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authorzsloan2016-12-15 15:13:02 -0600
committerGitHub2016-12-15 15:13:02 -0600
commit7ea8ee22074c297925335cc048777f0ce8cb3912 (patch)
treec499ba97a0dcffe4383a0b7a6adc4efa6919ac34 /wqflask/maintenance
parent45c7ffe78337e0ef051ee96a751d4ee8cf809acb (diff)
parentb88eb7fcbd24462efb34fd3e30bfb64483223935 (diff)
downloadgenenetwork2-7ea8ee22074c297925335cc048777f0ce8cb3912.tar.gz
Merge pull request #234 from zsloan/master
Various changes
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/gen_select_dataset.py33
1 files changed, 17 insertions, 16 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 542c0d83..e5726656 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -95,13 +95,13 @@ def get_groups(species):
for species_name, _species_full_name in species:
Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet,
Species,
- ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s
+ ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = '%s'
and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and
(PublishFreeze.InbredSetId = InbredSet.Id
or GenoFreeze.InbredSetId = InbredSet.Id
or ProbeFreeze.InbredSetId = InbredSet.Id)
group by InbredSet.Name
- order by InbredSet.Name""", (species_name))
+ order by InbredSet.Name""" % species_name)
groups[species_name] = list(Cursor.fetchall())
return groups
@@ -133,7 +133,7 @@ def get_types(groups):
def phenotypes_exist(group_name):
#print("group_name:", group_name)
Cursor.execute("""select Name from PublishFreeze
- where PublishFreeze.Name = %s""", (group_name+"Publish"))
+ where PublishFreeze.Name = '%s'""" % (group_name+"Publish"))
results = Cursor.fetchone()
#print("RESULTS:", results)
@@ -146,7 +146,7 @@ def phenotypes_exist(group_name):
def genotypes_exist(group_name):
#print("group_name:", group_name)
Cursor.execute("""select Name from GenoFreeze
- where GenoFreeze.Name = %s""", (group_name+"Geno"))
+ where GenoFreeze.Name = '%s'""" % (group_name+"Geno"))
results = Cursor.fetchone()
#print("RESULTS:", results)
@@ -166,13 +166,14 @@ def build_types(species, group):
Cursor.execute("""select distinct Tissue.Name
from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
- where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
- InbredSet.Name = %s and
+ where Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
+ InbredSet.Name = '%s' and
ProbeFreeze.TissueId = Tissue.Id and
ProbeFreeze.InbredSetId = InbredSet.Id and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
- ProbeSetFreeze.public > 0
- order by Tissue.Name""", (species, group))
+ ProbeSetFreeze.public > 0 and
+ ProbeSetFreeze.confidentiality < 1
+ order by Tissue.Name""" % (species, group))
results = []
for result in Cursor.fetchall():
@@ -205,12 +206,12 @@ def build_datasets(species, group, type_name):
if type_name == "Phenotypes":
print("GROUP:", group)
Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
- InbredSet.Name = %s and
+ InbredSet.Name = '%s' and
PublishFreeze.InbredSetId = InbredSet.Id and
InfoFiles.InfoPageName = PublishFreeze.Name and
PublishFreeze.public > 0 and
PublishFreeze.confidentiality < 1 order by
- PublishFreeze.CreateTime desc""", (group))
+ PublishFreeze.CreateTime desc""" % group)
results = Cursor.fetchone()
if results != None:
@@ -225,12 +226,12 @@ def build_datasets(species, group, type_name):
elif type_name == "Genotypes":
Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
- InbredSet.Name = %s and
+ InbredSet.Name = '%s' and
GenoFreeze.InbredSetId = InbredSet.Id and
InfoFiles.InfoPageName = GenoFreeze.ShortName and
GenoFreeze.public > 0 and
GenoFreeze.confidentiality < 1 order by
- GenoFreeze.CreateTime desc""", (group))
+ GenoFreeze.CreateTime desc""" % group)
results = Cursor.fetchone()
if results != None:
@@ -245,12 +246,12 @@ def build_datasets(species, group, type_name):
else:
Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
- Species.Name = %s and Species.Id = InbredSet.SpeciesId and
- InbredSet.Name = %s and
- ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s and
+ Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
+ InbredSet.Name = '%s' and
+ ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '%s' and
ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and
ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0 order by
- ProbeSetFreeze.CreateTime desc""", (species, group, type_name))
+ ProbeSetFreeze.CreateTime desc""" % (species, group, type_name))
dataset_results = Cursor.fetchall()
datasets = []