diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 22 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 18 |
2 files changed, 21 insertions, 19 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index acfee3d4..d46e4363 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -392,6 +392,12 @@ class DatasetGroup(object): Redis.set(key, json.dumps(self.samplelist)) Redis.expire(key, 60*5) + def all_samples_ordered(self): + result = [] + lists = (self.parlist, self.f1list, self.samplelist) + [result.extend(l) for l in lists if l] + return result + def read_genotype_file(self): '''Read genotype from .geno file instead of database''' #if self.group == 'BXD300': @@ -805,11 +811,11 @@ class PhenotypeDataSet(DataSet): WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND - PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id + PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id Order BY Strain.Name - """ % (trait, self.id) - results = g.db.execute(query).fetchall() + """ + results = g.db.execute(query, (trait, self.id)).fetchall() return results @@ -892,15 +898,17 @@ class GenotypeDataSet(DataSet): 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 + Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = '%s' AND + GenoFreeze.Name = %s AND GenoXRef.DataId = GenoData.Id AND GenoData.StrainId = Strain.Id Order BY Strain.Name - """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name) - results = g.db.execute(query).fetchall() + """ + results = g.db.execute(query, + (webqtlDatabaseFunction.retrieve_species_id(self.group.name), + trait, self.name)).fetchall() return results diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7f1170a9..4a088bc8 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -251,14 +251,7 @@ class GeneralTrait(object): # Todo: is this necessary? If not remove self.data.clear() - if self.dataset.group.parlist: - all_samples_ordered = (self.dataset.group.parlist + - self.dataset.group.f1list + - self.dataset.group.samplelist) - elif self.dataset.group.f1list: - all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist - else: - all_samples_ordered = self.dataset.group.samplelist + all_samples_ordered = self.dataset.group.all_samples_ordered() if results: for item in results: @@ -299,6 +292,7 @@ class GeneralTrait(object): """ % (self.name, self.dataset.id) print("query is:", query) + assert self.name.isdigit() trait_info = g.db.execute(query).fetchone() #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name @@ -337,10 +331,10 @@ class GeneralTrait(object): trait_info = g.db.execute(query).fetchone() #print("trait_info is: ", pf(trait_info)) else: #Temp type - query = """SELECT %s FROM %s WHERE Name = %s - """ % (string.join(self.dataset.display_fields,','), - self.dataset.type, self.name) - trait_info = g.db.execute(query).fetchone() + query = """SELECT %s FROM %s WHERE Name = %s""" + trait_info = g.db.execute(query, + (string.join(self.dataset.display_fields,','), + self.dataset.type, self.name)).fetchone() if trait_info: self.haveinfo = True |