annotate rgToolFactory.py @ 33:ca60c96f0beb draft

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author fubar
date Thu, 28 Aug 2014 02:27:03 -0400
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1 # rgToolFactory.py
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2 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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9 #
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10 # march 2014
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11 # had to remove dependencies because cross toolshed dependencies are not possible - can't pre-specify a toolshed url for graphicsmagick and ghostscript
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12 # grrrrr - night before a demo
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13 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
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14 #
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15 # added ghostscript and graphicsmagick as dependencies
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16 # fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
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17 # errors ensued
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18 #
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19 # august 2013
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20 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
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21 #
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22 # july 2013
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23 # added ability to combine images and individual log files into html output
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24 # just make sure there's a log file foo.log and it will be output
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25 # together with all images named like "foo_*.pdf
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26 # otherwise old format for html
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27 #
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28 # January 2013
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29 # problem pointed out by Carlos Borroto
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30 # added escaping for <>$ - thought I did that ages ago...
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31 #
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32 # August 11 2012
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33 # changed to use shell=False and cl as a sequence
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34
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35 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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36 # It also serves as the wrapper for the new tool.
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37 #
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38 # you paste and run your script
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39 # Only works for simple scripts that read one input from the history.
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40 # Optionally can write one new history dataset,
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41 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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42
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43 # DO NOT install on a public or important site - please.
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44
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45 # installed generated tools are fine if the script is safe.
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46 # They just run normally and their user cannot do anything unusually insecure
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47 # but please, practice safe toolshed.
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48 # Read the fucking code before you install any tool
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49 # especially this one
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50
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51 # After you get the script working on some test data, you can
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52 # optionally generate a toolshed compatible gzip file
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53 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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54 # safe and largely automated installation in a production Galaxy.
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55
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56 # If you opt for an HTML output, you get all the script outputs arranged
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57 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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58 # Ugly but really inexpensive.
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59 #
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60 # Patches appreciated please.
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61 #
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62 #
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63 # long route to June 2012 product
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64 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
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65 # derived from an integrated script model
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66 # called rgBaseScriptWrapper.py
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67 # Note to the unwary:
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68 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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69 # There is nothing stopping a malicious user doing whatever they choose
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70 # Extremely dangerous!!
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71 # Totally insecure. So, trusted users only
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72 #
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73 # preferred model is a developer using their throw away workstation instance - ie a private site.
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74 # 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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75 #
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76
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77 import sys
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78 import shutil
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79 import subprocess
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80 import os
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81 import time
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82 import tempfile
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83 import optparse
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84 import tarfile
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85 import re
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86 import shutil
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87 import math
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88
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89 progname = os.path.split(sys.argv[0])[1]
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90 myversion = 'V001.1 March 2014'
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91 verbose = False
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92 debug = False
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93 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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94
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95 # if we do html we need these dependencies specified in a tool_dependencies.xml file and referred to in the generated
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96 # tool xml
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97 toolhtmldepskel = """<?xml version="1.0"?>
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98 <tool_dependency>
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99 <package name="ghostscript" version="9.10">
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100 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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101 </package>
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102 <package name="graphicsmagick" version="1.3.18">
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103 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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104 </package>
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105 <readme>
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106 %s
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107 </readme>
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108 </tool_dependency>
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109 """
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110
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111 protorequirements = """<requirements>
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112 <requirement type="package" version="9.10">ghostscript</requirement>
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113 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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114 </requirements>"""
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115
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116 def timenow():
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117 """return current time as a string
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118 """
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119 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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120
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121 html_escape_table = {
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122 "&": "&amp;",
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123 ">": "&gt;",
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124 "<": "&lt;",
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125 "$": "\$"
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126 }
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127
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128 def html_escape(text):
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129 """Produce entities within text."""
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130 return "".join(html_escape_table.get(c,c) for c in text)
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131
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132 def cmd_exists(cmd):
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133 return subprocess.call("type " + cmd, shell=True,
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134 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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135
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136
30
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137 def parse_citations(citations_text):
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138 """
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139 """
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140 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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141 citation_tuples = []
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142 for citation in citations:
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143 if citation.startswith("doi"):
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144 citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
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145 else:
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146 citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
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147 return citation_tuples
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148
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149
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150 class ScriptRunner:
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151 """class is a wrapper for an arbitrary script
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152 """
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153
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154 def __init__(self,opts=None,treatbashSpecial=True):
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155 """
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156 cleanup inputs, setup some outputs
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157
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158 """
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159 self.useGM = cmd_exists('gm')
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160 self.useIM = cmd_exists('convert')
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161 self.useGS = cmd_exists('gs')
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162 self.temp_warned = False # we want only one warning if $TMP not set
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163 self.treatbashSpecial = treatbashSpecial
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164 if opts.output_dir: # simplify for the tool tarball
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165 os.chdir(opts.output_dir)
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166 self.thumbformat = 'png'
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167 self.opts = opts
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168 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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169 self.toolid = self.toolname
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170 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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171 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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172 self.xmlfile = '%s.xml' % self.toolname
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173 s = open(self.opts.script_path,'r').readlines()
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174 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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175 self.script = '\n'.join(s)
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176 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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177 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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178 tscript.write(self.script)
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179 tscript.close()
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180 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
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181 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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182 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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183 if opts.output_dir: # may not want these complexities
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184 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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185 art = '%s.%s' % (self.toolname,opts.interpreter)
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186 artpath = os.path.join(self.opts.output_dir,art) # need full path
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187 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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188 artifact.write(self.script)
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189 artifact.close()
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190 self.cl = []
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191 self.html = []
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192 a = self.cl.append
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193 a(opts.interpreter)
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194 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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195 a(self.sfile)
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196 else:
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197 a('-') # stdin
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198 a(opts.input_tab)
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199 a(opts.output_tab)
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200 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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201 self.inputFormats = 'tabular,txt' # TODO make this an option at tool generation time
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202 self.test1Input = '%s_test1_input.xls' % self.toolname
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203 self.test1Output = '%s_test1_output.xls' % self.toolname
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204 self.test1HTML = '%s_test1_output.html' % self.toolname
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205
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206 def makeXML(self):
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207 """
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208 Create a Galaxy xml tool wrapper for the new script as a string to write out
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209 fixme - use templating or something less fugly than this example of what we produce
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210
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211 <tool id="reverse" name="reverse" version="0.01">
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212 <description>a tabular file</description>
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213 <command interpreter="python">
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214 reverse.py --script_path "$runMe" --interpreter "python"
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215 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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216 </command>
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217 <inputs>
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218 <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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219
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220 </inputs>
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221 <outputs>
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222 <data format="tabular" name="tab_file" label="${job_name}"/>
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223
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224 </outputs>
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225 <help>
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226
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227 **What it Does**
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228
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229 Reverse the columns in a tabular file
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230
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231 </help>
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232 <configfiles>
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233 <configfile name="runMe">
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234
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235 # reverse order of columns in a tabular file
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236 import sys
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237 inp = sys.argv[1]
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238 outp = sys.argv[2]
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239 i = open(inp,'r')
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240 o = open(outp,'w')
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241 for row in i:
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242 rs = row.rstrip().split('\t')
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243 rs.reverse()
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244 o.write('\t'.join(rs))
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245 o.write('\n')
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246 i.close()
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247 o.close()
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248
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249
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250 </configfile>
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251 </configfiles>
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252 </tool>
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253
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254 """
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255 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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256 %(tooldesc)s
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257 %(requirements)s
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258 <command interpreter="python">
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259 %(command)s
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260 </command>
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261 <inputs>
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262 %(inputs)s
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263 </inputs>
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264 <outputs>
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265 %(outputs)s
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266 </outputs>
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267 <configfiles>
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268 <configfile name="runMe">
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269 %(script)s
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270 </configfile>
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271 </configfiles>
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272
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273 %(tooltests)s
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274
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275 <help>
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276
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277 %(help)s
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278
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279 </help>
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280 <citations>
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281 %(citations)s
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282 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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283 </citations>
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284 </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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285
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286 newCommand="""
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287 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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288 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
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289 # may NOT be an input or htmlout - appended later
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290 tooltestsTabOnly = """
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291 <tests>
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292 <test>
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293 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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294 <param name="job_name" value="test1"/>
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295 <param name="runMe" value="$runMe"/>
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296 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
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297 </test>
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298 </tests>
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299 """
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300 tooltestsHTMLOnly = """
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301 <tests>
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302 <test>
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303 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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304 <param name="job_name" value="test1"/>
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305 <param name="runMe" value="$runMe"/>
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306 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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307 </test>
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308 </tests>
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309 """
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310 tooltestsBoth = """<tests>
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311 <test>
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312 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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313 <param name="job_name" value="test1"/>
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314 <param name="runMe" value="$runMe"/>
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315 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
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316 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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317 </test>
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318 </tests>
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319 """
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320 xdict = {}
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321 xdict['requirements'] = ''
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322 if self.opts.make_HTML:
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323 if self.opts.include_dependencies == "yes":
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324 xdict['requirements'] = protorequirements
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325 xdict['tool_version'] = self.opts.tool_version
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326 xdict['test1Input'] = self.test1Input
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327 xdict['test1HTML'] = self.test1HTML
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328 xdict['test1Output'] = self.test1Output
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329 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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330 xdict['tooltests'] = tooltestsBoth % xdict
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331 elif self.opts.make_HTML:
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332 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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333 else:
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334 xdict['tooltests'] = tooltestsTabOnly % xdict
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335 xdict['script'] = self.escapedScript
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336 # configfile is least painful way to embed script to avoid external dependencies
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337 # but requires escaping of <, > and $ to avoid Mako parsing
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338 if self.opts.help_text:
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339 helptext = open(self.opts.help_text,'r').readlines()
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340 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
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341 xdict['help'] = ''.join([x for x in helptext])
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342 else:
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343 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
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344 if self.opts.citations:
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345 citationstext = open(self.opts.citations,'r').read()
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346 citation_tuples = parse_citations(citationstext)
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347 citations_xml = ""
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348 for citation_type, citation_content in citation_tuples:
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349 citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
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350 citations_xml += citation_xml
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351 xdict['citations'] = citations_xml
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352 else:
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353 xdict['citations'] = ""
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354 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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355 coda.append('\n')
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356 coda.append(self.indentedScript)
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357 coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
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358 coda.append('See %s for details of that project' % (toolFactoryURL))
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359 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
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360 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
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361 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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362 if self.opts.tool_desc:
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363 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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364 else:
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365 xdict['tooldesc'] = ''
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366 xdict['command_outputs'] = ''
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367 xdict['outputs'] = ''
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368 if self.opts.input_tab <> 'None':
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369 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
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370 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
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371 else:
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372 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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373 xdict['inputs'] = ''
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374 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
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375 xdict['toolname'] = self.toolname
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376 xdict['toolid'] = self.toolid
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377 xdict['interpreter'] = self.opts.interpreter
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378 xdict['scriptname'] = self.sfile
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379 if self.opts.make_HTML:
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380 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
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381 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
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382 else:
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383 xdict['command_outputs'] += ' --output_dir "./"'
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384 if self.opts.output_tab <> 'None':
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385 xdict['command_outputs'] += ' --output_tab "$tab_file"'
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386 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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387 xdict['command'] = newCommand % xdict
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388 xmls = newXML % xdict
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389 xf = open(self.xmlfile,'w')
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390 xf.write(xmls)
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391 xf.write('\n')
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392 xf.close()
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393 # ready for the tarball
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394
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395
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396 def makeTooltar(self):
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397 """
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398 a tool is a gz tarball with eg
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399 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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400 """
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401 retval = self.run()
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diff changeset
402 if retval:
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403 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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404 sys.exit(1)
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405 tdir = self.toolname
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diff changeset
406 os.mkdir(tdir)
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diff changeset
407 self.makeXML()
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408 if self.opts.make_HTML:
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diff changeset
409 if self.opts.help_text:
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410 hlp = open(self.opts.help_text,'r').read()
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411 else:
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412 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
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413 if self.opts.include_dependencies:
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414 tooldepcontent = toolhtmldepskel % hlp
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415 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
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416 depf.write(tooldepcontent)
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417 depf.write('\n')
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418 depf.close()
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419 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
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420 testdir = os.path.join(tdir,'test-data')
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421 os.mkdir(testdir) # make tests directory
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422 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
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423 if self.opts.output_tab <> 'None':
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424 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
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425 if self.opts.make_HTML:
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426 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
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427 if self.opts.output_dir:
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428 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
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429 outpif = '%s.py' % self.toolname # new name
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430 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
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431 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
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432 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
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433 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
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434 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
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435 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
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436 notes += pi
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437 outpi = open(outpiname,'w')
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438 outpi.write(''.join(notes))
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439 outpi.write('\n')
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440 outpi.close()
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441 stname = os.path.join(tdir,self.sfile)
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442 if not os.path.exists(stname):
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443 shutil.copyfile(self.sfile, stname)
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444 xtname = os.path.join(tdir,self.xmlfile)
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445 if not os.path.exists(xtname):
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diff changeset
446 shutil.copyfile(self.xmlfile,xtname)
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447 tarpath = "%s.gz" % self.toolname
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448 tar = tarfile.open(tarpath, "w:gz")
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449 tar.add(tdir,arcname=self.toolname)
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450 tar.close()
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451 shutil.copyfile(tarpath,self.opts.new_tool)
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452 shutil.rmtree(tdir)
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453 ## TODO: replace with optional direct upload to local toolshed?
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454 return retval
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diff changeset
455
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diff changeset
456
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457 def compressPDF(self,inpdf=None,thumbformat='png'):
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458 """need absolute path to pdf
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459 note that GS gets confoozled if no $TMP or $TEMP
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diff changeset
460 so we set it
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461 """
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462 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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463 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
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464 sto = open(hlog,'a')
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465 our_env = os.environ.copy()
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466 our_tmp = our_env.get('TMP',None)
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467 if not our_tmp:
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468 our_tmp = our_env.get('TEMP',None)
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469 if not (our_tmp and os.path.exists(our_tmp)):
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470 newtmp = os.path.join(self.opts.output_dir,'tmp')
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471 try:
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472 os.mkdir(newtmp)
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473 except:
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474 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
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475 our_env['TEMP'] = newtmp
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476 if not self.temp_warned:
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477 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
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478 self.temp_warned = True
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479 outpdf = '%s_compressed' % inpdf
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480 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
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481 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
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482 retval1 = x.wait()
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diff changeset
483 sto.close()
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diff changeset
484 if retval1 == 0:
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diff changeset
485 os.unlink(inpdf)
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diff changeset
486 shutil.move(outpdf,inpdf)
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diff changeset
487 os.unlink(hlog)
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488 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
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489 sto = open(hlog,'w')
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diff changeset
490 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
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diff changeset
491 if self.useGM:
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492 cl2 = ['gm', 'convert', inpdf, outpng]
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493 else: # assume imagemagick
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diff changeset
494 cl2 = ['convert', inpdf, outpng]
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diff changeset
495 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
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496 retval2 = x.wait()
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diff changeset
497 sto.close()
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498 if retval2 == 0:
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diff changeset
499 os.unlink(hlog)
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diff changeset
500 retval = retval1 or retval2
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501 return retval
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diff changeset
502
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diff changeset
503
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504 def getfSize(self,fpath,outpath):
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505 """
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506 format a nice file size string
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507 """
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508 size = ''
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509 fp = os.path.join(outpath,fpath)
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diff changeset
510 if os.path.isfile(fp):
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diff changeset
511 size = '0 B'
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diff changeset
512 n = float(os.path.getsize(fp))
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diff changeset
513 if n > 2**20:
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514 size = '%1.1f MB' % (n/2**20)
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515 elif n > 2**10:
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diff changeset
516 size = '%1.1f KB' % (n/2**10)
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517 elif n > 0:
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diff changeset
518 size = '%d B' % (int(n))
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519 return size
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diff changeset
520
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521 def makeHtml(self):
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522 """ Create an HTML file content to list all the artifacts found in the output_dir
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523 """
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diff changeset
524
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525 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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526 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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diff changeset
527 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
528 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
529 <title></title>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
530 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
531 </head>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
532 <body>
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
533 <div class="toolFormBody">
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
534 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
535 galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>"""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
536 galhtmlpostfix = """</div></body></html>\n"""
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
537
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
538 flist = os.listdir(self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
539 flist = [x for x in flist if x <> 'Rplots.pdf']
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
540 flist.sort()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
541 html = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
542 html.append(galhtmlprefix % progname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
543 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
544 fhtml = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
545 if len(flist) > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
546 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
547 logfiles.sort()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
548 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
549 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
550 pdflist = []
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
551 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
552 for rownum,fname in enumerate(flist):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
553 dname,e = os.path.splitext(fname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
554 sfsize = self.getfSize(fname,self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
555 if e.lower() == '.pdf' : # compress and make a thumbnail
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
556 thumb = '%s.%s' % (dname,self.thumbformat)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
557 pdff = os.path.join(self.opts.output_dir,fname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
558 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
559 if retval == 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
560 pdflist.append((fname,thumb))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
561 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
562 pdflist.append((fname,fname))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
563 if (rownum+1) % 2 == 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
564 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
565 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
566 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
567 for logfname in logfiles: # expect at least tlog - if more
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
568 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
569 sectionname = 'All tool run'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
570 if (len(logfiles) > 1):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
571 sectionname = 'Other'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
572 ourpdfs = pdflist
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
573 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
574 realname = os.path.basename(logfname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
575 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
576 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
577 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
578 nacross = 1
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
579 npdf = len(ourpdfs)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
580
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
581 if npdf > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
582 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
583 if int(nacross)**2 != npdf:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
584 nacross += 1
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
585 nacross = int(nacross)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
586 width = min(400,int(1200/nacross))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
587 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
588 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
589 ntogo = nacross # counter for table row padding with empty cells
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
590 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
591 for i,paths in enumerate(ourpdfs):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
592 fname,thumb = paths
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
593 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
594 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
595 if ((i+1) % nacross == 0):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
596 s += '</tr>\n'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
597 ntogo = 0
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
598 if i < (npdf - 1): # more to come
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
599 s += '<tr>'
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
600 ntogo = nacross
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
601 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
602 ntogo -= 1
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
603 html.append(s)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
604 if html[-1].strip().endswith('</tr>'):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
605 html.append('</table></div>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
606 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
607 if ntogo > 0: # pad
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
608 html.append('<td>&nbsp;</td>'*ntogo)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
609 html.append('</tr></table></div>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
610 logt = open(logfname,'r').readlines()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
611 logtext = [x for x in logt if x.strip() > '']
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
612 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
613 if len(logtext) > 1:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
614 html.append('\n<pre>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
615 html += logtext
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
616 html.append('\n</pre>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
617 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
618 html.append('%s is empty<br/>' % logfname)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
619 if len(fhtml) > 0:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
620 fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
621 fhtml.append('</table></div><br/>')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
622 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
623 html += fhtml # add all non-pdf files to the end of the display
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
624 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
625 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
626 html.append(galhtmlpostfix)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
627 htmlf = file(self.opts.output_html,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
628 htmlf.write('\n'.join(html))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
629 htmlf.write('\n')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
630 htmlf.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
631 self.html = html
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
632
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
633
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
634 def run(self):
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
635 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
636 scripts must be small enough not to fill the pipe!
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
637 """
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
638 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
639 retval = self.runBash()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
640 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
641 if self.opts.output_dir:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
642 ste = open(self.elog,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
643 sto = open(self.tlog,'w')
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
644 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
645 sto.flush()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
646 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
647 else:
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
648 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
649 p.stdin.write(self.script)
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
650 p.stdin.close()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
651 retval = p.wait()
bff4c9bfabc7 Fixes for escaping all xml characters in help and code - thanks to Marius van den Beek for pointing these out
fubar
parents:
diff changeset
652 if self.opts.output_dir:
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653 sto.close()
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654 ste.close()
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655 err = open(self.elog,'r').readlines()
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656 if retval <> 0 and err: # problem
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657 print >> sys.stderr,err
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658 if self.opts.make_HTML:
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659 self.makeHtml()
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660 return retval
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661
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662 def runBash(self):
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663 """
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664 cannot use - for bash so use self.sfile
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665 """
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666 if self.opts.output_dir:
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667 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
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668 sto = open(self.tlog,'w')
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669 sto.write(s)
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670 sto.flush()
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671 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
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672 else:
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673 p = subprocess.Popen(self.cl,shell=False)
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674 retval = p.wait()
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675 if self.opts.output_dir:
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676 sto.close()
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677 if self.opts.make_HTML:
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678 self.makeHtml()
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679 return retval
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680
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681
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682 def main():
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683 u = """
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684 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
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685 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
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686 </command>
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687 """
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688 op = optparse.OptionParser()
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689 a = op.add_option
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690 a('--script_path',default=None)
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691 a('--tool_name',default=None)
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692 a('--interpreter',default=None)
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693 a('--output_dir',default='./')
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694 a('--output_html',default=None)
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695 a('--input_tab',default="None")
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696 a('--output_tab',default="None")
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697 a('--user_email',default='Unknown')
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698 a('--bad_user',default=None)
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699 a('--make_Tool',default=None)
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700 a('--make_HTML',default=None)
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701 a('--help_text',default=None)
30
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702 a('--citations',default=None)
29
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703 a('--tool_desc',default=None)
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704 a('--new_tool',default=None)
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705 a('--tool_version',default=None)
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706 a('--include_dependencies',default=None)
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707 opts, args = op.parse_args()
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708 assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
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709 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
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710 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
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711 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
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712 if opts.output_dir:
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713 try:
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714 os.makedirs(opts.output_dir)
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715 except:
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716 pass
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717 r = ScriptRunner(opts)
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718 if opts.make_Tool:
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719 retcode = r.makeTooltar()
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720 else:
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721 retcode = r.run()
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722 os.unlink(r.sfile)
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723 if retcode:
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724 sys.exit(retcode) # indicate failure to job runner
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725
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726
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727 if __name__ == "__main__":
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728 main()
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729
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730