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1 # rgToolFactory.py
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2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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9
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10 # August 11 2012
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11 # changed to use shell=False and cl as a sequence
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12
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13 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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14 # It also serves as the wrapper for the new tool.
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15 #
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16 # you paste and run your script
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17 # Only works for simple scripts that read one input from the history.
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18 # Optionally can write one new history dataset,
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19 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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20
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21 # DO NOT install on a public or important site - please.
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22
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23 # installed generated tools are fine if the script is safe.
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24 # They just run normally and their user cannot do anything unusually insecure
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25 # but please, practice safe toolshed.
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26 # Read the fucking code before you install any tool
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27 # especially this one
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28
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29 # After you get the script working on some test data, you can
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30 # optionally generate a toolshed compatible gzip file
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31 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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32 # safe and largely automated installation in a production Galaxy.
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33
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34 # If you opt for an HTML output, you get all the script outputs arranged
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35 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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36 # Ugly but really inexpensive.
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37 #
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38 # Patches appreciated please.
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39 #
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40 #
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41 # long route to June 2012 product
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42 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
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43 # derived from an integrated script model
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44 # called rgBaseScriptWrapper.py
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45 # Note to the unwary:
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46 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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47 # There is nothing stopping a malicious user doing whatever they choose
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48 # Extremely dangerous!!
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49 # Totally insecure. So, trusted users only
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50 #
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51 # preferred model is a developer using their throw away workstation instance - ie a private site.
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52 # no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
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53 #
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54
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55 import sys
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56 import shutil
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57 import subprocess
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58 import os
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59 import time
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60 import tempfile
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61 import optparse
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62 import tarfile
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63 import re
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64 import shutil
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65 import math
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66
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67 progname = os.path.split(sys.argv[0])[1]
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68 myversion = 'V000.2 June 2012'
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69 verbose = False
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70 debug = False
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71 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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72
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73 def timenow():
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74 """return current time as a string
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75 """
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76 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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77
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78
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79 class ScriptRunner:
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80 """class is a wrapper for an arbitrary script
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81 """
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82
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83 def __init__(self,opts=None):
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84 """
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85 cleanup inputs, setup some outputs
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86
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87 """
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88 if opts.output_dir: # simplify for the tool tarball
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89 os.chdir(opts.output_dir)
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90 self.thumbformat = 'jpg'
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91 self.opts = opts
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92 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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93 self.toolid = self.toolname
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94 s = open(self.opts.script_path,'r').readlines()
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95 self.script = ''.join(s)
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96 self.indentedScript = ''.join([' %s' % x for x in s]) # for restructured text in help
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97 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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98 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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99 self.xmlfile = '%s.xml' % self.toolname
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100 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
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101 if opts.output_dir: # may not want these complexities
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102 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
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103 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
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104 artifact = open(artifactpath,'w')
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105 artifact.write(self.script)
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106 artifact.write('\n')
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107 artifact.close()
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108 if opts.make_Tool: # need this code and the user script for the tarball
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109 localscript = open(self.sfile,'w')
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110 localscript.write(self.script)
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111 localscript.close()
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112 self.cl = []
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113 self.html = []
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114 a = self.cl.append
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115 a(opts.interpreter)
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116 a('-') # use stdin
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117 a(opts.input_tab)
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118 a(opts.output_tab)
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119 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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120 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
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121 self.test1Input = '%s_test1_input.xls' % self.toolname
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122 self.test1Output = '%s_test1_output.xls' % self.toolname
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123 self.test1HTML = '%s_test1_output.html' % self.toolname
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124
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125 def makeXML(self):
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126 """
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127 Create a Galaxy xml tool wrapper for the new script as a string to write out
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128 fixme - use templating or something less fugly than this example of what we produce
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129
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130 <tool id="reverse" name="reverse" version="0.01">
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131 <description>a tabular file</description>
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132 <command interpreter="python">
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133 reverse.py --script_path "$runMe" --interpreter "python"
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134 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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135 </command>
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136 <inputs>
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137 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
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138
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139 </inputs>
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140 <outputs>
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141 <data format="tabular" name="tab_file" label="${job_name}"/>
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142
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143 </outputs>
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144 <help>
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145
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146 **What it Does**
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147
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148 Reverse the columns in a tabular file
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149
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150 </help>
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151 <configfiles>
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152 <configfile name="runMe">
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153
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154 # reverse order of columns in a tabular file
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155 import sys
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156 inp = sys.argv[1]
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157 outp = sys.argv[2]
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158 i = open(inp,'r')
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159 o = open(outp,'w')
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160 for row in i:
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161 rs = row.rstrip().split('\t')
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162 rs.reverse()
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163 o.write('\t'.join(rs))
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164 o.write('\n')
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165 i.close()
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166 o.close()
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167
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168
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169 </configfile>
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170 </configfiles>
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171 </tool>
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172
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173 """
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174 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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175 %(tooldesc)s
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176 %(command)s
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177 <inputs>
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178 %(inputs)s
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179 </inputs>
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180 <outputs>
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181 %(outputs)s
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182 </outputs>
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183 <configfiles>
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184 <configfile name="runMe">
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185 %(script)s
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186 </configfile>
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187 </configfiles>
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188 %(tooltests)s
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189 <help>
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190 %(help)s
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191 </help>
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192 </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
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193
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194 newCommand="""<command interpreter="python">
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195 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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196 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
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197 </command>""" # may NOT be an input or htmlout
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198 tooltestsTabOnly = """<tests><test>
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199 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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200 <param name="job_name" value="test1"/>
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201 <param name="runMe" value="$runMe"/>
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202 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
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203 </test></tests>"""
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204 tooltestsHTMLOnly = """<tests><test>
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205 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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206 <param name="job_name" value="test1"/>
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207 <param name="runMe" value="$runMe"/>
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208 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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209 </test></tests>"""
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210 tooltestsBoth = """<tests><test>
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211 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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212 <param name="job_name" value="test1"/>
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213 <param name="runMe" value="$runMe"/>
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214 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
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215 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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216 </test></tests>"""
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217 xdict = {}
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218 xdict['tool_version'] = self.opts.tool_version
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219 xdict['test1Input'] = self.test1Input
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220 xdict['test1HTML'] = self.test1HTML
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221 xdict['test1Output'] = self.test1Output
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222 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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223 xdict['tooltests'] = tooltestsBoth % xdict
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224 elif self.opts.make_HTML:
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225 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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226 else:
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227 xdict['tooltests'] = tooltestsTabOnly % xdict
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228 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
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229 if self.opts.help_text:
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230 xdict['help'] = open(self.opts.help_text,'r').read()
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231 else:
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232 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
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233 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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234 coda.append(self.indentedScript)
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235 coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
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236 coda.append('See %s for details of that project' % (toolFactoryURL))
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237 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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238 if self.opts.tool_desc:
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239 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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240 else:
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241 xdict['tooldesc'] = ''
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242 xdict['command_outputs'] = ''
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243 xdict['outputs'] = ''
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244 if self.opts.input_tab <> 'None':
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245 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
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246 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
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247 else:
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248 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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249 xdict['inputs'] = ''
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250 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
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251 xdict['toolname'] = self.toolname
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252 xdict['toolid'] = self.toolid
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253 xdict['interpreter'] = self.opts.interpreter
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254 xdict['scriptname'] = self.sfile
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255 if self.opts.make_HTML:
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256 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
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257 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
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258 if self.opts.output_tab <> 'None':
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259 xdict['command_outputs'] += ' --output_tab "$tab_file"'
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260 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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261 xdict['command'] = newCommand % xdict
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262 xmls = newXML % xdict
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263 xf = open(self.xmlfile,'w')
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264 xf.write(xmls)
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265 xf.write('\n')
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266 xf.close()
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267 # ready for the tarball
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268
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269
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270 def makeTooltar(self):
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271 """
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272 a tool is a gz tarball with eg
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273 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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274 """
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275 retval = self.run()
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276 if retval:
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277 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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278 sys.exit(1)
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279 self.makeXML()
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280 tdir = self.toolname
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281 os.mkdir(tdir)
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282 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
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283 testdir = os.path.join(tdir,'test-data')
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284 os.mkdir(testdir) # make tests directory
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285 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
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286 if self.opts.output_tab <> 'None':
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287 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
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288 if self.opts.make_HTML:
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289 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
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290 if self.opts.output_dir:
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291 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
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292 op = '%s.py' % self.toolname # new name
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293 outpiname = os.path.join(tdir,op) # path for the tool tarball
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294 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
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295 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
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296 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
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297 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
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298 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
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299 notes += pi
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300 outpi = open(outpiname,'w')
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301 outpi.write(''.join(notes))
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302 outpi.write('\n')
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303 outpi.close()
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304 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
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305 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
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306 tarpath = "%s.gz" % self.toolname
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307 tar = tarfile.open(tarpath, "w:gz")
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308 tar.add(tdir,arcname=self.toolname)
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309 tar.close()
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310 shutil.copyfile(tarpath,self.opts.new_tool)
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311 shutil.rmtree(tdir)
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312 ## TODO: replace with optional direct upload to local toolshed?
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313 return retval
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314
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315 def compressPDF(self,inpdf=None,thumbformat='png'):
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316 """need absolute path to pdf
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317 """
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318 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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319 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
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320 sto = open(hlog,'w')
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321 outpdf = '%s_compressed' % inpdf
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322 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
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323 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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324 retval1 = x.wait()
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325 if retval1 == 0:
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326 os.unlink(inpdf)
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327 shutil.move(outpdf,inpdf)
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328 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
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329 cl2 = ['convert', inpdf, outpng]
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330 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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331 retval2 = x.wait()
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332 sto.close()
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333 retval = retval1 or retval2
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334 return retval
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335
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336
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337 def getfSize(self,fpath,outpath):
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338 """
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339 format a nice file size string
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340 """
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341 size = ''
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342 fp = os.path.join(outpath,fpath)
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343 if os.path.isfile(fp):
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344 size = '0 B'
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345 n = float(os.path.getsize(fp))
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346 if n > 2**20:
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347 size = '%1.1f MB' % (n/2**20)
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348 elif n > 2**10:
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349 size = '%1.1f KB)' % (n/2**10)
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350 elif n > 0:
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351 size = '%d B' % (int(n))
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352 return size
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353
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354 def makeHtml(self):
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355 """ Create an HTML file content to list all the artefacts found in the output_dir
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356 """
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357
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358 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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359 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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360 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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361 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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362 <title></title>
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363 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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364 </head>
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365 <body>
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366 <div class="toolFormBody">
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367 """
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368 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
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369 galhtmlpostfix = """</div></body></html>\n"""
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370
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371 flist = os.listdir(self.opts.output_dir)
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372 flist = [x for x in flist if x <> 'Rplots.pdf']
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373 flist.sort()
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374 html = []
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375 html.append(galhtmlprefix % progname)
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376 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
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377 fhtml = []
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378 if len(flist) > 0:
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379 pdflist = []
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380 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
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381 nacross = 1
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382 if npdf > 0:
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383 nacross = int(round(math.log(npdf,2)))
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384 nacross = max(1,nacross)
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385 width = min(400,int(1200/nacross))
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386 for rownum,fname in enumerate(flist):
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387 dname,e = os.path.splitext(fname)
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388 sfsize = self.getfSize(fname,self.opts.output_dir)
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389 if e.lower() == '.pdf' : # compress and make a thumbnail
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390 thumb = '%s.%s' % (dname,self.thumbformat)
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391 pdff = os.path.join(self.opts.output_dir,fname)
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392 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
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393 if retval == 0:
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394 pdflist.append((fname,thumb))
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395 if (rownum+1) % 2 == 0:
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396 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
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397 else:
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398 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
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399 ntogo = nacross # counter for table row padding with empty cells
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400 if len(pdflist) > 0:
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401 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
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402 for i,paths in enumerate(pdflist):
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403 fname,thumb = paths
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404 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
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405 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
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406 if ((i+1) % nacross == 0):
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407 s += '</tr>\n'
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408 ntogo = 0
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409 if i < (npdf - 1): # more to come
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410 s += '<tr>'
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411 ntogo = nacross
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412 else:
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413 ntogo -= 1
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414 html.append(s)
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415 if html[-1].strip().endswith('</tr>'):
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416 html.append('</table></div>\n')
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417 else:
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418 if ntogo > 0: # pad
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419 html.append('<td> </td>'*ntogo)
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420 html.append('</tr></table></div>\n')
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421 if len(fhtml) > 0:
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422 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
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423 fhtml.append('</table></div><br/>')
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424 html += fhtml # add all non-pdf files to the end of the display
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425 else:
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426 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
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427 rlog = open(self.tlog,'r').readlines()
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428 rlog = [x for x in rlog if x.strip() > '']
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429 if len(rlog) > 1:
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430 html.append('<div class="toolFormTitle">%s log</div><pre>\n' % self.opts.interpreter)
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431 html += rlog
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432 html.append('</pre>\n')
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433 html.append(galhtmlattr % (self.toolname))
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434 html.append(galhtmlpostfix)
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435 htmlf = file(self.opts.output_html,'w')
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436 htmlf.write('\n'.join(html))
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437 htmlf.write('\n')
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438 htmlf.close()
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439 self.html = html
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440
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441
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442 def run(self):
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443 """
|
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444 scripts must be small enough not to fill the pipe!
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445 """
|
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446 if self.opts.output_dir:
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447 sto = open(self.tlog,'w')
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448 sto.write('## FastQC generated command line = %s\n' % ' '.join(self.cl))
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449 sto.flush()
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450 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
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451 else:
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452 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
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453 p.stdin.write(self.script)
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454 p.stdin.close()
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455 retval = p.wait()
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456 if self.opts.output_dir:
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457 sto.close()
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458 if self.opts.make_HTML:
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459 self.makeHtml()
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460 return retval
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461
|
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462
|
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463 def main():
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464 u = """
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465 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
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466 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
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467 </command>
|
|
|
468 """
|
|
|
469 op = optparse.OptionParser()
|
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|
470 a = op.add_option
|
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|
471 a('--script_path',default=None)
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|
472 a('--tool_name',default=None)
|
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473 a('--interpreter',default=None)
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474 a('--output_dir',default=None)
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475 a('--output_html',default=None)
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476 a('--input_tab',default="None")
|
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477 a('--output_tab',default="None")
|
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478 a('--user_email',default='Unknown')
|
|
|
479 a('--bad_user',default=None)
|
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|
480 a('--make_Tool',default=None)
|
|
|
481 a('--make_HTML',default=None)
|
|
|
482 a('--help_text',default=None)
|
|
|
483 a('--tool_desc',default=None)
|
|
|
484 a('--new_tool',default=None)
|
|
|
485 a('--tool_version',default=None)
|
|
|
486 opts, args = op.parse_args()
|
|
|
487 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
|
|
|
488 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
|
|
|
489 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
|
|
|
490 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
|
|
|
491 if opts.output_dir:
|
|
|
492 try:
|
|
|
493 os.makedirs(opts.output_dir)
|
|
|
494 except:
|
|
|
495 pass
|
|
|
496 r = ScriptRunner(opts)
|
|
|
497 if opts.make_Tool:
|
|
|
498 retcode = r.makeTooltar()
|
|
|
499 else:
|
|
|
500 retcode = r.run()
|
|
|
501 if retcode:
|
|
|
502 sys.exit(retcode) # indicate failure to job runner
|
|
|
503
|
|
|
504
|
|
|
505 if __name__ == "__main__":
|
|
|
506 main()
|
|
|
507
|
|
|
508
|
