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authorLei Yan2014-02-22 23:03:21 -0600
committerLei Yan2014-02-22 23:03:21 -0600
commit1e92d78d574956d88fef648cbde4306d78952626 (patch)
tree73b22bd2bca731ceafb9d08b5cf40d75887109f3 /wqflask/maintenance/dataset/datastructure.py
parentaf92bb48b2589d2804569863bc0306f787df1c60 (diff)
downloadgenenetwork2-1e92d78d574956d88fef648cbde4306d78952626.tar.gz
On branch master
Diffstat (limited to 'wqflask/maintenance/dataset/datastructure.py')
-rw-r--r--wqflask/maintenance/dataset/datastructure.py41
1 files changed, 33 insertions, 8 deletions
diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py
index e1d88df2..f436d32c 100644
--- a/wqflask/maintenance/dataset/datastructure.py
+++ b/wqflask/maintenance/dataset/datastructure.py
@@ -94,7 +94,8 @@ def get_nextdataid_phenotype():
dataid += 1
return dataid
-def insert_strain(speciesid, strainname):
+def insert_strain(inbredsetid, strainname, updatestrainxref=None):
+ speciesid = get_species(inbredsetid)
cursor, con = utilities.get_cursor()
sql = """
INSERT INTO Strain
@@ -104,8 +105,32 @@ def insert_strain(speciesid, strainname):
Strain.`SpeciesId`=%s
"""
cursor.execute(sql, (strainname, strainname, speciesid))
+ strainid = con.insert_id()
+ if updatestrainxref:
+ sql = """
+ SELECT StrainXRef.`OrderId`
+ FROM StrainXRef
+ where StrainXRef.`InbredSetId`=%s
+ ORDER BY StrainXRef.`OrderId` DESC
+ LIMIT 1
+ """
+ cursor.execute(sql, (inbredsetid))
+ re = cursor.fetchone()
+ orderid = re[0] + 1
+ #
+ sql = """
+ INSERT INTO StrainXRef
+ SET
+ StrainXRef.`InbredSetId`=%s,
+ StrainXRef.`StrainId`=%s,
+ StrainXRef.`OrderId`=%s,
+ StrainXRef.`Used_for_mapping`=%s,
+ StrainXRef.`PedigreeStatus`=%s
+ """
+ cursor.execute(sql, (inbredsetid, strainid, orderid, "N", None))
-def get_strain(speciesid, strainname):
+def get_strain(inbredsetid, strainname):
+ speciesid = get_species(inbredsetid)
cursor, con = utilities.get_cursor()
sql = """
SELECT Strain.`Id`, Strain.`Name`
@@ -116,15 +141,15 @@ def get_strain(speciesid, strainname):
cursor.execute(sql, (speciesid, strainname))
return cursor.fetchone()
-def get_strain_sure(speciesid, strainname):
- strain = get_strain(speciesid, strainname)
+def get_strain_sure(inbredsetid, strainname, updatestrainxref=None):
+ strain = get_strain(inbredsetid, strainname)
if not strain:
- insert_strain(speciesid, strainname)
- strain = get_strain(speciesid, strainname)
+ insert_strain(inbredsetid, strainname, updatestrainxref)
+ strain = get_strain(inbredsetid, strainname)
return strain
-def get_strains_bynames(speciesid, strainnames):
+def get_strains_bynames(inbredsetid, strainnames, updatestrainxref=None):
strains = []
for strainname in strainnames:
- strains.append(get_strain_sure(speciesid, strainname))
+ strains.append(get_strain_sure(inbredsetid, strainname, updatestrainxref))
return strains