet.`SpeciesId`=Species.`Id`
+        """
+    cursor.execute(sql, (inbredsetid))
+    return cursor.fetchone()
 
 def get_nextdataid_phenotype():
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         SELECT PublishData.`Id`
         FROM PublishData
@@ -60,7 +71,7 @@ def get_nextdataid_phenotype():
     return dataid
 
 def insert_strain(speciesid, strainname):
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         INSERT INTO Strain
         SET
@@ -71,7 +82,7 @@ def insert_strain(speciesid, strainname):
     cursor.execute(sql, (strainname, strainname, speciesid))
 
 def get_strain(speciesid, strainname):
-    cursor = utilities.get_cursor()
+    cursor, con = utilities.get_cursor()
     sql = """
         SELECT Strain.`Id`, Strain.`Name`
         FROM Strain
diff --git a/wqflask/maintenance/dataset/load_phenotypes.py b/wqflask/maintenance/dataset/load_phenotypes.py
index 77133d0c..e74f8725 100644
--- a/wqflask/maintenance/dataset/load_phenotypes.py
+++ b/wqflask/maintenance/dataset/load_phenotypes.py
@@ -2,6 +2,7 @@ import sys
 import csv
 
 import utilities
+import datastructure
 
 def main(argv):
     # config
@@ -11,14 +12,21 @@ def main(argv):
         print "\t%s" % (str(item))
     # var
     inbredsetid = config.get('config', 'inbredsetid')
-    dataid = utilities.get_nextdataid_phenotype()
-    cursor, con = utilities.get_cursor()
     print "inbredsetid: %s" % inbredsetid
+    species = datastructure.get_species(inbredsetid)
+    speciesid = species[0]
+    print "speciesid: %s" % speciesid
+    dataid = datastructure.get_nextdataid_phenotype()
+    print "next data id: %s" % dataid
+    cursor, con = utilities.get_cursor()
     # datafile
     datafile = open(config.get('config', 'datafile'), 'r')
     phenotypedata = csv.reader(datafile, delimiter='\t', quotechar='"')
     phenotypedata_head = phenotypedata.next()
     print "phenotypedata head:\n\t%s" % phenotypedata_head
+    strainnames = phenotypedata_head[1:]
+    strains = datastructure.get_strains_bynames(speciesid, strainnames)
+    print "%s" % strains
     # metafile
     metafile = open(config.get('config', 'metafile'), 'r')
     phenotypemeta = csv.reader(metafile, delimiter='\t', quotechar='"')
@@ -102,6 +110,8 @@ def main(argv):
             rowcount = cursor.rowcount
             publicationid = con.insert_id()
             print "INSERT INTO Publication: %d record: %d" % (rowcount, publicationid)
+        # data
+        
 
 if __name__ == "__main__":
     print "command line arguments:\n\t%s" % sys.argv