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1 # rgToolFactory.py
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2 # https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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3
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4 # this is a tool factory for simple scripts in python, R or whatever ails ye.
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5 # you paste and run your script
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6 # Only works for simple scripts that read one input from the history.
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7 # Optionally can write one new history dataset,
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8 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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9
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10 # DO NOT install on a public or important site - please.
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11
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12 # installed generated tools are fine if the script is safe.
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13 # They just run normally and their user cannot do anything unusually insecure
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14 # but please, practice safe toolshed.
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15 # Read the fucking code before you install any tool
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16 # especially this one
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17
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18 # After you get the script working on some test data, you can
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19 # optionally generate a toolshed compatible gzip file
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20 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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21 # safe and largely automated installation in a production Galaxy.
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22
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23 # If you opt for an HTML output, you get all the script outputs arranged
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24 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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25 # Ugly but really inexpensive.
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26 #
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27 # Patches appreciated please.
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28 #
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29 #
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30 # long route to June 2012 product
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31 # Behold the awesome power of Galaxy and the toolshed with the tool factory binds to bind them
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32 # derived from an integrated script model
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33 # called rgBaseScriptWrapper.py
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34 # Note to the unwary:
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35 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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36 # There is nothing stopping a malicious user doing whatever they choose
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37 # Extremely dangerous!!
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38 # Totally insecure. So, trusted users only
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39 #
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40 # preferred model is a developer using their throw away workstation instance - ie a private site.
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41 # 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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42 #
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43
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44 #
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45 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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46 #
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47 # all rights reserved
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48 # Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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49
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50 import sys
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51 import shutil
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52 import subprocess
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53 import os
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54 import time
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55 import tempfile
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56 import optparse
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57 import tarfile
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58 import re
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59 import shutil
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60
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61 progname = os.path.split(sys.argv[0])[1]
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62 myversion = 'V000.1 May 2012'
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63 verbose = False
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64 debug = False
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65
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66
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67 def timenow():
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68 """return current time as a string
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69 """
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70 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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71 # characters that are allowed but need to be escaped
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72
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73 class ScriptRunner:
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74 """class is a wrapper for an arbitrary script
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75 """
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76
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77 def __init__(self,opts=None):
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78 """
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79 cleanup inputs, setup some outputs
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80
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81 """
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82 if opts.output_dir: # simplify for the tool tarball
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83 os.chdir(opts.output_dir)
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84 self.thumbformat = 'jpg'
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85 self.opts = opts
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86 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
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87 self.toolid = self.toolname
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88 s = open(self.opts.script_path,'r').read()
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89 self.script = s
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90 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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91 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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92 self.xmlfile = '%s.xml' % self.toolname
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93 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
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94 if opts.output_dir: # may not want these complexities
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95 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
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96 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
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97 artifact = open(artifactpath,'w')
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98 artifact.write(self.script)
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99 artifact.write('\n')
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100 artifact.close()
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101 if opts.make_Tool: # need this code and the user script for the tarball
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102 localscript = open(self.sfile,'w')
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103 localscript.write(self.script)
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104 localscript.close()
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105 shutil.copyfile(self.myname,'%s.py' % self.toolname) # for tool and for user
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106 self.cl = []
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107 self.html = []
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108 a = self.cl.append
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109 a(opts.interpreter)
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110 a('-') # use stdin
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111 a(opts.input_tab)
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112 a(opts.output_tab)
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113 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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114 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
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115 self.test1Input = 'test1_input.xls'
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116 self.test1Output = 'test1_output.xls'
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117 self.test1HTML = 'test1_output.html'
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118
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119 def makeXML(self):
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120 """
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121 Create a Galaxy xml tool wrapper for the new script as a string to write out
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122 fixme - use templating or something less fugly than this example of what we produce
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123
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124 <tool id="reverse" name="reverse" version="0.01">
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125 <description>a tabular file</description>
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126 <command interpreter="python">
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127 reverse.py --script_path "$runMe" --interpreter "python"
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128 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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129 </command>
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130 <inputs>
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131 <param name="input1" type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
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132
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133 </inputs>
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134 <outputs>
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135 <data format="tabular" name="tab_file" label="${job_name}"/>
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136
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137 </outputs>
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138 <help>
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139
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140 **What it Does**
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141
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142 Reverse the columns in a tabular file
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143
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144 </help>
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145 <configfiles>
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146 <configfile name="runMe">
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147
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148 # reverse order of columns in a tabular file
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149 import sys
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150 inp = sys.argv[1]
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151 outp = sys.argv[2]
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152 i = open(inp,'r')
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153 o = open(outp,'w')
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154 for row in i:
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155 rs = row.rstrip().split('\t')
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156 rs.reverse()
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157 o.write('\t'.join(rs))
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158 o.write('\n')
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159 i.close()
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160 o.close()
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161
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162
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163 </configfile>
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164 </configfiles>
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165 </tool>
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166
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167 """
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168 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
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169 %(tooldesc)s
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170 %(command)s
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171 <inputs>
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172 %(inputs)s
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173 </inputs>
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174 <outputs>
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175 %(outputs)s
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176 </outputs>
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177 <help>
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178 %(help)s
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179 </help>
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180 <configfiles>
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181 <configfile name="runMe">
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182 %(script)s
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183 </configfile>
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184 </configfiles>
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185 </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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186
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187 newCommand="""<command interpreter="python">
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188 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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189 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
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190 </command>""" # may NOT be an input or htmlout
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191 tooltests = """<tests><test>
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192 <param name="input1" value="%s" ftype="%s"/>
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193 <param name="job_name" value="test1"/>
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194 <param name="runMe" value="$runMe"/>
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195 </test><tests>"""
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196 xdict = {}
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197 xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
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198 if self.opts.help_text:
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199 xdict['help'] = open(self.opts.help_text,'r').read()
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200 else:
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201 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
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202 if self.opts.tool_desc:
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203 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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204 else:
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205 xdict['tooldesc'] = ''
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206 xdict['command_outputs'] = ''
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207 xdict['outputs'] = ''
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208 if self.opts.input_tab <> 'None':
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209 xdict['command_inputs'] = '--input_tab "$input1"'
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210 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/>' % self.inputFormats
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211 else:
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212 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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213 xdict['inputs'] = ''
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214 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/>\n' % self.toolname
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215 xdict['toolname'] = self.toolname
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216 xdict['toolid'] = self.toolid
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217 xdict['interpreter'] = self.opts.interpreter
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218 xdict['scriptname'] = self.sfile
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219 if self.opts.make_HTML:
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220 xdict['command_outputs'] += '--output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
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221 xdict['outputs'] += '<data format="html" name="html_file" label="${job_name}.html"/>\n'
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222 if self.opts.output_tab <> 'None':
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223 xdict['command_outputs'] += '--output_tab "$tab_file"'
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224 xdict['outputs'] += '<data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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225 xdict['command'] = newCommand % xdict
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226 xmls = newXML % xdict
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227 xf = open(self.xmlfile,'w')
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228 xf.write(xmls)
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229 xf.write('\n')
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230 xf.close()
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231 # ready for the tarball
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232
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233
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234 def makeTooltar(self):
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235 """
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236 a tool is a gz tarball with eg
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237 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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238 """
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239 retval = self.run()
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240 if retval:
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241 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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242 sys.exit(1)
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243 self.makeXML()
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244 tdir = self.toolname
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245 os.mkdir(tdir)
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246 if self.opts.input_tab <> 'None': # we may have test data?
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247 testdir = os.path.join(tdir,'test-data')
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248 os.mkdir(testdir) # make tests directory
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249 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
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250 if self.opts.output_tab <> 'None':
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251 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
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252 if self.opts.make_HTML:
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253 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
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254 if self.opts.output_dir:
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255 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
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256 shutil.copyfile(self.xmlfile,os.path.join(tdir,self.xmlfile))
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257 shutil.copyfile(self.pyfile,os.path.join(tdir,'%s.py' % self.toolname))
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258 shutil.copyfile(self.sfile,os.path.join(tdir,self.sfile))
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259 tarpath = "%s.gz" % self.toolname
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260 tar = tarfile.open(tarpath, "w:gz")
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261 tar.add(tdir,arcname=self.toolname)
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262 tar.close()
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263 shutil.copy(tarpath,self.opts.new_tool)
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264 shutil.rmtree(tdir)
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265 ## TODO: replace with optional direct upload to local toolshed?
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266 return retval
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267
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268 def compressPDF(self,inpdf=None,thumbformat='png'):
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269 """need absolute path to pdf
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270 """
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271 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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272 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
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273 sto = open(hlog,'w')
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274 outpdf = '%s_compressed' % inpdf
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275 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
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276 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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277 retval1 = x.wait()
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278 if retval1 == 0:
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279 os.unlink(inpdf)
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280 shutil.move(outpdf,inpdf)
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281 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
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282 cl2 = ['convert', inpdf, outpng]
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283 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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284 retval2 = x.wait()
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285 sto.close()
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286 retval = retval1 or retval2
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287 return retval
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288
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289
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290 def getfSize(self,fpath,outpath):
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291 """
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292 format a nice file size string
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293 """
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294 size = ''
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295 fp = os.path.join(outpath,fpath)
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296 if os.path.isfile(fp):
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297 n = float(os.path.getsize(fp))
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298 if n > 2**20:
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299 size = ' (%1.1f MB)' % (n/2**20)
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300 elif n > 2**10:
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301 size = ' (%1.1f KB)' % (n/2**10)
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302 elif n > 0:
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303 size = ' (%d B)' % (int(n))
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304 return size
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305
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306 def makeHtml(self):
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307 """ Create an HTML file content to list all the artefacts found in the output_dir
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308 """
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309
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310 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
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311 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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312 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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313 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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314 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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315 <title></title>
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316 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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317 </head>
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318 <body>
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319 <div class="document">
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320 """
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321 galhtmlattr = """<hr/><b><a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory Script Wrapper</a> tool output %s run at %s</b><br/>"""
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322 galhtmlpostfix = """</div></body></html>\n"""
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323
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324 flist = os.listdir(self.opts.output_dir)
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325 flist = [x for x in flist if x <> 'Rplots.pdf']
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326 flist.sort()
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327 html = [galhtmlprefix % progname,]
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328 html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow()))
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329 fhtml = []
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330 if len(flist) > 0:
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331 html.append('<table cellpadding="3" cellspacing="3">\n')
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332 for fname in flist:
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333 dname,e = os.path.splitext(fname)
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334 sfsize = self.getfSize(fname,self.opts.output_dir)
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335 if e.lower() == '.pdf' : # compress and make a thumbnail
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336 thumb = '%s.%s' % (dname,self.thumbformat)
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337 pdff = os.path.join(self.opts.output_dir,fname)
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338 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
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339 if retval == 0:
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340 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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341 html.append(s)
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342 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
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343 else:
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344 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
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345 html.append('</table>\n')
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346 if len(fhtml) > 0:
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347 fhtml.insert(0,'<ul>')
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348 fhtml.append('</ul><br/>')
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349 html += fhtml # add all non-pdf files to the end of the display
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350 else:
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351 html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
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352 html.append('<h3>%s log follows below</h3><hr/><pre><br/>\n' % self.opts.interpreter)
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353 rlog = open(self.tlog,'r').readlines()
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354 html += rlog
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355 html.append('<br/>%s CL = %s<br/>\n' % (self.toolname,' '.join(sys.argv)))
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356 html.append('</pre>\n')
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357 html.append(galhtmlattr % (progname,timenow()))
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358 html.append(galhtmlpostfix)
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359 htmlf = file(self.opts.output_html,'w')
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360 htmlf.write('\n'.join(html))
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361 htmlf.write('\n')
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362 htmlf.close()
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363 self.html = html
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364
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365
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366 def run(self):
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367 """
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368 """
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369 if self.opts.output_dir:
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370 sto = open(self.tlog,'w')
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371 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
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372 else:
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373 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
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374 p.stdin.write(self.script)
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375 p.stdin.close()
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376 retval = p.wait()
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377 if self.opts.output_dir:
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|
378 sto.close()
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379 if self.opts.make_HTML:
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380 self.makeHtml()
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381 return retval
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382
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383
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|
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384 def main():
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385 u = """
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386 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
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387 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
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388 </command>
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|
|
389 """
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390 op = optparse.OptionParser()
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391 a = op.add_option
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392 a('--script_path',default=None)
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393 a('--tool_name',default=None)
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394 a('--interpreter',default=None)
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395 a('--output_dir',default=None)
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396 a('--output_html',default=None)
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397 a('--input_tab',default="None")
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|
|
398 a('--output_tab',default="None")
|
|
|
399 a('--user_email',default=None)
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|
|
400 a('--bad_user',default=None)
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|
|
401 a('--make_Tool',default=None)
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|
|
402 a('--make_HTML',default=None)
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|
|
403 a('--help_text',default=None)
|
|
|
404 a('--tool_desc',default=None)
|
|
|
405 a('--new_tool',default=None)
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|
|
406 opts, args = op.parse_args()
|
|
|
407 assert not opts.bad_user,'%s is NOT authorized to use this tool. Please ask your friendly admin to add their ID to admin_users in universe_wsgi.ini' % (opts.bad_user)
|
|
|
408 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
|
|
|
409 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
|
|
|
410 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
|
|
|
411 if opts.output_dir:
|
|
|
412 try:
|
|
|
413 os.makedirs(opts.output_dir)
|
|
|
414 except:
|
|
|
415 pass
|
|
|
416 r = ScriptRunner(opts)
|
|
|
417 if opts.make_Tool:
|
|
|
418 retcode = r.makeTooltar()
|
|
|
419 else:
|
|
|
420 retcode = r.run()
|
|
|
421 if retcode:
|
|
|
422 sys.exit(retcode) # indicate failure to job runner
|
|
|
423
|
|
|
424
|
|
|
425 if __name__ == "__main__":
|
|
|
426 main()
|
|
|
427
|
|
|
428
|
