diff options
Diffstat (limited to 'wqflask/maintenance/dataset/datastructure.py')
| -rw-r--r-- | wqflask/maintenance/dataset/datastructure.py | 41 |
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 |