annotate rgToolFactory.py @ 22:2983106e1460 draft

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author fubar
date Sun, 23 Mar 2014 08:17:32 -0400
parents abeec897b2d7
children f87139fe5e09
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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
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137 class ScriptRunner:
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138 """class is a wrapper for an arbitrary script
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139 """
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140
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141 def __init__(self,opts=None,treatbashSpecial=True):
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142 """
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143 cleanup inputs, setup some outputs
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144
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145 """
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146 self.useGM = cmd_exists('gm')
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147 self.useIM = cmd_exists('convert')
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148 self.useGS = cmd_exists('gs')
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149 self.temp_warned = False # we want only one warning if $TMP not set
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150 self.treatbashSpecial = treatbashSpecial
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151 if opts.output_dir: # simplify for the tool tarball
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152 os.chdir(opts.output_dir)
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153 self.thumbformat = 'png'
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154 self.opts = opts
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155 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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156 self.toolid = self.toolname
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157 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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158 self.pyfile = self.myname # crude but efficient - the cruft won't hurt muchself.tooldepfile)
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159 self.xmlfile = '%s.xml' % self.toolname
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160 s = open(self.opts.script_path,'r').readlines()
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161 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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162 s = [x.lstrip() for x in s] # and left padding
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163 self.script = '\n'.join(s)
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164 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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165 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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166 tscript.write(self.script)
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167 tscript.close()
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168 self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
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169 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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170 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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171 if opts.output_dir: # may not want these complexities
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172 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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173 art = '%s.%s' % (self.toolname,opts.interpreter)
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174 artpath = os.path.join(self.opts.output_dir,art) # need full path
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175 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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176 artifact.write(self.script)
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177 artifact.close()
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178 self.cl = []
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179 self.html = []
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180 a = self.cl.append
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181 a(opts.interpreter)
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182 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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183 a(self.sfile)
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184 else:
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185 a('-') # stdin
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186 a(opts.input_tab)
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187 a(opts.output_tab)
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188 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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189 self.inputFormats = 'tabular,txt' # TODO make this an option at tool generation time
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190 self.test1Input = '%s_test1_input.xls' % self.toolname
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191 self.test1Output = '%s_test1_output.xls' % self.toolname
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192 self.test1HTML = '%s_test1_output.html' % self.toolname
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193
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194 def makeXML(self):
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195 """
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196 Create a Galaxy xml tool wrapper for the new script as a string to write out
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197 fixme - use templating or something less fugly than this example of what we produce
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198
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199 <tool id="reverse" name="reverse" version="0.01">
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200 <description>a tabular file</description>
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201 <command interpreter="python">
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202 reverse.py --script_path "$runMe" --interpreter "python"
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203 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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204 </command>
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205 <inputs>
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206 <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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207
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208 </inputs>
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209 <outputs>
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210 <data format="tabular" name="tab_file" label="${job_name}"/>
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211
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212 </outputs>
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213 <help>
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214
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215 **What it Does**
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216
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217 Reverse the columns in a tabular file
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218
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219 </help>
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220 <configfiles>
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221 <configfile name="runMe">
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222
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223 # reverse order of columns in a tabular file
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224 import sys
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225 inp = sys.argv[1]
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226 outp = sys.argv[2]
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227 i = open(inp,'r')
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228 o = open(outp,'w')
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229 for row in i:
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230 rs = row.rstrip().split('\t')
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231 rs.reverse()
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232 o.write('\t'.join(rs))
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233 o.write('\n')
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234 i.close()
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235 o.close()
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236
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237
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238 </configfile>
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239 </configfiles>
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240 </tool>
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241
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242 """
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243 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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244 %(tooldesc)s
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245 %(requirements)s
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246 %(command)s
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247 <inputs>
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248 %(inputs)s
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249 </inputs>
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250 <outputs>
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251 %(outputs)s
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252 </outputs>
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253 <configfiles>
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254 <configfile name="runMe">
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255 %(script)s
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256 </configfile>
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257 </configfiles>
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258
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259 %(tooltests)s
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260
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261 <help>
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262
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263 %(help)s
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264
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265 </help>
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266 </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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267
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268 newCommand="""<command interpreter="python">
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269 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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270 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
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271 </command>""" # may NOT be an input or htmlout
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272 tooltestsTabOnly = """
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273 <tests>
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274 <test>
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275 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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276 <param name="job_name" value="test1"/>
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277 <param name="runMe" value="$runMe"/>
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278 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
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279 </test>
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280 </tests>
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281 """
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282 tooltestsHTMLOnly = """
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283 <tests>
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284 <test>
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285 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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286 <param name="job_name" value="test1"/>
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287 <param name="runMe" value="$runMe"/>
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288 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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289 </test>
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290 </tests>
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291 """
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292 tooltestsBoth = """<tests>
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293 <test>
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294 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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295 <param name="job_name" value="test1"/>
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296 <param name="runMe" value="$runMe"/>
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297 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
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298 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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299 </test>
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300 </tests>
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301 """
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302 xdict = {}
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303 xdict['requirements'] = ''
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304 if self.opts.make_HTML:
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305 xdict['requirements'] = protorequirements
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306 xdict['tool_version'] = self.opts.tool_version
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307 xdict['test1Input'] = self.test1Input
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308 xdict['test1HTML'] = self.test1HTML
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309 xdict['test1Output'] = self.test1Output
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310 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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311 xdict['tooltests'] = tooltestsBoth % xdict
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312 elif self.opts.make_HTML:
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313 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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314 else:
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315 xdict['tooltests'] = tooltestsTabOnly % xdict
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316 xdict['script'] = self.escapedScript
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317 # configfile is least painful way to embed script to avoid external dependencies
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318 # but requires escaping of <, > and $ to avoid Mako parsing
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319 if self.opts.help_text:
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320 xdict['help'] = open(self.opts.help_text,'r').readlines()
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321 xdict['help'] = ''.join([x.lstrip(x) for x in xdict['help']])
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322 else:
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323 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation\n'
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324 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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325 coda.append('\n')
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326 coda.append(self.indentedScript)
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327 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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328 coda.append('See %s for details of that project' % (toolFactoryURL))
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329 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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330 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
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331 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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332 if self.opts.tool_desc:
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333 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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334 else:
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335 xdict['tooldesc'] = ''
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336 xdict['command_outputs'] = ''
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337 xdict['outputs'] = ''
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338 if self.opts.input_tab <> 'None':
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339 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
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340 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
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341 else:
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342 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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343 xdict['inputs'] = ''
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344 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
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345 xdict['toolname'] = self.toolname
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346 xdict['toolid'] = self.toolid
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347 xdict['interpreter'] = self.opts.interpreter
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348 xdict['scriptname'] = self.sfile
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349 if self.opts.make_HTML:
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350 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
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351 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
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352 if self.opts.output_tab <> 'None':
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353 xdict['command_outputs'] += ' --output_tab "$tab_file"'
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354 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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355 xdict['command'] = newCommand % xdict
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356 xmls = newXML % xdict
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357 xf = open(self.xmlfile,'w')
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diff changeset
358 xf.write(xmls)
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diff changeset
359 xf.write('\n')
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diff changeset
360 xf.close()
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diff changeset
361 # ready for the tarball
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362
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363
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364 def makeTooltar(self):
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365 """
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366 a tool is a gz tarball with eg
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367 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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368 """
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369 retval = self.run()
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370 if retval:
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diff changeset
371 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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372 sys.exit(1)
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373 tdir = self.toolname
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374 os.mkdir(tdir)
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375 self.makeXML()
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376 if self.opts.make_HTML:
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377 if self.opts.help_text:
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378 hlp = open(self.opts.help_text,'r').read()
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379 else:
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380 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
18
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diff changeset
381 if self.opts.include_dependencies:
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382 tooldepcontent = toolhtmldepskel % hlp
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diff changeset
383 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
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diff changeset
384 depf.write(tooldepcontent)
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diff changeset
385 depf.write('\n')
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diff changeset
386 depf.close()
7
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387 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
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388 testdir = os.path.join(tdir,'test-data')
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389 os.mkdir(testdir) # make tests directory
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390 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
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391 if self.opts.output_tab <> 'None':
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392 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
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393 if self.opts.make_HTML:
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394 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
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395 if self.opts.output_dir:
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396 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
12
a898ba82496e Uploaded
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397 outpif = '%s.py' % self.toolname # new name
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398 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
7
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399 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
13
d5a5f9c2c108 Uploaded
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400 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
7
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401 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
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402 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
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diff changeset
403 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
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diff changeset
404 notes += pi
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diff changeset
405 outpi = open(outpiname,'w')
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diff changeset
406 outpi.write(''.join(notes))
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diff changeset
407 outpi.write('\n')
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diff changeset
408 outpi.close()
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diff changeset
409 stname = os.path.join(tdir,self.sfile)
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diff changeset
410 if not os.path.exists(stname):
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diff changeset
411 shutil.copyfile(self.sfile, stname)
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diff changeset
412 xtname = os.path.join(tdir,self.xmlfile)
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diff changeset
413 if not os.path.exists(xtname):
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diff changeset
414 shutil.copyfile(self.xmlfile,xtname)
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diff changeset
415 tarpath = "%s.gz" % self.toolname
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diff changeset
416 tar = tarfile.open(tarpath, "w:gz")
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diff changeset
417 tar.add(tdir,arcname=self.toolname)
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418 tar.close()
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diff changeset
419 shutil.copyfile(tarpath,self.opts.new_tool)
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diff changeset
420 shutil.rmtree(tdir)
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diff changeset
421 ## TODO: replace with optional direct upload to local toolshed?
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422 return retval
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diff changeset
423
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diff changeset
424
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diff changeset
425 def compressPDF(self,inpdf=None,thumbformat='png'):
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diff changeset
426 """need absolute path to pdf
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diff changeset
427 note that GS gets confoozled if no $TMP or $TEMP
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diff changeset
428 so we set it
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diff changeset
429 """
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diff changeset
430 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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diff changeset
431 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
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diff changeset
432 sto = open(hlog,'a')
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diff changeset
433 our_env = os.environ.copy()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
434 our_tmp = our_env.get('TMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
435 if not our_tmp:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
436 our_tmp = our_env.get('TEMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
437 if not (our_tmp and os.path.exists(our_tmp)):
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diff changeset
438 newtmp = os.path.join(self.opts.output_dir,'tmp')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
439 try:
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diff changeset
440 os.mkdir(newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
441 except:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
442 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
443 our_env['TEMP'] = newtmp
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
444 if not self.temp_warned:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
445 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
446 self.temp_warned = True
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
447 outpdf = '%s_compressed' % inpdf
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
448 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
449 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
450 retval1 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
451 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
452 if retval1 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
453 os.unlink(inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
454 shutil.move(outpdf,inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
455 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
456 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
457 sto = open(hlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
458 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
459 if self.useGM:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
460 cl2 = ['gm', 'convert', inpdf, outpng]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
461 else: # assume imagemagick
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
462 cl2 = ['convert', inpdf, outpng]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
463 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
464 retval2 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
465 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
466 if retval2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
467 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
468 retval = retval1 or retval2
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
469 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
470
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
471
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
472 def getfSize(self,fpath,outpath):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
473 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
474 format a nice file size string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
475 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
476 size = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
477 fp = os.path.join(outpath,fpath)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
478 if os.path.isfile(fp):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
479 size = '0 B'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
480 n = float(os.path.getsize(fp))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
481 if n > 2**20:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
482 size = '%1.1f MB' % (n/2**20)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
483 elif n > 2**10:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
484 size = '%1.1f KB' % (n/2**10)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
485 elif n > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
486 size = '%d B' % (int(n))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
487 return size
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
488
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
489 def makeHtml(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
490 """ Create an HTML file content to list all the artifacts found in the output_dir
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
491 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
492
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
493 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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diff changeset
494 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
495 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
496 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
497 <title></title>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
498 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
499 </head>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
500 <body>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
501 <div class="toolFormBody">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
502 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
503 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/>"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
504 galhtmlpostfix = """</div></body></html>\n"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
505
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
506 flist = os.listdir(self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
507 flist = [x for x in flist if x <> 'Rplots.pdf']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
508 flist.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
509 html = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
510 html.append(galhtmlprefix % progname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
511 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
512 fhtml = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
513 if len(flist) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
514 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
515 logfiles.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
516 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
517 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
518 pdflist = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
519 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
520 for rownum,fname in enumerate(flist):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
521 dname,e = os.path.splitext(fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
522 sfsize = self.getfSize(fname,self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
523 if e.lower() == '.pdf' : # compress and make a thumbnail
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
524 thumb = '%s.%s' % (dname,self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
525 pdff = os.path.join(self.opts.output_dir,fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
526 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
527 if retval == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
528 pdflist.append((fname,thumb))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
529 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
530 pdflist.append((fname,fname))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
531 if (rownum+1) % 2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
532 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
533 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
534 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
535 for logfname in logfiles: # expect at least tlog - if more
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
536 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
537 sectionname = 'All tool run'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
538 if (len(logfiles) > 1):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
539 sectionname = 'Other'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
540 ourpdfs = pdflist
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
541 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
542 realname = os.path.basename(logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
543 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
544 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
545 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
546 nacross = 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
547 npdf = len(ourpdfs)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
548
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
549 if npdf > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
550 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
551 if int(nacross)**2 != npdf:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
552 nacross += 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
553 nacross = int(nacross)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
554 width = min(400,int(1200/nacross))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
555 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
556 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
557 ntogo = nacross # counter for table row padding with empty cells
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
558 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
559 for i,paths in enumerate(ourpdfs):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
560 fname,thumb = paths
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
561 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
562 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
563 if ((i+1) % nacross == 0):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
564 s += '</tr>\n'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
565 ntogo = 0
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
566 if i < (npdf - 1): # more to come
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
567 s += '<tr>'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
568 ntogo = nacross
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
569 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
570 ntogo -= 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
571 html.append(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
572 if html[-1].strip().endswith('</tr>'):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
573 html.append('</table></div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
574 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
575 if ntogo > 0: # pad
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
576 html.append('<td>&nbsp;</td>'*ntogo)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
577 html.append('</tr></table></div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
578 logt = open(logfname,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
579 logtext = [x for x in logt if x.strip() > '']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
580 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
581 if len(logtext) > 1:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
582 html.append('\n<pre>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
583 html += logtext
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
584 html.append('\n</pre>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
585 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
586 html.append('%s is empty<br/>' % logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
587 if len(fhtml) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
588 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')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
589 fhtml.append('</table></div><br/>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
590 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
591 html += fhtml # add all non-pdf files to the end of the display
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
592 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
593 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
594 html.append(galhtmlpostfix)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
595 htmlf = file(self.opts.output_html,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
596 htmlf.write('\n'.join(html))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
597 htmlf.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
598 htmlf.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
599 self.html = html
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
600
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
601
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
602 def run(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
603 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
604 scripts must be small enough not to fill the pipe!
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
605 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
606 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
607 retval = self.runBash()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
608 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
609 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
610 ste = open(self.elog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
611 sto = open(self.tlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
612 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
613 sto.flush()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
614 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
615 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
616 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
617 p.stdin.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
618 p.stdin.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
619 retval = p.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
620 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
621 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
622 ste.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
623 err = open(self.elog,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
624 if retval <> 0 and err: # problem
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
625 print >> sys.stderr,err
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
626 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
627 self.makeHtml()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
628 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
629
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
630 def runBash(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
631 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
632 cannot use - for bash so use self.sfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
633 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
634 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
635 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
636 sto = open(self.tlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
637 sto.write(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
638 sto.flush()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
639 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
640 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
641 p = subprocess.Popen(self.cl,shell=False)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
642 retval = p.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
643 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
644 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
645 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
646 self.makeHtml()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
647 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
648
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
649
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
650 def main():
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
651 u = """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
652 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
653 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
654 </command>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
655 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
656 op = optparse.OptionParser()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
657 a = op.add_option
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
658 a('--script_path',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
659 a('--tool_name',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
660 a('--interpreter',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
661 a('--output_dir',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
662 a('--output_html',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
663 a('--input_tab',default="None")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
664 a('--output_tab',default="None")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
665 a('--user_email',default='Unknown')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
666 a('--bad_user',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
667 a('--make_Tool',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
668 a('--make_HTML',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
669 a('--help_text',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
670 a('--tool_desc',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
671 a('--new_tool',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
672 a('--tool_version',default=None)
18
a986c9f88d38 removed dependencies
fubar
parents: 17
diff changeset
673 a('--include_dependencies',default=None)
7
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
674 opts, args = op.parse_args()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
675 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)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
676 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
677 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
678 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
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679 if opts.output_dir:
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680 try:
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681 os.makedirs(opts.output_dir)
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682 except:
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683 pass
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684 r = ScriptRunner(opts)
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685 if opts.make_Tool:
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686 retcode = r.makeTooltar()
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687 else:
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688 retcode = r.run()
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689 os.unlink(r.sfile)
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690 if retcode:
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691 sys.exit(retcode) # indicate failure to job runner
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692
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693
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694 if __name__ == "__main__":
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695 main()
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696
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697