1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
|
import utilities
def get_probesetfreezes(inbredsetid):
cursor = 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 = 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 = 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 = 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_nextdataid_phenotype():
cursor = 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(speciesid, strainname):
cursor = utilities.get_cursor()
sql = """
INSERT INTO Strain
SET
Strain.`Name`=%s,
Strain.`Name2`=%s,
Strain.`SpeciesId`=%s
"""
cursor.execute(sql, (strainname, strainname, speciesid))
def get_strain(speciesid, strainname):
cursor = 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(speciesid, strainname):
strain = get_strain(speciesid, strainname)
if not strain:
insert_strain(speciesid, strainame)
strain = get_strain(speciesid, strainname)
return strain
def get_strains_bynames(speciesid, strainnames):
strains = []
for strainname in strainnames:
strains.append(get_strain_sure(speciesid, strainname))
return strains
|
