diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/webqtlFormData.py | 99 |
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
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