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1 # To change this template, choose Tools | Templates
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2 # and open the template in the editor.
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3
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4 __author__ = "Chaitanya Guttula"
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5
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6
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7 import os
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8 import sys
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9 from shutil import copytree, ignore_patterns
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10
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11 galaxyhome=os.environ.get('GALAXY_HOME')
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12 #print galaxyhome
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13
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14 #os.mkdir(galaxyhome+'/GAL')
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15 dirfilelist=os.listdir(galaxyhome+'/tools')
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16 exist = False
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17 for dirfile in dirfilelist:
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18 if dirfile == 'WebServiceToolWorkflow_REST_SOAP':
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19 exist = True
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20 break
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21
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22 if exist:
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23 print 'WebServiceToolWorkflow_REST_SOAP is already present in '+galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP'
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24 else:
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25 copytree('WebServiceToolWorkflow_REST_SOAP',galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP', ignore=ignore_patterns('*.pyc', 'tmp*'))
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26 print 'Copied the folder \'WebServiceToolWorkflow_REST_SOAP\' to '+galaxyhome+'/tools'
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27
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28 f1=open(galaxyhome+'/tool_conf.xml','r')
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29 f1.seek(0,0)
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30 f2=open(galaxyhome+'/tool_conf_backup.xml','w')
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31 f2.seek(0,0)
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32
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33 #copy the first line <toolbox> into another file f2
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34 line = f1.readline()
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35 #f2.write(line)
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36
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37 lineStripped=line.lstrip()
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38 lineStripped=lineStripped.rstrip()
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39
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40 #Flags for verifying that the tool is not already installed
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41 tool_present = False
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42 webservice_present = False
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43 workflow_present = False
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44
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45 # Check of the tools are already installed or not
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46 # and sets the flags to true if they are already installed
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47 while not lineStripped == '</toolbox>':
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48 line = f1.readline()
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49 lineStripped = line.lstrip()
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50 lineStripped=lineStripped.rstrip()
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51 if(lineStripped.find('<!--')>-1):
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52 line = f1.readline()
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53 while(not line.find('-->')>-1):
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54 line = f1.readline()
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55
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56 if lineStripped == '<section name="Add Web service tool" id="RegisterWebService">':
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57 tool_present = True
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58 elif lineStripped == '<section name="Web Service Tools" id="WebServices">':
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59 webservice_present = True
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60 elif lineStripped == '<section name="Web Service Workflow Tools" id="WebServiceWorkflow">':
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61 workflow_present = True
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62
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63
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64 f1.seek(0,0)
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65 line = f1.readline()
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66 f2.write(line)
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67
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68 lineStripped=line.lstrip()
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69 lineStripped=lineStripped.rstrip()
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70
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71 # copy to the file f2 till <toolbox>
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72 while not lineStripped == '<toolbox>':
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73 line = f1.readline()
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74 f2.write(line)
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75 lineStripped = line.lstrip()
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76 lineStripped = lineStripped.rstrip()
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77
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78 # Check if the tool is not installed and then add it to the file f2
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79 if not tool_present:
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80 f2.write(' <section name="Add Web service tool" id="RegisterWebService">\n')
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81 f2.write(' <tool file="WebServiceToolWorkflow_REST_SOAP/WebServiceTool_input_url_REST_SOAP.xml"/>\n')
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82 f2.write(' <tool file="WebServiceToolWorkflow_REST_SOAP/WebServiceTool_input_method_REST_SOAP.xml"/>\n')
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83 f2.write(' <tool file="WebServiceToolWorkflow_REST_SOAP/refreshTool.xml"/>\n')
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84 f2.write(' </section>\n')
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85 print 'The "Add Web Service Tool" added successfully'
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86 else:
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87 print 'The "Add Web service tool" tool is already present'
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88
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89
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90 # Check if the section "Web Service Tools" is not installed and then add it to the file f2
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91 if not webservice_present:
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92 f2.write(' <section name="Web Service Tools" id="WebServices">\n')
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93 f2.write('\n')
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94 f2.write(' </section>\n')
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95 print 'The "Web Service Tools" added successfully'
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96 else:
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97 print 'The section "Web Service Tools" is already present'
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98
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99
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100 # Check if the Section "Web Service Workflow Tools" is not installed and then add it to the file f2
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101 if not workflow_present:
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102 f2.write(' <section name="Web Service Workflow Tools" id="WebServiceWorkflow">\n')
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103 f2.write('\n')
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104 f2.write(' </section>\n')
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105 print 'The section "Web Service Workflow Tools" is added successfully'
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106 else:
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107 print 'The section "Web Service Workflow Tools" is already present'
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108
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109
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110 #copy rest of tool_conf.xml file to f2
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111 while not lineStripped == '</toolbox>':
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112 line = f1.readline()
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113 f2.write(line)
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114 lineStripped = line.lstrip()
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115 lineStripped=lineStripped.rstrip()
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116 #else:
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117 # print line
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118
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119 ##close f1 and f2
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120 f1.close()
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121 f2.close()
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122
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123 ##interchange modes of f1 and f2
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124 f1=open(galaxyhome+'/tool_conf.xml','w')
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125 f1.seek(0,0)
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126 f2=open(galaxyhome+'/tool_conf_backup.xml','r')
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127 f2.seek(0,0)
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128
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129 line = f2.readline()
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130 f1.write(line)
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131
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132 lineStripped=line.lstrip()
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133 lineStripped = lineStripped.rstrip()
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134
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135 ##write entire f2 into f1 (reverse roles)
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136 while not lineStripped == '</toolbox>':
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137 line = f2.readline()
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138 f1.write(line)
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139 lineStripped = line.lstrip()
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140 lineStripped = lineStripped.rstrip()
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141 #else:
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142 # print line
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143
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144 f1.close()
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145 f2.close()
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146
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147
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148 # Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for disabling Web service stand alone tools in Workflows
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149 f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
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150 f1.seek(0,0)
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151
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152 exist = False
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153 line = f1.readline()
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154 linestripped = line.lstrip()
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155 linestripped = linestripped.rstrip()
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156 while line != '':
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157 # if(linsetripped.find('\'\'\'')>-1):
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158 # line = f1.readline()
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159 # while(not line.find('\'\'\'')>-1):
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160 # line = f1.readline()
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161 if(linestripped == 'if self.id.find("WebService")>-1:'):
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162 exist = True
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163 break
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164 line = f1.readline()
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165 linestripped = line.lstrip()
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166 linestripped = linestripped.rstrip()
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167
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168 if exist :
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169 print 'Workflow code is already present in __init__.py'
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170 else:
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171 f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
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172 f2.seek(0,0)
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173 f1.seek(0,0)
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174 line = f1.readline()
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175 f2.write(line)
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176 linestripped = line.lstrip()
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177 linestripped = linestripped.rstrip()
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178 while not (linestripped.find('def check_workflow_compatible(')>-1):
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179 line = f1.readline()
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180 linestripped = line.lstrip()
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181 linestripped = linestripped.rstrip()
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182 f2.write(line)
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183 if line.find('(')>-1:
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184 while not line.find(')')>-1:
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185 line = f1.readline()
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186 f2.write(line)
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187
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188 line = f1.readline()
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189 while line.find('#')>-1:
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190 f2.write(line)
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191 line = f1.readline()
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192
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193 indent=0
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194 while (line[indent] == ' '):
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195 indent = indent+1
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196
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197 space = ''
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198 for i in range(0,indent):
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199 space +=' '
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200
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201 f2.write(space+'#############\n')
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202 f2.write(space+'#added by Chaitany Guttula, chaitu86@uga.edu - to disable webservice standalone tools in Workflows\n')
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203 f2.write(space+'if self.id.find("WebService")>-1:\n')
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204 f2.write(space+' return False\n')
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205 f2.write(space+'#############\n')
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206
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207 f2.write(line)
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208 line = f1.readline()
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209 f2.write(line)
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210
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211 while line != '':
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212 line = f1.readline()
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213 f2.write(line)
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214
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215 f1.close()
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216 f2.close()
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217
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218 f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
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219 f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')
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220
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221 line = f1.readline()
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222 f2.write(line)
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223
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224 while line != '':
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225 line = f1.readline()
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226 f2.write(line)
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227
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228 f1.close()
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229 f2.close()
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230 print 'Workflow disabling Code added to __init__.py'
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231
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232
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233
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234 # Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for invoking the refresh functionality
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235 f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
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236 f1.seek(0,0)
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237
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238 exist = False
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239 line = f1.readline()
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240 linestripped = line.lstrip()
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241 linestripped = linestripped.rstrip()
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242 while line != '':
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243 # if(linsetripped.find('\'\'\'')>-1):
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244 # line = f1.readline()
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245 # while(not line.find('\'\'\'')>-1):
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246 # line = f1.readline()
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247 if(linestripped == 'if self.id == \'WebService_REFRESH_ID\':'):
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248 exist = True
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249 break
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250 line = f1.readline()
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251 linestripped = line.lstrip()
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252 linestripped = linestripped.rstrip()
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253
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254 if exist :
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255 print 'Refresh code is already present in __init__.py'
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256 else:
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257 f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
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258 f2.seek(0,0)
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259 f1.seek(0,0)
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260 line = f1.readline()
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261 f2.write(line)
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262 linestripped = line.lstrip()
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263 linestripped = linestripped.rstrip()
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264 while not (linestripped.find('def execute(')>-1):
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265 line = f1.readline()
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266 linestripped = line.lstrip()
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267 linestripped = linestripped.rstrip()
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268 f2.write(line)
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269 if line.find('(')>-1:
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270 while not line.find(')')>-1:
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271 line = f1.readline()
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272 f2.write(line)
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273
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274 line = f1.readline()
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275 while line.find('#')>-1:
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276 f2.write(line)
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277 line = f1.readline()
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278
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279 indent=0
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280 while (line[indent] == ' '):
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281 indent = indent+1
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282
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283 space = ''
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284 for i in range(0,indent):
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285 space +=' '
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286
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287 f2.write(space+'#############\n')
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288 f2.write(space+'#add code to verify if user has administrative privileges\n')
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289 f2.write(space+'#added by sumedha ganjoo, sganjoo@uga.edu - to refresh toolbox\n')
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290 f2.write(space+'if self.id == \'WebService_REFRESH_ID\':\n')
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291 f2.write(space+' self.app.refreshToolBox()\n')
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292 f2.write(space+'#############\n')
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293
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294 f2.write(line)
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295 line = f1.readline()
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296 f2.write(line)
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297
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298 while line != '':
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299 line = f1.readline()
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300 f2.write(line)
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301
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302 f1.close()
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303 f2.close()
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304
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305 f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
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306 f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')
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307
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308 line = f1.readline()
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309 f2.write(line)
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310
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311 while line != '':
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312 line = f1.readline()
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313 f2.write(line)
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314
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315 f1.close()
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316 f2.close()
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317 print 'Refresh Code added to __init__.py'
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318
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319
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320 # Adding Code to app.py in lib/galaxy folder in Galaxy for invoking the refresh functionality
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321 f1 = open(galaxyhome+'/lib/galaxy/app.py','r')
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322
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323 f1.seek(0,0)
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324
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325 exist = False
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326 line = f1.readline()
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327 linestripped = line.lstrip()
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328 linestripped = linestripped.rstrip()
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329 while line != '':
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330 if(linestripped == 'def refreshToolBox( self ):'):
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331 exist = True
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332 break
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333 line = f1.readline()
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334 linestripped = line.lstrip()
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335 linestripped = linestripped.rstrip()
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336
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337 if exist:
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338 print 'Refresh code is already present in app.py'
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339 else:
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340 f2 = open(galaxyhome+'/lib/galaxy/app_backup.py','w')
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341 f2.seek(0,0)
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342 f1.seek(0,0)
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343 line = f1.readline()
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344 f2.write(line)
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345 linestripped = line.lstrip()
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346 linestripped = linestripped.rstrip()
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347 while not (line.find('class UniverseApplication')>-1):
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348 line = f1.readline()
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349 linestripped = line.lstrip()
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350 linestripped = linestripped.rstrip()
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351 f2.write(line)
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352 if line.find('(')>-1:
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353 while not line.find(')')>-1:
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354 line = f1.readline()
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355 f2.write(line)
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356
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357 line = f1.readline()
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358
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359 while line.find('#')>-1:
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360 f2.write(line)
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361 line = f1.readline()
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362
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363
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364 indent=0
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365 while (line[indent] == ' '):
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366 indent = indent+1
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367
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368 space = ''
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369 for i in range(0,indent):
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370 space +=' '
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371
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372 f2.write(space+'#############\n')
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373 f2.write(space+'#added by sumedha ganjoo, sganjoo@uga.edu\n')
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374 f2.write(space+'def refreshToolBox( self ):\n')
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375 f2.write(space+' self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )\n')
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376 f2.write(space+'#############\n\n')
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377
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378 f2.write(line)
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379 line = f1.readline()
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380 f2.write(line)
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381
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382 while line != '':
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383 line = f1.readline()
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384 f2.write(line)
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385
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386 f1.close()
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387 f2.close()
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388
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389 f1 = open(galaxyhome+'/lib/galaxy/app_backup.py','r')
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390 f2 = open(galaxyhome+'/lib/galaxy/app.py','w')
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391
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392 line = f1.readline()
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393 f2.write(line)
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394
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395 while line != '':
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396 line = f1.readline()
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397 f2.write(line)
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398
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399 f1.close()
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400 f2.close()
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401 print 'Refresh code is added to app.py'
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402
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403
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404
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405 print '****Installation of tool is complete. Now reload galaxy to use the installed tool****'
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406
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