diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 119 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait_page.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 6 |
3 files changed, 72 insertions, 57 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 84e41cae..c94dbe53 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -24,7 +24,7 @@ # # Last updated by GeneNetwork Core Team 2010/10/20 -from mod_python import Cookie +#from mod_python import Cookie import string import os @@ -47,7 +47,9 @@ class webqtlFormData: #XZ: Attention! All attribute values must be picklable! - def __init__(self, req = None, mod_python_session=None, FieldStorage_formdata=None): + def __init__(self, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None): + + self.__dict__.update(start_vars) for item in self.attrs: setattr(self,item, None) @@ -62,34 +64,35 @@ class webqtlFormData: 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') + #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)) - #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 = "" self.mpolar = "" if self.RISet: try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet] except: f1 = f12 = self.mpolar = self.ppolar = None - + try: self.nperm = int(self.nperm) self.nboot = int(self.nboot) @@ -101,12 +104,21 @@ class webqtlFormData: self.allstrainlist = map(string.strip, string.split(self.allstrainlist)) #self.readGenotype() #self.readData() - + if self.RISet == 'BXD300': self.RISet = 'BXD' else: pass - + + def __getitem__(self, key): + 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: @@ -114,7 +126,7 @@ class webqtlFormData: rstr += '%s:%s\n' % (item,str(getattr(self,item))) return rstr - + def readGenotype(self): 'read genotype from .geno file' if self.RISet == 'BXD300': @@ -127,15 +139,15 @@ class webqtlFormData: self.genotype_1 = reaper.Dataset() self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')) try: - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; + # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet] except: _f1 = _f12 = _mat = _pat = None - + self.genotype_2 =self.genotype_1 if self.genotype_1.type == "riset" 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 @@ -148,7 +160,7 @@ class webqtlFormData: self.f1list = [_f1, _f12] if _mat and _pat: self.parlist = [_mat, _pat] - + def readData(self, strainlst=[], incf1=[]): 'read user input data or from trait data and analysis form' @@ -158,16 +170,16 @@ class webqtlFormData: if incf1: strainlst = self.f1list + self.strainlist else: - strainlst = self.strainlist - - + strainlst = self.strainlist + + traitfiledata = self.formdata.getfirst('traitfile') traitpastedata = self.formdata.getfirst('traitpaste') variancefiledata = self.formdata.getfirst('variancefile') variancepastedata = self.formdata.getfirst('variancepaste') Nfiledata = self.formdata.getfirst('Nfile') - + if traitfiledata: tt = string.split(traitfiledata) vals = map(webqtlUtil.StringAsFloat, tt) @@ -183,8 +195,8 @@ class webqtlFormData: vals = vals[:len(strainlst)] else: pass - - + + if variancefiledata: tt = string.split(variancefiledata) vars = map(webqtlUtil.StringAsFloat, tt) @@ -200,7 +212,7 @@ class webqtlFormData: vars = vars[:len(strainlst)] else: pass - + if Nfiledata: tt = string.split(Nfiledata) nstrains = map(webqtlUtil.IntAsFloat, tt) @@ -208,14 +220,14 @@ class webqtlFormData: nstrains += [None]*(len(strainlst) - len(nstrains)) else: nstrains = map(self.FormNAsFloat, strainlst) - + ##vals, vars, nstrains is obsolete self.allTraitData = {} for i, _strain in enumerate(strainlst): if vals[i] != None: self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i]) - + def informativeStrains(self, strainlst=[], incVars = 0): '''if readData was called, use this to output the informative strains @@ -241,26 +253,26 @@ class webqtlFormData: return strains, vals, vars, len(strains) - + def FormDataAsFloat(self, key): try: return float(self.formdata.getfirst(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.RISet = 'BXD' @@ -273,17 +285,16 @@ class webqtlFormData: #self.genotype.ReadMM('AXBXAforQTL') #self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy) #self.strainlist.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), + 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)} - diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py index a34c20cf..d4019fd5 100644 --- a/wqflask/wqflask/show_trait/show_trait_page.py +++ b/wqflask/wqflask/show_trait/show_trait_page.py @@ -56,8 +56,8 @@ class ShowTraitPage(DataEditingPage): else: print("j2.3") print("fd is:", fd) - database = fd['database'] - ProbeSetID = fd['ProbeSetID'] + database = fd['database'][0] + ProbeSetID = fd['ProbeSetID'][0] print("j2.4") CellID = fd.get('CellID') print("j2.6") diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 611cc05b..3457f0ff 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -7,6 +7,8 @@ from flask import render_template, request from wqflask import search_results from wqflask.show_trait import show_trait_page +from base import webqtlFormData + from pprint import pformat as pf @app.route("/") @@ -21,5 +23,7 @@ def search(): @app.route("/showDatabaseBXD") def showDatabaseBXD(): - template_vars = show_trait_page.ShowTraitPage(request.args) + # Here it's currently too complicated not to use an fd that is a webqtlFormData + fd = webqtlFormData.webqtlFormData(request.args) + template_vars = show_trait_page.ShowTraitPage(fd) return render_template("trait_data_and_analysis.html") |