Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.py @ 16:36df24947ab3

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readme changes
author Ross Lazarus <ross.lazarus@gmail.com>
date Mon, 04 Jun 2012 16:22:51 +1000
parents 8594478e8d2c
children a87a262220a4
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1 # rgToolFactory.py
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2 # derived from
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3 # rgBaseScriptWrapper.py
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4 # but designed to run arbitrary user supplied code
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5 # extremely dangerous!!
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6 # trusted users only - private site only
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7 # a list in the xml is searched for users permitted to run this tool.
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8 # DO NOT install on a public or important site - local instance only
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9 # generated tools are fine as they just run normally and their user cannot do anything unusually insecure
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10 #
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11 # copyright ross lazarus (ross.lazarus@gmail.com) May 2012
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12 #
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13 # all rights reserved
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14 # Licensed under the LGPL for your pleasure
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15 # Derived from rgDGE.py in May 2012
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16 # generalized to run required interpreter
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17 # to make your own tools based on a given script and interpreter such as perl or python
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18 # clone this and the corresponding xml wrapper
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19 # replace the parameters/inputs/outputs and the configfile contents with your script
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20 # Use the $foo syntax to place your parameter values inside the script to assign them - at run time, the script will be used as a template
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21 # and returned as part of the output to the user - with the right values for all the parameters.
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22 # Note that this assumes you want all the outputs arranged as a single Html file output
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23 # after this generic script runner runs your script with the specified interpreter,
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24 # it will collect all output files into the specified output_html, making thumbnails for all the pdfs it finds and making links for all the other files.
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25
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26 import sys
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27 import shutil
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28 import subprocess
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29 import os
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30 import time
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31 import tempfile
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32 import optparse
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33 import tarfile
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34 import re
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35 import shutil
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36
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37 progname = os.path.split(sys.argv[0])[1]
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38 myversion = 'V000.1 May 2012'
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39 verbose = False
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40 debug = False
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42
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43 def timenow():
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44 """return current time as a string
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45 """
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46 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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47 # characters that are allowed but need to be escaped
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48
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49 class ScriptRunner:
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50 """class is a wrapper for an arbitrary script
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51 """
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52
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53 def __init__(self,opts=None):
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54 """
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55 run the script
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56
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57 """
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58 if opts.output_dir: # simplify for the tool tarball
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59 os.chdir(opts.output_dir)
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60 self.thumbformat = 'jpg'
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61 self.opts = opts
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62 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
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63 self.toolid = self.toolname
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64 s = open(self.opts.script_path,'r').read()
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65 self.script = s
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66 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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67 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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68 self.xmlfile = '%s.xml' % self.toolname
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69 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
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70 if opts.output_dir: # may not want these complexities
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71 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
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72 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
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73 artifact = open(artifactpath,'w')
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74 artifact.write(self.script)
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75 artifact.write('\n')
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76 artifact.close()
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77 if opts.make_Tool: # need this code and the user script for the tarball
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78 localscript = open(self.sfile,'w')
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79 localscript.write(self.script)
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80 localscript.close()
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81 shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user
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82 self.cl = []
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83 self.html = []
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84 a = self.cl.append
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85 a(opts.interpreter)
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86 a('-') # use stdin
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87 a(opts.input_tab)
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88 a(opts.output_tab)
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89 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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90 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
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91
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92
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93 def makeXML(self):
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94 """
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95 Create a Galaxy xml tool wrapper for the new script as a string to write out
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96 fixme - use templating or something less fugly than this.
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97 Here's an example of what we produce
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98
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99 <tool id="reverse" name="reverse" version="0.01">
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100 <description>a tabular file</description>
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101 <command interpreter="python">
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102 reverse.py --script_path "$runMe" --interpreter "python"
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103 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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104 </command>
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105 <inputs>
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106 <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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107
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108 </inputs>
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109 <outputs>
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110 <data format="tabular" name="tab_file" label="${job_name}"/>
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111
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112 </outputs>
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113 <help>
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114
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115 **What it Does**
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116
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117 Reverse the columns in a tabular file
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118
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119 </help>
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120 <configfiles>
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121 <configfile name="runMe">
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122
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123 # reverse order of columns in a tabular file
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124 import sys
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125 inp = sys.argv[1]
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126 outp = sys.argv[2]
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127 i = open(inp,'r')
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128 o = open(outp,'w')
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129 for row in i:
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130 rs = row.rstrip().split('\t')
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131 rs.reverse()
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132 o.write('\t'.join(rs))
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133 o.write('\n')
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134 i.close()
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135 o.close()
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136
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137
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138 </configfile>
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139 </configfiles>
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140 </tool>
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141
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142 """
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143 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
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144 %(tooldesc)s
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145 %(command)s
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146 <inputs>
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147 %(inputs)s
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148 </inputs>
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149 <outputs>
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150 %(outputs)s
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151 </outputs>
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152 <help>
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153 %(help)s
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154 </help>
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155 <configfiles>
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156 <configfile name="runMe">
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157 %(script)s
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158 </configfile>
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159 </configfiles>
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160 </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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161
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162 newCommand="""<command interpreter="python">
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163 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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164 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
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165 </command>""" # may NOT be an input or htmlout
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166 tooltests = """<tests><test>
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167 <param name="input1" value="%s" ftype="%s"/>
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168 <param name="job_name" value="test1"/>
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169 <param name="runMe" value="$runMe"/>
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170 </test><tests>"""
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171 xdict = {}
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172 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
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173 if self.opts.help_text:
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174 xdict['help'] = open(self.opts.help_text,'r').read()
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175 else:
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176 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
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177 if self.opts.tool_desc:
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178 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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179 else:
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180 xdict['tooldesc'] = ''
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181 xdict['command_outputs'] = ''
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182 xdict['outputs'] = ''
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183 if self.opts.input_tab <> 'None':
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184 xdict['command_inputs'] = '--input_tab "$input1"'
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185 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
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186 else:
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187 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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188 xdict['inputs'] = ''
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189 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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190 xdict['toolname'] = self.toolname
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191 xdict['toolid'] = self.toolid
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192 xdict['interpreter'] = self.opts.interpreter
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193 xdict['scriptname'] = self.sfile
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194 if self.opts.make_HTML:
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195 xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
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196 xdict['outputs'] += '<data format="html" name="html_file" label="${job_name}.html"/>\n'
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197 if self.opts.output_tab <> 'None':
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198 xdict['command_outputs'] += '--output_tab "$tab_file"'
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199 xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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200 xdict['command'] = newCommand % xdict
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201 xmls = newXML % xdict
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202 xf = open(self.xmlfile,'w')
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203 xf.write(xmls)
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204 xf.write('\n')
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205 xf.close()
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206 # ready for the tarball
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207
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208
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209 def makeTooltar(self):
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210 """
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211 a tool is a gz tarball with eg
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212 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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213 """
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214 retval = self.run()
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215 if retval:
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216 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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217 sys.exit(1)
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218 self.makeXML()
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219 tdir = self.toolname
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220 os.mkdir(tdir)
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221 if self.opts.input_tab <> 'None': # we may have test data?
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222 testdir = os.path.join(tdir,'test-data')
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223 os.mkdir(testdir) # make tests directory
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224 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,'test1_in.tab'))
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225 if self.opts.output_tab <> 'None':
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226 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,'test1_out.tab'))
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227 if self.opts.make_HTML:
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228 shutil.copyfile(self.opts.output_html,os.path.join(testdir,'test1_out.html'))
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229 if self.opts.output_dir:
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230 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
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231 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
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232 shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
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233 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
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234 tarpath = "%s.gz" % self.toolname
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235 tar = tarfile.open(tarpath, "w:gz")
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236 tar.add(tdir,arcname=self.toolname)
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237 tar.close()
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238 shutil.copy(tarpath,self.opts.new_tool)
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239 shutil.rmtree(tdir)
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240 ## TODO: replace with optional direct upload to local toolshed?
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241 return retval
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242
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243 def compressPDF(self,inpdf=None,thumbformat='png'):
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244 """need absolute path to pdf
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245 """
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246 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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247 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
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248 sto = open(hlog,'w')
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249 outpdf = '%s_compressed' % inpdf
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250 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
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251 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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252 retval1 = x.wait()
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253 if retval1 == 0:
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254 os.unlink(inpdf)
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255 shutil.move(outpdf,inpdf)
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256 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
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257 cl2 = ['convert', inpdf, outpng]
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258 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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259 retval2 = x.wait()
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260 sto.close()
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261 retval = retval1 or retval2
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262 return retval
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263
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264
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265 def getfSize(self,fpath,outpath):
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266 """
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267 format a nice file size string
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268 """
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269 size = ''
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diff changeset
270 fp = os.path.join(outpath,fpath)
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diff changeset
271 if os.path.isfile(fp):
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diff changeset
272 n = float(os.path.getsize(fp))
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diff changeset
273 if n > 2**20:
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274 size = ' (%1.1f MB)' % (n/2**20)
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diff changeset
275 elif n > 2**10:
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276 size = ' (%1.1f KB)' % (n/2**10)
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diff changeset
277 elif n > 0:
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diff changeset
278 size = ' (%d B)' % (int(n))
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diff changeset
279 return size
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diff changeset
280
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diff changeset
281 def makeHtml(self):
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diff changeset
282 """ Create an HTML file content to list all the artefacts found in the output_dir
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283 """
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284
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285 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
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286 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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287 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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288 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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289 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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diff changeset
290 <title></title>
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diff changeset
291 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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292 </head>
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293 <body>
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294 <div class="document">
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295 """
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296 galhtmlattr = """<hr/><b><a href="http://rgenetics.org">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>"""
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297 galhtmlpostfix = """</div></body></html>\n"""
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298
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299 flist = os.listdir(self.opts.output_dir)
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300 flist = [x for x in flist if x <> 'Rplots.pdf']
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301 flist.sort()
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302 html = [galhtmlprefix % progname,]
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303 html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow()))
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304 fhtml = []
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305 if len(flist) > 0:
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306 html.append('<table cellpadding="3" cellspacing="3">\n')
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diff changeset
307 for fname in flist:
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308 dname,e = os.path.splitext(fname)
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309 sfsize = self.getfSize(fname,self.opts.output_dir)
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310 if e.lower() == '.pdf' : # compress and make a thumbnail
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311 thumb = '%s.%s' % (dname,self.thumbformat)
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312 pdff = os.path.join(self.opts.output_dir,fname)
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313 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
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diff changeset
314 if retval == 0:
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315 s= '<tr><td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="10" width="600"></a></td></tr>\n' % (fname,thumb,fname)
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diff changeset
316 html.append(s)
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diff changeset
317 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
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diff changeset
318 else:
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319 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
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320 html.append('</table>\n')
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diff changeset
321 if len(fhtml) > 0:
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diff changeset
322 fhtml.insert(0,'<ul>')
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diff changeset
323 fhtml.append('</ul><br/>')
8
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diff changeset
324 html += fhtml # add all non-pdf files to the end of the display
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diff changeset
325 else:
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diff changeset
326 html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
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diff changeset
327 html.append('<h3>%s log follows below</h3><hr/><pre><br/>\n' % self.opts.interpreter)
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328 rlog = open(self.tlog,'r').readlines()
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329 html += rlog
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330 html.append('<br/>%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
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331 html.append('</pre>\n')
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diff changeset
332 html.append(galhtmlattr % (progname,timenow()))
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diff changeset
333 html.append(galhtmlpostfix)
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334 htmlf = file(self.opts.output_html,'w')
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diff changeset
335 htmlf.write('\n'.join(html))
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diff changeset
336 htmlf.write('\n')
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diff changeset
337 htmlf.close()
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diff changeset
338 self.html = html
7
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339
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diff changeset
340
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341 def run(self):
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342 """
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343 """
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344 if self.opts.output_dir:
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345 sto = open(self.tlog,'w')
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346 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
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347 else:
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348 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
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349 p.stdin.write(self.script)
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350 p.stdin.close()
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351 retval = p.wait()
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diff changeset
352 if self.opts.output_dir:
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353 sto.close()
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diff changeset
354 if self.opts.make_HTML:
7
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355 self.makeHtml()
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356 return retval
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diff changeset
357
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parents:
diff changeset
358
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parents:
diff changeset
359 def main():
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360 u = """
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361 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
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362 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
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363 </command>
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364 """
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365 op = optparse.OptionParser()
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366 a = op.add_option
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367 a('--script_path',default=None)
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diff changeset
368 a('--tool_name',default=None)
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diff changeset
369 a('--interpreter',default=None)
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370 a('--output_dir',default=None)
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diff changeset
371 a('--output_html',default=None)
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diff changeset
372 a('--input_tab',default="None")
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diff changeset
373 a('--output_tab',default="None")
7
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374 a('--user_email',default=None)
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375 a('--bad_user',default=None)
8
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diff changeset
376 a('--make_Tool',default=None)
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377 a('--make_HTML',default=None)
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diff changeset
378 a('--help_text',default=None)
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diff changeset
379 a('--tool_desc',default=None)
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diff changeset
380 a('--new_tool',default=None)
7
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381 opts, args = op.parse_args()
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382 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin' % opts.bad_user
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383 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
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384 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
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385 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
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diff changeset
386 if opts.output_dir:
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diff changeset
387 try:
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diff changeset
388 os.makedirs(opts.output_dir)
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diff changeset
389 except:
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diff changeset
390 pass
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391 r = ScriptRunner(opts)
8
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diff changeset
392 if opts.make_Tool:
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393 retcode = r.makeTooltar()
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diff changeset
394 else:
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395 retcode = r.run()
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diff changeset
396 if retcode:
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397 sys.exit(retcode) # indicate failure to job runner
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diff changeset
398
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parents:
diff changeset
399
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diff changeset
400 if __name__ == "__main__":
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diff changeset
401 main()
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diff changeset
402
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parents:
diff changeset
403