Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 358 insertions, 0 deletions

diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
new file mode 100755
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--- /dev/null
+++ b/wqflask/base/webqtlFormData.py
@@ -0,0 +1,358 @@
+# 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
+import cookieData
+import sessionData
+from cgiData import cgiData
+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 = os.path.join(webqtlConfig.GENODIR, self.group + '.geno')
+
+        # 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)}