# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. # # This program is free software: you can redistribute it and/or modify it # under the terms of the GNU Affero General Public License # as published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # See the GNU Affero General Public License for more details. # # This program is available from Source Forge: at GeneNetwork Project # (sourceforge.net/projects/genenetwork/). # # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) # at rwilliams@uthsc.edu and xzhou15@uthsc.edu # # # # This module is used by GeneNetwork project (www.genenetwork.org) # # Created by GeneNetwork Core Team 2010/08/10 # # 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 import string import os import reaper import webqtlConfig from webqtlCaseData import webqtlCaseData from utility import webqtlUtil class webqtlFormData(object): 'Represents data from a WebQTL form page, needed to generate the next page' attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance' 'suggestive','significance','submitID','identification', 'enablevariance', 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo') #XZ: Attention! All attribute values must be picklable! def __init__(self, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=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: self.remote_ip = req.connection.remote_ip 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 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): if key in self.__dict__: return self.__dict__[key] else: return default def __str__(self): rstr = '' for item in self.attrs: if item != 'genotype': rstr += '%s:%s\n' % (item,str(getattr(self,item))) return rstr def readGenotype(self): '''read genotype from .geno file''' if self.group == 'BXD300': self.group = 'BXD' assert self.group, "self.group needs to be set" #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() full_filename = locate(self.group + '.geno','genotype') # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(full_filename) self.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.group] except KeyError: _f1 = _f12 = _mat = _pat = 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) #determine default genotype object if self.incparentsf1 and self.genotype_1.type != "intercross": self.genotype = self.genotype_2 else: self.incparentsf1 = 0 self.genotype = self.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] def readData(self, samplelist, incf1=None): '''read user input data or from trait data and analysis form''' if incf1 == None: incf1 = [] if not self.genotype: self.readGenotype() if not samplelist: if incf1: 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) variancepastedata = getattr(self, "variancepaste", None) Nfiledata = getattr(self, "Nfile", None) #### Todo: Rewrite below when we get to someone submitting their own trait ##### def to_float(item): try: return float(item) except ValueError: return None print("bottle samplelist is:", samplelist) if traitfiledata: tt = traitfiledata.split() values = map(webqtlUtil.StringAsFloat, tt) elif traitpastedata: tt = traitpastedata.split() values = map(webqtlUtil.StringAsFloat, tt) else: 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() variances = map(webqtlUtil.StringAsFloat, tt) elif variancepastedata: tt = variancepastedata.split() variances = map(webqtlUtil.StringAsFloat, tt) else: variances = map(self.FormVarianceAsFloat, samplelist) if len(variances) < len(samplelist): variances += [None]*(len(samplelist) - len(variances)) elif len(variances) > len(samplelist): variances = variances[:len(samplelist)] if Nfiledata: tt = string.split(Nfiledata) nsamples = map(webqtlUtil.IntAsFloat, tt) if len(nsamples) < len(samplelist): nsamples += [None]*(len(samplelist) - len(nsamples)) else: nsamples = map(self.FormNAsFloat, samplelist) ##values, variances, nsamples is obsolete self.allTraitData = {} for i, _sample in enumerate(samplelist): 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)''' if not samplelist: samplelist = self.samplelist samples = [] 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 if _val != None: if include_variances: if _var != None: samples.append(sample) values.append(_val) variances.append(_var) else: samples.append(sample) values.append(_val) variances.append(None) 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)) except: return None def FormNAsFloat(self, key): 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)}