path: root/wqflask/base/webqtlFormData.py

# 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)}