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1 #!/usr/bin/env python
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2
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3 # Copyright (c) 2003-2004 The Regents of the University of California.
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4 # Copyright (c) 2005 Gavin E. Crooks
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5 # Copyright (c) 2006, The Regents of the University of California, through
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6 # Lawrence Berkeley National Laboratory (subject to receipt of any required
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7 # approvals from the U.S. Dept. of Energy). All rights reserved.
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8
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9 # This software is distributed under the new BSD Open Source License.
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10 # <http://www.opensource.org/licenses/bsd-license.html>
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11 #
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12 # Redistribution and use in source and binary forms, with or without
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13 # modification, are permitted provided that the following conditions are met:
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14 #
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15 # (1) Redistributions of source code must retain the above copyright notice,
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16 # this list of conditions and the following disclaimer.
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17 #
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18 # (2) Redistributions in binary form must reproduce the above copyright
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19 # notice, this list of conditions and the following disclaimer in the
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20 # documentation and or other materials provided with the distribution.
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21 #
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22 # (3) Neither the name of the University of California, Lawrence Berkeley
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23 # National Laboratory, U.S. Dept. of Energy nor the names of its contributors
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24 # may be used to endorse or promote products derived from this software
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25 # without specific prior written permission.
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26 #
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27 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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28 # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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29 # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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30 # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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31 # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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32 # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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33 # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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34 # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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35 # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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36 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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37 # POSSIBILITY OF SUCH DAMAGE.
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38
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39 import sys
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40 import cgi as cgilib
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41 import cgitb; cgitb.enable()
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42
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43 #print "Content-Type: text/html\n\n"
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44 #print "HELLO WORLD"
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45 #print __name__
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46
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47 from StringIO import StringIO
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48 from color import *
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49 from colorscheme import ColorScheme, ColorGroup
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50
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51 import weblogolib
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52 from corebio.utils import *
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53 from corebio._future import Template
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54
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55
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56 # TODO: Check units
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57
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58 # TODO: In WebLogo2: why slash create.cgi? I think this was a workaround
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59 # for some browser quirk
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60 #<form method="post" action="/create.cgi" enctype="multipart/form-data">
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61
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62 def resource_string(resource, basefilename) :
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63 import os
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64 fn = os.path.join(os.path.dirname(basefilename), resource)
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65 return open( fn ).read()
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66
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67 mime_type = {
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68 'eps': 'application/postscript',
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69 'pdf': 'application/pdf',
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70 'png': 'image/png',
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71 'png_print': 'image/png',
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72 'txt' : 'text/plain',
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73 'jpeg' : 'image/jpeg',
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74 }
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75
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76 extension = {
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77 'eps': 'eps',
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78 'pdf': 'pdf',
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79 'png': 'png',
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80 'png_print': 'png',
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81 'txt' : 'txt',
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82 'jpeg' : 'png'
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83 }
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84
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85
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86 alphabets = {
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87 'alphabet_auto': None,
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88 'alphabet_protein': weblogolib.unambiguous_protein_alphabet,
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89 'alphabet_rna': weblogolib.unambiguous_rna_alphabet,
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90 'alphabet_dna': weblogolib.unambiguous_dna_alphabet}
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91
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92 color_schemes = {}
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93 for k in weblogolib.std_color_schemes.keys():
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94 color_schemes[ 'color_'+k.replace(' ', '_')] = weblogolib.std_color_schemes[k]
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95
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96
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97 composition = {'comp_none' : 'none',
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98 'comp_auto' : 'auto',
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99 'comp_equiprobable':'equiprobable',
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100 'comp_CG': 'percentCG',
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101 'comp_Celegans' : 'C. elegans',
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102 'comp_Dmelanogaster' : 'D. melanogaster',
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103 'comp_Ecoli' : 'E. coli',
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104 'comp_Hsapiens': 'H. sapiens',
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105 'comp_Mmusculus' : 'M. musculus',
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106 'comp_Scerevisiae': 'S. cerevisiae'
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107 }
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108
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109 class Field(object) :
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110 """ A representation of an HTML form field."""
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111 def __init__(self, name, default=None, conversion= None, options=None, errmsg="Illegal value.") :
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112 self.name = name
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113 self.default = default
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114 self.value = default
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115 self.conversion = conversion
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116 self.options = options
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117 self.errmsg = errmsg
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118
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119 def get_value(self) :
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120 if self.options :
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121 if not self.value in self.options :
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122 raise ValueError, (self.name, self.errmsg)
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123
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124 if self.conversion :
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125 try :
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126 return self.conversion(self.value)
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127 except ValueError, e :
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128 raise ValueError, (self.name, self.errmsg)
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129 else:
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130 return self.value
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131
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132
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133 def string_or_none(value) :
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134 if value is None or value == 'auto':
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135 return None
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136 return str(value)
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137
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138 def truth(value) :
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139 if value== "true" : return True
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140 return bool(value)
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141
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142 def int_or_none(value) :
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143 if value =='' or value is None or value == 'auto':
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144 return None
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145 return int(value)
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146
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147 def float_or_none(value) :
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148 if value =='' or value is None or value == 'auto':
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149 return None
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150 return float(value)
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151
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152
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153 def main(htdocs_directory = None) :
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154
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155 logooptions = weblogolib.LogoOptions()
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156
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157 # A list of form fields.
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158 # The default for checkbox values must be False (irrespective of
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159 # the default in logooptions) since a checked checkbox returns 'true'
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160 # but an unchecked checkbox returns nothing.
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161 controls = [
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162 Field( 'sequences', ''),
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163 Field( 'format', 'png', weblogolib.formatters.get ,
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164 options=['png_print', 'png', 'jpeg', 'eps', 'pdf', 'txt'] ,
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165 errmsg="Unknown format option."),
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166 Field( 'stacks_per_line', logooptions.stacks_per_line , int,
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167 errmsg='Invalid number of stacks per line.'),
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168 Field( 'size','medium', weblogolib.std_sizes.get,
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169 options=['small', 'medium', 'large'], errmsg='Invalid logo size.'),
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170 Field( 'alphabet','alphabet_auto', alphabets.get,
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171 options=['alphabet_auto', 'alphabet_protein', 'alphabet_dna',
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172 'alphabet_rna'],
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173 errmsg="Unknown sequence type."),
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174 Field( 'unit_name', 'bits',
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175 options=[ 'probability', 'bits', 'nats', 'kT', 'kJ/mol',
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176 'kcal/mol']),
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177 Field( 'first_index', 1, int_or_none),
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178 Field( 'logo_start', '', int_or_none),
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179 Field( 'logo_end', '', int_or_none),
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180 Field( 'composition', 'comp_auto', composition.get,
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181 options=['comp_none','comp_auto','comp_equiprobable','comp_CG',
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182 'comp_Celegans','comp_Dmelanogaster','comp_Ecoli',
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183 'comp_Hsapiens','comp_Mmusculus','comp_Scerevisiae'],
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184 errmsg= "Illegal sequence composition."),
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185 Field( 'percentCG', '', float_or_none, errmsg="Invalid CG percentage."),
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186 Field( 'show_errorbars', False , truth),
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187 Field( 'altype', False , truth),
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188 Field( 'logo_title', logooptions.logo_title ),
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189 Field( 'logo_label', logooptions.logo_label ),
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190 Field( 'show_xaxis', False, truth),
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191 Field( 'xaxis_label', logooptions.xaxis_label ),
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192 Field( 'show_yaxis', False, truth),
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193 Field( 'yaxis_label', logooptions.yaxis_label, string_or_none ),
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194 Field( 'yaxis_scale', logooptions.yaxis_scale , float_or_none,
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195 errmsg="The yaxis scale must be a positive number." ),
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196 Field( 'yaxis_tic_interval', logooptions.yaxis_tic_interval ,
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197 float_or_none),
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198 Field( 'show_ends', False, truth),
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199 Field( 'show_fineprint', False , truth),
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200 Field( 'color_scheme', 'color_auto', color_schemes.get,
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201 options=color_schemes.keys() ,
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202 errmsg = 'Unknown color scheme'),
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203 Field( 'color0', ''),
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204 Field( 'symbols0', ''),
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205 Field( 'desc0', ''),
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206 Field( 'color1', ''),
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207 Field( 'symbols1', ''),
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208 Field( 'desc1', ''),
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209 Field( 'color2', ''),
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210 Field( 'symbols2', ''),
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211 Field( 'desc2', ''),
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212 Field( 'color3', ''),
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213 Field( 'symbols3', ''),
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214 Field( 'desc3', ''),
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215 Field( 'color4', ''),
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216 Field( 'symbols4', ''),
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217 Field( 'desc4', ''),
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218 Field( 'ignore_lower_case', False, truth),
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219 Field( 'altype', False, truth),
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220 Field( 'scale_width', False, truth),
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221 ]
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222
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223 form = {}
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224 for c in controls :
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225 form[c.name] = c
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226
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227
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228 form_values = cgilib.FieldStorage()
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229
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230 # Send default form?
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231 if len(form_values) ==0 or form_values.has_key("cmd_reset"):
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232 # Load default truth values now.
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233 form['show_errorbars'].value = logooptions.show_errorbars
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234 form['show_xaxis'].value = logooptions.show_xaxis
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235 form['show_yaxis'].value = logooptions.show_yaxis
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236 form['show_ends'].value = logooptions.show_ends
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237 form['show_fineprint'].value = logooptions.show_fineprint
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238 form['scale_width'].value = logooptions.scale_width
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239 form['altype'].value = logooptions.altype
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240
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241 send_form(controls, htdocs_directory = htdocs_directory)
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242 return
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243
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244 # Get form content
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245 for c in controls :
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246 c.value = form_values.getfirst( c.name, c.default)
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247
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248
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249 options_from_form = ['format', 'stacks_per_line', 'size',
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250 'alphabet', 'unit_name', 'first_index', 'logo_start','logo_end',
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251 'composition',
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252 'show_errorbars', 'logo_title', 'logo_label', 'show_xaxis',
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253 'xaxis_label',
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254 'show_yaxis', 'yaxis_label', 'yaxis_scale', 'yaxis_tic_interval',
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255 'show_ends', 'show_fineprint', 'scale_width','altype']
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256
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257 errors = []
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258 for optname in options_from_form :
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259 try :
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260 value = form[optname].get_value()
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261 if value!=None : setattr(logooptions, optname, value)
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262 except ValueError, err :
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263 errors.append(err.args)
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264
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265 #check if using codons or not.
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266 if logooptions.altype!=True:
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267 weblogolib.altype = ""
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268 print >> sys.stderr,logooptions.altype
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269 print >> sys.stderr, "--nn-"
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270
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271 # Construct custom color scheme
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272 custom = ColorScheme()
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273 for i in range(0,5) :
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274 color = form["color%d"%i].get_value()
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275 symbols = form["symbols%d"%i].get_value()
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276 desc = form["desc%d"%i].get_value()
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277
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278 if color :
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279 try :
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280 custom.groups.append(weblogolib.ColorGroup(symbols, color, desc))
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281 except ValueError, e :
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282 errors.append( ('color%d'%i, "Invalid color: %s" % color) )
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283
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284 if form["color_scheme"].value == 'color_custom' :
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285 logooptions.color_scheme = custom
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286 else :
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287 try :
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288 logooptions.color_scheme = form["color_scheme"].get_value()
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289 except ValueError, err :
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290 errors.append(err.args)
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291
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292 sequences = None
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293
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294 # FIXME: Ugly fix: Must check that sequence_file key exists
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295 # FIXME: Sending malformed or missing form keys should not cause a crash
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296 # sequences_file = form["sequences_file"]
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297 if form_values.has_key("sequences_file") :
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298 sequences = form_values.getvalue("sequences_file")
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299 assert type(sequences) == str
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300
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301 if not sequences or len(sequences) ==0:
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302 sequences = form["sequences"].get_value()
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303
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304 if not sequences or len(sequences) ==0:
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305 errors.append( ("sequences", "Please enter a multiple-sequence alignment in the box above, or select a file to upload."))
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306
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307
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308
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309 # If we have uncovered errors or we want the chance to edit the logo
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310 # ("cmd_edit" command from examples page) then we return the form now.
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311 # We do not proceed to the time consuming logo creation step unless
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312 # required by a 'create' or 'validate' command, and no errors have been
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313 # found yet.
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314 if form_values.has_key("cmd_edit") or errors :
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315 send_form(controls, errors, htdocs_directory)
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316 return
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317
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318
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319
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320
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321 # We write the logo into a local buffer so that we can catch and
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322 # handle any errors. Once the "Content-Type:" header has been sent
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323 # we can't send any useful feedback
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324 logo = StringIO()
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325 try :
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326 comp = form["composition"].get_value()
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327 percentCG = form["percentCG"].get_value()
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328 ignore_lower_case = form_values.has_key("ignore_lower_case")
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329 seqs = weblogolib.read_seq_data(StringIO( sequences),
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330 alphabet=logooptions.alphabet,
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331 ignore_lower_case=ignore_lower_case
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332 )
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333 if comp=='percentCG': comp = str(percentCG/100)
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334 prior = weblogolib.parse_prior(comp, seqs.alphabet)
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335 data = weblogolib.LogoData.from_seqs(seqs, prior)
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336 logoformat = weblogolib.LogoFormat(data, logooptions)
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337 format = form["format"].value
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338 weblogolib.formatters[format](data, logoformat, logo)
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339 except ValueError, err :
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340 errors.append( err.args )
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341 except IOError, err :
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342 errors.append( err.args)
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343 except RuntimeError, err :
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344 errors.append( err.args )
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345
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346 if form_values.has_key("cmd_validate") or errors :
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347 send_form(controls, errors, htdocs_directory)
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348 return
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349
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350
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351 #
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352 # RETURN LOGO OVER HTTP
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353 #
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354
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355 print "Content-Type:", mime_type[format]
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356 # Content-Disposition: inline Open logo in browser window
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357 # Content-Disposition: attachment Download logo
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358 if form_values.has_key("download") :
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359 print 'Content-Disposition: attachment; ' \
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360 'filename="logo.%s"' % extension[format]
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361 else :
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362 print 'Content-Disposition: inline; ' \
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363 'filename="logo.%s"' % extension[format]
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364
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365
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366 # Seperate header from data
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367 print
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368
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369 # Finally, and at last, send the logo.
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370 print logo.getvalue()
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371
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372
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373 def send_form(controls, errors=[], htdocs_directory=None) :
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374 if htdocs_directory is None :
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375 htdocs_directory = os.path.join(
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376 os.path.dirname(__file__, "htdocs") )
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377
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378 subsitutions = {}
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379 subsitutions["version"] = weblogolib.release_description
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380
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381 for c in controls :
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382 if c.options :
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383 for opt in c.options :
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384 subsitutions[opt.replace('/','_')] = ''
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385 subsitutions[c.value.replace('/','_')] = 'selected'
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386 else :
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387 value = c.value
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388 if value == None : value = 'auto'
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389 if value=='true':
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390 subsitutions[c.name] = 'checked'
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391 elif type(value)==bool :
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392 if value :
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393 subsitutions[c.name] = 'checked'
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394 else :
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395 subsitutions[c.name] = ''
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396 else :
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397 subsitutions[c.name] = str(value)
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398 subsitutions[c.name+'_err'] = ''
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399
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400 if errors :
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401 print >>sys.stderr, errors
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402 error_message = []
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403 for e in errors :
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404 if type(e) is str :
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405 msg = e
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406 elif len(e)==2:
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407 subsitutions[e[0]+"_err"] = "class='error'"
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408 msg = e[1]
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409 else :
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410 msg = e[0]
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411
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412
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413 error_message += "ERROR: "
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414 error_message += msg
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415 error_message += ' <br />'
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416
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417 error_message += \
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418 "<input style='float:right; font-size:small' type='submit' name='cmd_validate' value='Clear Error' /> "
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419 subsitutions["error_message"] = ''.join(error_message)
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420 else :
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421 subsitutions["error_message"] = ""
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422
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423
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424 template = resource_string("create_html_template.html", htdocs_directory)
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425 html = Template(template).safe_substitute(subsitutions) #FIXME
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426
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427 print "Content-Type: text/html\n\n"
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428 print html
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429
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430 # DEBUG
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431 # keys = subsitutions.keys()
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432 # keys.sort()
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433 # for k in keys :
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434 # print k,"=", subsitutions[k], " <br />"
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435
|
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436 #for k in controls :
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437 # print k.name,"=", k.get_value(), " <br />"
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438
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439
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440
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441 if __name__=="__main__" :
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442 main()
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443
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444
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445
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446
|
