Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty sure also isn't used any more.

Also removed some other unused code from the files listed

1 files changed, 0 insertions, 257 deletions

diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
deleted file mode 100644
index 1b41b2fc..00000000
--- a/wqflask/base/webqtlFormData.py
+++ /dev/null
@@ -1,257 +0,0 @@
-# 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 __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):
-        # Todo: rework this whole thing
-        for item in webqtlFormData.attrs:
-            self.__dict__[item] = None
-
-        for item in start_vars:
-            self.__dict__[item] = start_vars[item]
-
-        #Todo: This can't be good below...rework
-        try:
-            self.remote_ip = req.connection.remote_ip
-        except:
-            self.remote_ip = '1.2.3.4'
-
-        self.ppolar = None
-        self.mpolar = None
-
-        if self.group:
-            _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
-
-        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 = self.allsamplelist.split()
-
-        if self.group == 'BXD300':
-            self.group = 'BXD'
-
-    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:
-            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
-
-        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]
-
-
-        if len(values) < len(samplelist):
-            values += [None] * (len(samplelist) - len(values))
-        elif len(values) > len(samplelist):
-            values = values[:len(samplelist)]
-
-        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])
-
-    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 = []
-
-        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 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
\ No newline at end of file