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-rw-r--r--wqflask/base/webqtlFormData.py99
1 files changed, 2 insertions, 97 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 10251756..1b41b2fc 100644
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -24,8 +24,6 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-#from mod_python import Cookie
-
from __future__ import print_function
from pprint import pformat as pf
@@ -49,20 +47,13 @@ class webqtlFormData(object):
def __init__(self,
start_vars = None,
- req = None,
- mod_python_session=None,
- FieldStorage_formdata=None):
+ req = None):
# Todo: rework this whole thing
- print("in webqtlFormData start_vars are:", pf(start_vars))
for item in webqtlFormData.attrs:
self.__dict__[item] = None
- #ZS: This is only used in DataEditingPage.py (as far as I know)
- self.varianceDispName = None
-
for item in start_vars:
self.__dict__[item] = start_vars[item]
- print(" Now self.dict is:", pf(self.__dict__))
#Todo: This can't be good below...rework
try:
@@ -70,42 +61,11 @@ class webqtlFormData(object):
except:
self.remote_ip = '1.2.3.4'
- if req and req.headers_in.has_key('referer'):
- self.refURL = req.headers_in['referer']
- else:
- self.refURL = None
-
- # For now let's just comment all this out - Sam
-
- #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie.
- #
- ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable.
- #self.input_session_data = sessionData.sessionData( mod_python_session )
- #
- ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data.
- #self.formdata = cgiData( FieldStorage_formdata )
- #
- ##get Form ID
- #self.formID = self.formdata.getfirst('FormID')
- #
- ##get rest of the attributes
- #if self.formID:
- # for item in self.attrs:
- # value = self.formdata.getfirst(item)
- # if value != None:
- # setattr(self,item,string.strip(value))
-
self.ppolar = None
self.mpolar = None
- print("[yellow] self.group is:", self.group)
if self.group:
- #try:
- # # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
_f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
- #except:
- # f1 = f12 = self.mpolar = self.ppolar = None
-
def set_number(stringy):
return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
@@ -113,22 +73,13 @@ class webqtlFormData(object):
self.nperm = set_number(self.nperm)
self.nboot = set_number(self.nboot)
-
- #if self.allsamplelist:
- # self.allsamplelist = map(string.strip, string.split(self.allsamplelist))
- print("self.allsamplelist is:", self.allsamplelist)
if self.allsamplelist:
self.allsamplelist = self.allsamplelist.split()
- print("now self.allsamplelist is:", self.allsamplelist)
- #self.readGenotype()
- #self.readData()
if self.group == 'BXD300':
self.group = 'BXD'
-
def __getitem__(self, key):
- print("in __getitem__")
return self.__dict__[key]
def get(self, key, default=None):
@@ -206,8 +157,6 @@ class webqtlFormData(object):
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)
@@ -233,15 +182,12 @@ class webqtlFormData(object):
print("mapping formdataasfloat")
#values = map(self.FormDataAsFloat, samplelist)
values = [to_float(getattr(self, key)) for key in samplelist]
- print("rocket values is:", values)
if len(values) < len(samplelist):
values += [None] * (len(samplelist) - len(values))
elif len(values) > len(samplelist):
values = values[:len(samplelist)]
- print("now values is:", values)
-
if variancefiledata:
tt = variancefiledata.split()
@@ -271,9 +217,6 @@ class webqtlFormData(object):
if values[i] != None:
self.allTraitData[_sample] = webqtlCaseData(
_sample, values[i], variances[i], nsamples[i])
- print("allTraitData is:", pf(self.allTraitData))
-
-
def informativeStrains(self, samplelist=None, include_variances = None):
'''if readData was called, use this to output informative samples (sample with values)'''
@@ -285,8 +228,6 @@ class webqtlFormData(object):
values = []
variances = []
- #print("self.allTraitData is:", pf(self.allTraitData))
-
for sample in samplelist:
if sample in self.allTraitData:
_val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
@@ -303,16 +244,6 @@ class webqtlFormData(object):
return samples, values, variances, len(samples)
-
-
- #def FormDataAsFloat(self, key):
- #
- # #try:
- # # return float(self.key)
- # #except:
- # # return None
-
-
def FormVarianceAsFloat(self, key):
try:
return float(self.formdata.getfirst('V' + key))
@@ -323,30 +254,4 @@ class webqtlFormData(object):
try:
return int(self.formdata.getfirst('N' + key))
except:
- return None
-
- def Sample(self):
- 'Create some dummy data for testing'
- self.group = 'BXD'
- self.incparentsf1 = 'on'
- #self.display = 9.2
- #self.significance = 16.1
- self.readGenotype()
- self.identification = 'BXD : Coat color example by Lu Lu, et al'
- #self.readGenotype()
- #self.genotype.ReadMM('AXBXAforQTL')
- #self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
- #self.samplelist.sort()
- self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2),
- 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2),
- 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4),
- 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2),
- 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3),
- 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3),
- 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2),
- 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4),
- 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4),
- 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1),
- 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4),
- 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4),
- 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)}
+ return None \ No newline at end of file