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-rwxr-xr-xwqflask/base/trait.py102
1 files changed, 3 insertions, 99 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index d0158ebd..8c9e3b10 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -258,113 +258,15 @@ class GeneralTrait:
#else:
results = self.dataset.retrieve_sample_data(self)
- #if self.dataset.type == 'Temp':
- # query = '''
- # SELECT
- # Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
- # FROM
- # TempData, Temp, Strain
- # WHERE
- # TempData.StrainId = Strain.Id AND
- # TempData.Id = Temp.DataId AND
- # Temp.name = '%s'
- # Order BY
- # Strain.Name
- # ''' % self.name
- ##XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
- #elif self.dataset.type == 'Publish':
- # query = '''
- # SELECT
- # Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
- # FROM
- # (PublishData, Strain, PublishXRef, PublishFreeze)
- # left join PublishSE on
- # (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
- # left join NStrain on
- # (NStrain.DataId = PublishData.Id AND
- # NStrain.StrainId = PublishData.StrainId)
- # WHERE
- # PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
- # PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
- # PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
- # Order BY
- # Strain.Name
- # ''' % (self.name, self.dataset.id)
-
- #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
- #elif self.cellid:
-
- #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
- #elif self.dataset.type == 'ProbeSet':
- # #ProbeSet Data
- # query = '''
- # SELECT
- # Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
- # FROM
- # (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
- # left join ProbeSetSE on
- # (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
- # WHERE
- # ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- # ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- # ProbeSetFreeze.Name = '%s' AND
- # ProbeSetXRef.DataId = ProbeSetData.Id AND
- # ProbeSetData.StrainId = Strain.Id
- # Order BY
- # Strain.Name
- # ''' % (self.name, self.dataset.name)
- ##XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
- #else:
- # #Geno Data
- # #XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search.
- # query = '''
- # SELECT
- # Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
- # FROM
- # (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
- # left join GenoSE on
- # (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
- # WHERE
- # Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
- # GenoXRef.GenoFreezeId = GenoFreeze.Id AND
- # GenoFreeze.Name = '%s' AND
- # GenoXRef.DataId = GenoData.Id AND
- # GenoData.StrainId = Strain.Id
- # Order BY
- # Strain.Name
- # ''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group), self.name, self.dataset.name)
-
-
- #self.cursor.execute(query)
- #results = self.cursor.fetchall()
-
# Todo: is this necessary? If not remove
self.data.clear()
if results:
- #self.mysqlid = results[0][-1]
- #if samplelist:
for item in results:
#name, value, variance, num_cases = item
if not samplelist or (samplelist and name in samplelist):
- #if value != None:
- # num_cases = None
- # if self.dataset.type in ('Publish', 'Temp'):
- # ndata = item[3]
name = item[0]
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
- #end for
- # else:
- # for item in results:
- # val = item[1]
- # if val != None:
- # var = item[2]
- # ndata = None
- # if self.dataset.type in ('Publish', 'Temp'):
- # ndata = item[3]
- # self.data[item[0]] = webqtlCaseData(val, var, ndata)
- # #end for
- # #end if
#def keys(self):
# return self.__dict__.keys()
@@ -429,7 +331,9 @@ class GeneralTrait:
GenoXRef.GenoId = Geno.Id AND
GenoFreeze.Name = '%s' AND
Geno.Name = '%s'
- """ % (escape(display_fields_string), escape(self.dataset.name), escape(self.name))
+ """ % (escape(display_fields_string),
+ escape(self.dataset.name),
+ escape(self.name))
traitInfo = g.db.execute(query).fetchone()
print("traitInfo is: ", pf(traitInfo))
else: #Temp type