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authorZachary Sloan2012-12-06 16:50:20 -0600
committerZachary Sloan2012-12-06 16:50:20 -0600
commit41721f0d386c034470fe68e0017295474242ab48 (patch)
tree169d5ca3d895326ce2dc1e3f95dae72ccd2cffe1 /wqflask/base/data_set.py
parent2ec627563efa9fdf4fc74cb4764bfebb5ab90933 (diff)
downloadgenenetwork2-41721f0d386c034470fe68e0017295474242ab48.tar.gz
Added minimum/maximum to basic statistics table
Continued bug-shooting related to getting show_trait running with phenotype traits
Diffstat (limited to 'wqflask/base/data_set.py')
-rwxr-xr-xwqflask/base/data_set.py32
1 files changed, 23 insertions, 9 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 9f0f3fac..2182fe9e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -30,6 +30,7 @@ from htmlgen import HTMLgen2 as HT
import reaper
import webqtlConfig
+from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
from MySQLdb import escape_string as escape
@@ -72,10 +73,12 @@ class DatasetGroup(object):
"""
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
- self.name, self.group_id = g.db.execute(dataset.query).fetchone()
+ self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
if self.name == 'BXD300':
self.name = "BXD"
+ self.species = webqtlDatabaseFunction.retrieve_species(self.name)
+
self.incparentsf1 = False
self.f1list = None
self.parlist = None
@@ -151,14 +154,25 @@ class DataSet(object):
self.check_confidentiality()
- self.retrieve_name()
+ self.retrieve_other_names()
self.group = DatasetGroup(self) # sets self.group and self.group_id
def get_desc(self):
"""Gets overridden later, at least for Temp...used by trait's get_given_name"""
return None
-
+
+ #@staticmethod
+ #def get_by_trait_id(trait_id):
+ # """Gets the dataset object given the trait id"""
+ #
+ #
+ #
+ # name = g.db.execute(""" SELECT
+ #
+ # """)
+ #
+ # return DataSet(name)
# Delete this eventually
@property
@@ -175,7 +189,7 @@ class DataSet(object):
- def retrieve_name(self):
+ def retrieve_other_names(self):
"""
If the data set name parameter is not found in the 'Name' field of the data set table,
check if it is actually the FullName or ShortName instead.
@@ -326,7 +340,7 @@ class PhenotypeDataSet(DataSet):
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id
+ Strain.Name, PublishData.value, PublishSE.error, NStrain.count
FROM
(PublishData, Strain, PublishXRef, PublishFreeze)
left join PublishSE on
@@ -340,7 +354,7 @@ class PhenotypeDataSet(DataSet):
PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
Order BY
Strain.Name
- """ % (self.trait.name, self.id)
+ """ % (trait.name, self.id)
results = g.db.execute(query).fetchall()
return results
@@ -368,7 +382,7 @@ class GenotypeDataSet(DataSet):
# Todo: Obsolete or rename this field
self.type = 'Geno'
- self.query = '''
+ self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id
FROM
@@ -418,7 +432,7 @@ class GenotypeDataSet(DataSet):
GenoData.StrainId = Strain.Id
Order BY
Strain.Name
- """ % (webqtlDatabaseFunction.retrieve_species_id(self.group), trait.name, self.name)
+ """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait.name, self.name)
results = g.db.execute(query).fetchall()
return results
@@ -476,7 +490,7 @@ class MrnaAssayDataSet(DataSet):
# Todo: Obsolete or rename this field
self.type = 'ProbeSet'
- self.query = '''
+ self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id
FROM