Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate rgToolFactory.py @ 7:7221619caefa

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Updated name and added crude gzip generator for toolshed TODO: add tests and new XML tool descriptor as soon as Greg has it nailed down.
author ross lazarus ross.lazarus@gmail.com
date Sat, 02 Jun 2012 10:43:08 +1000
parents
children 220885b2d7ee
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7
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1 # rgDynamicScriptWrapper.py
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2 # derived from
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3 # rgBaseScriptWrapper.py
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4 # to run some 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 - only users in the list can run this tool.
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8 #
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9 # copyright ross lazarus (ross.lazarus@gmail.com) May 2012
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10 #
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11 # all rights reserved
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12 # Licensed under the LGPL for your pleasure
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13 # Derived from rgDGE.py in May 2012
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14 # generalized to run required interpreter
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15 # to make your own tools based on a given script and interpreter such as perl or python
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16 # clone this and the corresponding xml wrapper
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17 # replace the parameters/inputs/outputs and the configfile contents with your script
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18 # 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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19 # and returned as part of the output to the user - with the right values for all the parameters.
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20 # Note that this assumes you want all the outputs arranged as a single Html file output
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21 # after this generic script runner runs your script with the specified interpreter,
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22 # 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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23
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24 import sys
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25 import shutil
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26 import subprocess
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27 import os
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28 import time
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29 import tempfile
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30 import optparse
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31 import tarfile
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32 import re
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33 progname = os.path.split(sys.argv[0])[1]
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34 myversion = 'V000.1 May 2012'
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35 verbose = False
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36 debug = False
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37
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38
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39 galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
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40 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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41 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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42 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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43 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
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44 <title></title>
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45 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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46 </head>
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47 <body>
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48 <div class="document">
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49 """
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50 galhtmlattr = """<b><a href="http://rgenetics.org">Galaxy Rgenetics Base Script Wrapper based </a> tool output %s run at %s</b><br/>"""
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51 galhtmlpostfix = """</div></body></html>\n"""
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52
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53 def timenow():
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54 """return current time as a string
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55 """
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56 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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57 # characters that are allowed but need to be escaped
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58 mapped_chars = { '>' :'__gt__',
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59 '<' :'__lt__',
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60 "'" :'__sq__',
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61 '"' :'__dq__',
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62 '{' :'__oc__',
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63 '}' :'__cc__',
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64 '@' : '__at__',
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65 '\n' : '__cn__',
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66 '\r' : '__cr__',
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67 '\t' : '__tc__',
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68 '#' : '__pd__',
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69 '[' :'__ob__',
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70 ']' :'__cb__',
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71 '\t' : 'Xt',
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72 'systemCallsAreNotAllowed' : 'system'
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73 }
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74
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75 def restore_text(text):
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76 """Restores sanitized text"""
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77 if not text:
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78 return text
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79 for key, value in mapped_chars.items():
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80 text = text.replace(value, key)
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81 return text
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82
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83 class ScriptRunner:
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84 """class is a wrapper for an arbitrary script
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85 """
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86
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87 def __init__(self,opts=None):
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88 """
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89 run the script
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90 cheetah/galaxy will provide an escaped string so
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91 __pd__ your script goes here
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92 __cr____cn__ourargs __lt__- commandArgs(TRUE)
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93 __cr____cn__inf = ourargs[1]
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94 __cr____cn__outf = ourargs[2]
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95 __cr____cn__inp = read.table(inf,head=T,rownames=F,sep=__sq__Xt__sq__)
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96 __cr____cn__ write.table(inp,outf, quote=FALSE, sep=__dq__Xt__dq__,row.names=F)
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97 __cr____cn__sessionInfo()
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98 __cr____cn__
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99 """
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100 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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101 self.thumbformat = 'jpg'
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102 self.opts = opts
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103 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name)
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104 s = open(self.opts.script_path,'r').read()
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105 self.script = restore_text(s)
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106 self.pyfile = self.myname
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107 self.xmlfile = '%s.xml' % os.path.splitext(self.pyfile)[0] # punt
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108 self.sfile = '%s.%s' % (self.toolname,opts.interpreter)
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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 if opts.output_dir or self.opts.makeTool: # may not want these complexities if a simple script
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113 self.tlog = os.path.join(opts.output_dir,"%s_runner.log" % self.toolname)
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114 artifactpath = os.path.join(opts.output_dir,'%s_run.script' % self.toolname)
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115 artifact = open(artifactpath,'w')
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116 artifact.write(self.script)
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117 artifact.write('\n')
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118 artifact.close()
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119 self.cl = []
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120 self.html = []
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121 a = self.cl.append
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122 a(opts.interpreter)
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123 a('-') # use stdin
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124 a(opts.input_tab)
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125 a(opts.output_tab)
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126
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127 def makeTooltar(self):
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128 """
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129 a tool is a gz tarball with eg
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130 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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131 """
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132 retval = self.run()
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133 if retval:
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134 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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135 sys.exit(1)
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136 tarpath = os.path.join(self.opts.output_dir,"%s.gz" % self.toolname)
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137 tar = tarfile.open(tarpath, "w:gz")
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138 tar.add(self.xmlfile,arcname='%s.xml' % self.toolname)
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139 tar.add(self.pyfile,arcname=os.path.basename(self.pyfile))
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140 tar.add(self.sfile,arcname=self.sfile)
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141 tar.close()
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142 self.makeHtml()
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143 return retval
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144
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145 def compressPDF(self,inpdf=None,thumbformat='png'):
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146 """need absolute path to pdf
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147 """
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148 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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149 hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
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150 sto = open(hlog,'w')
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151 outpdf = '%s_compressed' % inpdf
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152 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH", "-sOutputFile=%s" % outpdf,inpdf]
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153 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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154 retval1 = x.wait()
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155 if retval1 == 0:
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diff changeset
156 os.unlink(inpdf)
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diff changeset
157 shutil.move(outpdf,inpdf)
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158 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
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159 cl2 = ['convert', inpdf, outpng]
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160 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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161 retval2 = x.wait()
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diff changeset
162 sto.close()
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163 retval = retval1 or retval2
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164 return retval
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165
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166
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167 def getfSize(self,fpath,outpath):
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168 """
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169 format a nice file size string
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170 """
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171 size = ''
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172 fp = os.path.join(outpath,fpath)
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173 if os.path.isfile(fp):
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174 n = float(os.path.getsize(fp))
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175 if n > 2**20:
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176 size = ' (%1.1f MB)' % (n/2**20)
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177 elif n > 2**10:
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178 size = ' (%1.1f KB)' % (n/2**10)
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179 elif n > 0:
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180 size = ' (%d B)' % (int(n))
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181 return size
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182
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183 def makeHtml(self):
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184 """
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185 """
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186 flist = os.listdir(self.opts.output_dir)
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187 flist = [x for x in flist if x <> 'Rplots.pdf']
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188 flist.sort()
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189 html = [galhtmlprefix % progname,]
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190 html.append('<h2>Galaxy %s outputs run at %s</h2><br/>\n' % (self.toolname,timenow()))
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191 fhtml = []
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192 if len(flist) > 0:
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193 html.append('<table cellpadding="3" cellspacing="3">\n')
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194 for fname in flist:
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195 dname,e = os.path.splitext(fname)
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196 sfsize = self.getfSize(fname,self.opts.output_dir)
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197 if e.lower() == '.pdf' : # compress and make a thumbnail
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198 thumb = '%s.%s' % (dname,self.thumbformat)
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199 pdff = os.path.join(self.opts.output_dir,fname)
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200 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
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201 if retval == 0:
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202 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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203 html.append(s)
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204 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
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205 else:
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206 fhtml.append('<li><a href="%s">%s %s</a></li>' % (fname,fname,sfsize))
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207 html.append('</table>\n')
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parents:
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208 if len(fhtml) > 0:
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parents:
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209 fhtml.insert(0,'<ul>')
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210 fhtml.append('</ul>')
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211 html += fhtml # add all non-pdf files to the end of the display
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212 else:
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213 html.append('<h2>### Error - %s returned no files - please confirm that parameters are sane</h1>' % self.opts.interpreter)
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214 html.append('<h3>%s log follows below</h3><hr><pre>\n' % self.opts.interpreter)
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215 rlog = open(self.tlog,'r').readlines()
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216 html += rlog
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217 html.append('%s CL = %s</br>\n' % (self.toolname,' '.join(sys.argv)))
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parents:
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218 html.append('CL = %s</br>\n' % (' '.join(self.cl)))
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diff changeset
219 html.append('</pre>\n')
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220 html.append(galhtmlattr % (progname,timenow()))
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parents:
diff changeset
221 html.append(galhtmlpostfix)
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222 htmlf = file(self.opts.output_html,'w')
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parents:
diff changeset
223 htmlf.write('\n'.join(html))
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diff changeset
224 htmlf.write('\n')
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diff changeset
225 htmlf.close()
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parents:
diff changeset
226 self.html = html
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diff changeset
227
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parents:
diff changeset
228
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diff changeset
229 def run(self):
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230 """
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parents:
diff changeset
231 """
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diff changeset
232 if self.opts.output_dir or self.opts.makeTool:
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parents:
diff changeset
233 sto = open(self.tlog,'w')
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diff changeset
234 p = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
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diff changeset
235 else:
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parents:
diff changeset
236 p = subprocess.Popen(' '.join(self.cl),shell=True,stdin=subprocess.PIPE)
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diff changeset
237 p.stdin.write(self.script)
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diff changeset
238 p.stdin.close()
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parents:
diff changeset
239 retval = p.wait()
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parents:
diff changeset
240 if self.opts.output_dir or self.opts.makeTool:
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parents:
diff changeset
241 sto.close()
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parents:
diff changeset
242 self.makeHtml()
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diff changeset
243 return retval
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parents:
diff changeset
244
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parents:
diff changeset
245
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parents:
diff changeset
246 def main():
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diff changeset
247 u = """
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parents:
diff changeset
248 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
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parents:
diff changeset
249 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
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parents:
diff changeset
250 </command>
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parents:
diff changeset
251 """
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parents:
diff changeset
252 op = optparse.OptionParser()
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parents:
diff changeset
253 a = op.add_option
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parents:
diff changeset
254 a('--script_path',default=None)
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parents:
diff changeset
255 a('--tool_name',default=None)
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parents:
diff changeset
256 a('--interpreter',default=None)
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parents:
diff changeset
257 a('--output_dir',default=None)
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parents:
diff changeset
258 a('--output_html',default=None)
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parents:
diff changeset
259 a('--input_tab',default='NONE')
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parents:
diff changeset
260 a('--output_tab',default='NONE')
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parents:
diff changeset
261 a('--user_email',default=None)
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parents:
diff changeset
262 a('--bad_user',default=None)
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parents:
diff changeset
263 a('--makeTool',default=None)
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diff changeset
264 opts, args = op.parse_args()
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parents:
diff changeset
265 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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diff changeset
266 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
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diff changeset
267 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
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268 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
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parents:
diff changeset
269 if opts.output_dir:
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parents:
diff changeset
270 try:
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parents:
diff changeset
271 os.makedirs(opts.output_dir)
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parents:
diff changeset
272 except:
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parents:
diff changeset
273 pass
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parents:
diff changeset
274 r = ScriptRunner(opts)
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parents:
diff changeset
275 if opts.makeTool:
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276 retcode = r.makeTooltar()
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diff changeset
277 else:
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278 retcode = r.run()
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279 if retcode:
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280 sys.exit(retcode) # indicate failure to job runner
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281
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282
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283 if __name__ == "__main__":
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284 main()
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285
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286