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authorZachary Sloan2012-12-04 18:08:09 -0600
committerZachary Sloan2012-12-04 18:08:09 -0600
commit01785471d63de156fa9787a0fb38c9df09824183 (patch)
tree00eaac20327dde5647bf58a87e5beb1ddd1a3360 /wqflask/base/data_set.py
parent0e17939e123ec80c4da3f665004b08347aa9480b (diff)
downloadgenenetwork2-01785471d63de156fa9787a0fb38c9df09824183.tar.gz
Changed parser to allow quotes (i.e. name="rw williams")
Renamed webqtlTrait to GeneralTrait and began rewriting parts Changed database code in many places to use simple sqlalchemy
Diffstat (limited to 'wqflask/base/data_set.py')
-rwxr-xr-xwqflask/base/data_set.py18
1 files changed, 8 insertions, 10 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cd9e810e..7833f5c1 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -68,13 +68,10 @@ class DataSet(object):
assert name
self.name = name
- #self.db_conn = db_conn
- #self.cursor = self.db_conn.cursor()
self.id = None
self.type = None
self.group = None
- #if self.cursor and self.id == 0:
self.setup()
self.check_confidentiality()
@@ -200,6 +197,7 @@ class PhenotypeDataSet(DataSet):
description = this_trait.post_publication_description
if this_trait.confidential:
+ continue # for now
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
description = this_trait.pre_publication_description
this_trait.description_display = description
@@ -217,13 +215,13 @@ class PhenotypeDataSet(DataSet):
this_trait.LRS_location_value = 1000000
if this_trait.lrs:
- self.cursor.execute("""
+ result = g.db.execute("""
select Geno.Chr, Geno.Mb from Geno, Species
- where Species.Name = '%s' and
- Geno.Name = '%s' and
+ where Species.Name = %s and
+ Geno.Name = %s and
Geno.SpeciesId = Species.Id
- """ % (species, this_trait.locus))
- result = self.cursor.fetchone()
+ """, (species, this_trait.locus)).fetchone()
+ #result = self.cursor.fetchone()
if result:
if result[0] and result[1]:
@@ -509,13 +507,13 @@ def geno_mrna_confidentiality(ob):
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table)
- ob.cursor.execute(query, ob.name)
+ result = g.db.execute(query, ob.name)
(dataset_id,
name,
full_name,
confidential,
- authorized_users) = ob.cursor.fetchall()[0]
+ authorized_users) = result.fetchall()[0]
if confidential:
# Allow confidential data later