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-rwxr-xr-xwqflask/base/data_set.py37
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py48
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py81
-rw-r--r--wqflask/wqflask/templates/show_trait.html2
4 files changed, 80 insertions, 88 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 14e4055e..9f0f3fac 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -77,6 +77,9 @@ class DatasetGroup(object):
self.name = "BXD"
self.incparentsf1 = False
+ self.f1list = None
+ self.parlist = None
+ self.allsamples = None
#def read_genotype(self):
@@ -95,39 +98,39 @@ class DatasetGroup(object):
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
- self.genotype_1 = reaper.Dataset()
+ genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
- self.genotype_1.read(full_filename)
+ genotype_1.read(full_filename)
print("Got to after read")
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.name]
+ f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
except KeyError:
- _f1 = _f12 = _mat = _pat = None
+ f1 = f12 = maternal = paternal = None
- self.genotype_2 = self.genotype_1
- if self.genotype_1.type == "group" and _mat and _pat:
- self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1)
+
+ if genotype_1.type == "group" and maternal and paternal:
+ genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal) #, F1=_f1)
+ else:
+ genotype_2 = genotype_1
#determine default genotype object
- if self.incparentsf1 and self.genotype_1.type != "intercross":
- self.genotype = self.genotype_2
+ if self.incparentsf1 and genotype_1.type != "intercross":
+ self.genotype = genotype_2
else:
self.incparentsf1 = 0
- self.genotype = self.genotype_1
+ self.genotype = genotype_1
self.samplelist = list(self.genotype.prgy)
- self.f1list = []
- self.parlist = []
- if _f1 and _f12:
- self.f1list = [_f1, _f12]
- if _mat and _pat:
- self.parlist = [_mat, _pat]
+ if f1 and f12:
+ self.f1list = [f1, f12]
+ if maternal and paternal:
+ self.parlist = [maternal, paternal]
class DataSet(object):
@@ -169,8 +172,6 @@ class DataSet(object):
# self.get_group()
#
# return self._group
-
-
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 53bb24fb..0c752617 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,5 +1,7 @@
from __future__ import absolute_import, print_function, division
+from flask import Flask, g
+
from base import webqtlCaseData
from utility import webqtlUtil, Plot, Bunch
from base.webqtlTrait import GeneralTrait
@@ -8,22 +10,19 @@ from pprint import pformat as pf
class SampleList(object):
def __init__(self,
- cursor,
dataset,
- variance_data_page,
sample_names,
this_trait,
sample_group_type,
header):
-
- self.cursor = cursor
+
self.dataset = dataset
self.this_trait = this_trait
self.sample_group_type = sample_group_type # primary or other
self.header = header
self.sample_list = [] # The actual list
-
+
self.get_attributes()
print("camera: attributes are:", pf(self.attributes))
@@ -54,7 +53,7 @@ class SampleList(object):
sample.this_id = "Other_" + str(counter)
#### For extra attribute columns; currently only used by several datasets - Zach
- if self.this_trait and self.this_trait.db and self.this_trait.db.type == 'ProbeSet':
+ if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
sample.extra_attributes = self.get_extra_attribute_values(sample_name)
print("sample.extra_attributes is", pf(sample.extra_attributes))
self.sample_list.append(sample)
@@ -88,27 +87,27 @@ class SampleList(object):
def get_attributes(self):
"""Finds which extra attributes apply to this dataset"""
- #ZS: Id and name values for this trait's extra attributes
- self.cursor.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
+ #ZS: Id and name values for this trait's extra attributes
+ case_attributes = g.db.execute('''SELECT CaseAttribute.Id, CaseAttribute.Name
FROM CaseAttribute, CaseAttributeXRef
WHERE CaseAttributeXRef.ProbeSetFreezeId = %s AND
CaseAttribute.Id = CaseAttributeXRef.CaseAttributeId
group by CaseAttributeXRef.CaseAttributeId''',
- (str(self.this_trait.db.id),))
+ (str(self.dataset.id),))
self.attributes = {}
- for key, value in self.cursor.fetchall():
+ for key, value in case_attributes.fetchall():
print("radish: %s - %s" % (key, value))
self.attributes[key] = Bunch()
self.attributes[key].name = value
- self.cursor.execute('''SELECT DISTINCT CaseAttributeXRef.Value
- FROM CaseAttribute, CaseAttributeXRef
- WHERE CaseAttribute.Name = %s AND
- CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))
+ attribute_values = g.db.execute('''SELECT DISTINCT CaseAttributeXRef.Value
+ FROM CaseAttribute, CaseAttributeXRef
+ WHERE CaseAttribute.Name = %s AND
+ CaseAttributeXRef.CaseAttributeId = CaseAttribute.Id''', (value,))
- self.attributes[key].distinct_values = [item[0] for item in self.cursor.fetchall()]
+ self.attributes[key].distinct_values = [item[0] for item in attribute_values.fetchall()]
self.attributes[key].distinct_values.sort(key=natural_sort_key)
@@ -119,27 +118,28 @@ class SampleList(object):
if self.attributes:
#ZS: Get StrainId value for the next query
- self.cursor.execute("""SELECT Strain.Id
+ result = g.db.execute("""SELECT Strain.Id
FROM Strain, StrainXRef, InbredSet
WHERE Strain.Name = %s and
StrainXRef.StrainId = Strain.Id and
InbredSet.Id = StrainXRef.InbredSetId and
- InbredSet.Name = %s""", (sample_name, self.dataset.group.name))
+ InbredSet.Name = %s""", (sample_name,
+ self.dataset.group.name))
- sample_id = self.cursor.fetchone()[0]
+ sample_id = result.fetchone().Id
for attribute in self.attributes:
#ZS: Add extra case attribute values (if any)
- self.cursor.execute("""SELECT Value
+ result = g.db.execute("""SELECT Value
FROM CaseAttributeXRef
- WHERE ProbeSetFreezeId = '%s' AND
- StrainId = '%s' AND
- CaseAttributeId = '%s'
- group by CaseAttributeXRef.CaseAttributeId""" % (
+ WHERE ProbeSetFreezeId = %s AND
+ StrainId = %s AND
+ CaseAttributeId = %s
+ group by CaseAttributeXRef.CaseAttributeId""", (
self.this_trait.db.id, sample_id, str(attribute)))
- attribute_value = self.cursor.fetchone()[0] #Trait-specific attributes, if any
+ attribute_value = result.fetchone().Value #Trait-specific attributes, if any
#ZS: If it's an int, turn it into one for sorting
#(for example, 101 would be lower than 80 if they're strings instead of ints)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 73b438d0..cd61d70c 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -55,7 +55,7 @@ class ShowTrait(templatePage):
#fd.readGenotype()
if not self.dataset.group.genotype:
- self.read_data(incf1=1)
+ self.read_data(include_f1=True) #incf1=1)
## determine data editing page format
#variance_data_page = 0
@@ -158,15 +158,15 @@ class ShowTrait(templatePage):
# print("Calling dispBasicStatistics")
# self.dispBasicStatistics(fd, this_trait)
- self.build_correlation_tools(args, this_trait)
+ self.build_correlation_tools(this_trait)
- self.make_sample_lists(args, variance_data_page, this_trait)
+ self.make_sample_lists(this_trait)
- if args['allsamplelist']:
- hddn['allsamplelist'] = string.join(args['allsamplelist'], ' ')
+ if self.dataset.group.allsamples:
+ hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
- if args['varianceDispName'] != 'Variance':
- hddn['isSE'] = "yes"
+ #if args['varianceDispName'] != 'Variance':
+ # hddn['isSE'] = "yes"
# We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
self.this_trait = this_trait
@@ -215,22 +215,20 @@ class ShowTrait(templatePage):
return this_trait
- def read_data(self):
+ def read_data(self, include_f1=False):
'''read user input data or from trait data and analysis form'''
- if incf1 == None:
- incf1 = []
+ #if incf1 == None:
+ # incf1 = []
if not self.genotype:
self.dataset.read_genotype_file()
if not samplelist:
- if incf1:
+ if include_f1:
samplelist = self.f1list + self.samplelist
else:
samplelist = self.samplelist
- #print("before traitfiledata self.traitfile is:", pf(self.traitfile))
-
traitfiledata = getattr(self, "traitfile", None)
traitpastedata = getattr(self, "traitpaste", None)
variancefiledata = getattr(self, "variancefile", None)
@@ -1174,39 +1172,34 @@ class ShowTrait(templatePage):
dataset_menu = []
print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
- query =
- self.cursor.execute('''SELECT PublishFreeze.FullName,PublishFreeze.Name FROM
+ results = g.db.execute("""SELECT PublishFreeze.FullName,PublishFreeze.Name FROM
PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = %s and PublishFreeze.public > %s''',
+ and InbredSet.Name = %s and PublishFreeze.public > %s""",
(this_group, webqtlConfig.PUBLICTHRESH))
- for item in self.cursor.fetchall():
+ for item in results.fetchall():
dataset_menu.append(dict(tissue=None,
datasets=[item]))
- self.cursor.execute('''SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,
+ results = g.db.execute("""SELECT GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze,
InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id and InbredSet.Name =
- %s and GenoFreeze.public > %s''',
+ %s and GenoFreeze.public > %s""",
(this_group, webqtlConfig.PUBLICTHRESH))
- for item in self.cursor.fetchall():
+ for item in results.fetchall():
dataset_menu.append(dict(tissue=None,
datasets=[item]))
#03/09/2009: Xiaodong changed the SQL query to order by Name as requested by Rob.
- self.cursor.execute('SELECT Id, Name FROM Tissue order by Name')
- for item in self.cursor.fetchall():
+ tissues = g.db.execute("SELECT Id, Name FROM Tissue order by Name")
+ for item in tissues.fetchall():
tissue_id, tissue_name = item
#databaseMenuSub = HT.Optgroup(label = '%s ------' % tissue_name)
#dataset_sub_menu = []
- print("phun9")
- self.cursor.execute('''SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze,
+ data_sets = g.db.execute('''SELECT ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze,
InbredSet WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeFreeze.TissueId = %s and
ProbeSetFreeze.public > %s and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s
order by ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId ''',
(tissue_id, webqtlConfig.PUBLICTHRESH, "%" + this_group + "%"))
- print("phun8")
- dataset_sub_menu = [item for item in self.cursor.fetchall() if item]
- #for item2 in self.cursor.fetchall():
- # dataset_sub_menu.append(item2)
+ dataset_sub_menu = [item for item in data_sets.fetchall() if item]
if dataset_sub_menu:
dataset_menu.append(dict(tissue=tissue_name,
datasets=dataset_sub_menu))
@@ -1612,11 +1605,13 @@ class ShowTrait(templatePage):
title4Body.append(submitTable)
- def make_sample_lists(self, fd, variance_data_page, this_trait):
- if args['parlist']:
- all_samples_ordered = args['parlist'] + args['f1list'] + args['samplelist']
+ def make_sample_lists(self, this_trait):
+ if self.dataset.group.parlist:
+ all_samples_ordered = (self.dataset.group.parlist +
+ self.dataset.group.f1list +
+ self.dataset.group.samplelist)
else:
- all_samples_ordered = args['f1list'] + args['samplelist']
+ all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
this_trait_samples = set(this_trait.data.keys())
@@ -1624,9 +1619,7 @@ class ShowTrait(templatePage):
print("-*- primary_samplelist is:", pf(primary_sample_names))
- primary_samples = SampleList(self.cursor,
- args=args,
- variance_data_page=variance_data_page,
+ primary_samples = SampleList(dataset = self.dataset,
sample_names=primary_sample_names,
this_trait=this_trait,
sample_group_type='primary',
@@ -1640,18 +1633,16 @@ class ShowTrait(templatePage):
other_sample_names.append(sample)
if other_sample_names:
- par_f1_samples = fd.parlist + fd.f1list
+ parent_f1_samples = self.dataset.group.parlist + self.dataset.group.f1list
other_sample_names.sort() #Sort other samples
- other_sample_names = par_f1_samples + other_sample_names
+ other_sample_names = parent_f1_samples + other_sample_names
- other_samples = SampleList(self.cursor,
- fd=fd,
- variance_data_page=variance_data_page,
- sample_names=other_sample_names,
- this_trait=this_trait,
- sample_group_type='other',
- header="Non-%s" % (fd.group))
+ other_samples = SampleList(dataset=self.dataset,
+ sample_names=other_sample_names,
+ this_trait=this_trait,
+ sample_group_type='other',
+ header="Non-%s" % (self.dataset.group.name))
self.sample_groups = (primary_samples, other_samples)
else:
@@ -1661,4 +1652,4 @@ class ShowTrait(templatePage):
#if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
# or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
# print("hjs")
- fd.allsamplelist = all_samples_ordered
+ self.dataset.group.allsamples = all_samples_ordered
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b5c1d6ac..163be69c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -19,7 +19,7 @@
<div class="container">
<div class="page-header">
<h1>{{ this_trait.species.capitalize() }} -
- {{ fd.RISet }} -
+ {{ dataset.group.name }} -
{{ this_trait.symbol }}
</h1>
</div>
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 17:19:08 +0000