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1 #!/usr/bin/env python
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2
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3 from galaxy import eggs
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4 import pkg_resources
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5 pkg_resources.require( "Cheetah" )
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6 from Cheetah.Template import Template
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7
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8 import errno
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9 import os
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10 from datetime import datetime
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11
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12 ################################################################################
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13
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14 def die(message):
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15 print >> sys.stderr, message
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16 sys.exit(1)
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17
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18 def mkdir_p(path):
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19 try:
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20 os.makedirs(path)
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21 except OSError, e:
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22 if e.errno <> errno.EEXIST:
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23 raise
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24
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25 ################################################################################
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26
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27 class Display(object):
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28 def display(self, parameter):
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29 print parameter
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30
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31 class DisplayFile(Display):
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32 def display(self, parameter):
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33 return '<a href="{0}">{1}</a>'.format(parameter.value, parameter.name)
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34
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35 class DisplayValue(Display):
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36 def display(self, parameter):
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37 if parameter.value is not None:
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38 return '{0}: {1}'.format(parameter.description, parameter.value)
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39 else:
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40 return '{0}'.format(parameter.description)
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41
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42 class DisplayTagList(Display):
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43 def display(self, parameter):
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44 rv = []
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45 if parameter.name:
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46 rv.append(parameter.name)
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47 rv.append('<ol>')
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48 for tag in parameter.value:
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49 col, individual_name = tag.split(':')
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50 rv.append('<li>{0}</li>'.format(individual_name))
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51 rv.append('</ol>')
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52 return '\n'.join(rv)
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53
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54 class DisplayPopulationList(Display):
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55 def display(self, parameter):
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56 rv = []
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57 rv.append('Populations')
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58 rv.append('<ul>')
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59 for population in parameter.value:
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60 rv.append('<li>')
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61 if population.name is not None:
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62 rv.append(population.name)
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63 rv.append('<ol>')
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64 for name in population.individual_names():
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65 rv.append('<li>{0}</li>'.format(name))
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66 rv.append('</ol>')
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67 rv.append('</li>')
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68 rv.append('</ul>')
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69 return '\n'.join(rv)
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70
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71 # def display(self, parameter, name=''):
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72 # print '<ul> {0}'.format(name)
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73 # for individual_name in parameter.individual_names():
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74 # print '<li>{0}>/li>'.format(individual_name)
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75 # print '</ul>'
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76
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77
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78 class Parameter(object):
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79 def __init__(self, name=None, value=None, description=None, display_type=None):
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80 self.name = name
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81 self.value = value
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82 self.description = description
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83 if display_type is None:
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84 self.display_type = Display()
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85 else:
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86 self.display_type = display_type
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87
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88 def display(self):
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89 return self.display_type.display(self)
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90
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91 class InfoPage(object):
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92 _realpath = os.path.realpath(__file__)
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93 _script_dir = os.path.dirname(_realpath)
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94 template_file = os.path.join(_script_dir, 'gd_composite_template.html')
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95 def __init__(self):
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96 self.timestamp = datetime.now().strftime('%Y-%m-%d %I:%M:%S %p')
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97 self.title = 'Genome Diversity Composite Dataset'
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98 self.inputs = []
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99 self.outputs = []
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100 self.misc = ''
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101 self.template = self.load_template()
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102
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103 def load_template(self):
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104 with open(self.template_file) as f:
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105 return f.read().rstrip('\r\n')
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106
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107 def set_title(self, title):
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108 self.title = title
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109
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110 def add_input_parameter(self, parameter):
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111 self.inputs.append(parameter)
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112
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113 def add_output_parameter(self, parameter):
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114 self.outputs.append(parameter)
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115
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116 def add_misc(self, misc):
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117 self.misc = misc
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118
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119 def render(self):
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120 return Template(self.template, searchList=[{'tool': self}])
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121
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122
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123
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124
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125
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126
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127
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128
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