Merge /home/zas1024/gene

1 files changed, 0 insertions, 155 deletions

diff --git a/wqflask/maintenance/dataset/datastructure.py b/wqflask/maintenance/dataset/datastructure.py
deleted file mode 100644
index 7139856f..00000000
--- a/wqflask/maintenance/dataset/datastructure.py
+++ /dev/null
@@ -1,155 +0,0 @@
-import utilities
-
-def get_probesetfreezes(inbredsetid):
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
-        FROM ProbeSetFreeze, ProbeFreeze
-        WHERE ProbeSetFreeze.`ProbeFreezeId`=ProbeFreeze.`Id`
-        AND ProbeFreeze.`InbredSetId`=%s
-        """
-    cursor.execute(sql, (inbredsetid))
-    return cursor.fetchall()
-
-def get_probesetfreeze(probesetfreezeid):
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT ProbeSetFreeze.`Id`, ProbeSetFreeze.`Name`, ProbeSetFreeze.`FullName`
-        FROM ProbeSetFreeze
-        WHERE ProbeSetFreeze.`Id`=%s
-        """
-    cursor.execute(sql, (probesetfreezeid))
-    return cursor.fetchone()
-    
-def get_strains(inbredsetid):
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT Strain.`Id`, Strain.`Name`
-        FROM StrainXRef, Strain
-        WHERE StrainXRef.`InbredSetId`=%s
-        AND StrainXRef.`StrainId`=Strain.`Id`
-        ORDER BY StrainXRef.`OrderId`
-        """
-    cursor.execute(sql, (inbredsetid))
-    return cursor.fetchall()
-
-def get_inbredset(probesetfreezeid):
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT InbredSet.`Id`, InbredSet.`Name`, InbredSet.`FullName`
-        FROM InbredSet, ProbeFreeze, ProbeSetFreeze
-        WHERE InbredSet.`Id`=ProbeFreeze.`InbredSetId`
-        AND ProbeFreeze.`Id`=ProbeSetFreeze.`ProbeFreezeId`
-        AND ProbeSetFreeze.`Id`=%s
-        """
-    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_genofreeze_byinbredsetid(inbredsetid):
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT GenoFreeze.`Id`, GenoFreeze.`Name`, GenoFreeze.`FullName`, GenoFreeze.`InbredSetId`
-        FROM GenoFreeze
-        WHERE GenoFreeze.`InbredSetId`=%s
-        """
-    cursor.execute(sql, (inbredsetid))
-    return cursor.fetchone()
-
-def get_nextdataid_genotype():
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT GenoData.`Id`
-        FROM GenoData
-        ORDER BY GenoData.`Id` DESC
-        LIMIT 1
-        """
-    cursor.execute(sql)
-    re = cursor.fetchone()
-    dataid = re[0]
-    dataid += 1
-    return dataid
-    
-def get_nextdataid_phenotype():
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT PublishData.`Id`
-        FROM PublishData
-        ORDER BY PublishData.`Id` DESC
-        LIMIT 1
-        """
-    cursor.execute(sql)
-    re = cursor.fetchone()
-    dataid = re[0]
-    dataid += 1
-    return dataid
-
-def insert_strain(inbredsetid, strainname, updatestrainxref=None):
-    speciesid = get_species(inbredsetid)[0]
-    cursor, con = utilities.get_cursor()
-    sql = """
-        INSERT INTO Strain
-        SET
-        Strain.`Name`=%s,
-        Strain.`Name2`=%s,
-        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(inbredsetid, strainname):
-    speciesid = get_species(inbredsetid)[0]
-    cursor, con = utilities.get_cursor()
-    sql = """
-        SELECT Strain.`Id`, Strain.`Name`
-        FROM Strain
-        WHERE Strain.`SpeciesId`=%s
-        AND Strain.`Name` LIKE %s
-        """
-    cursor.execute(sql, (speciesid, strainname))
-    return cursor.fetchone()
-
-def get_strain_sure(inbredsetid, strainname, updatestrainxref=None):
-    strain = get_strain(inbredsetid, strainname)
-    if not strain:
-        insert_strain(inbredsetid, strainname, updatestrainxref)
-        strain = get_strain(inbredsetid, strainname)
-    return strain
-
-def get_strains_bynames(inbredsetid, strainnames, updatestrainxref=None):
-    strains = []
-    for strainname in strainnames:
-        strains.append(get_strain_sure(inbredsetid, strainname, updatestrainxref))
-    return strains