annotate rgToolFactory.py @ 13:d5a5f9c2c108 draft

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author fubar
date Thu, 20 Mar 2014 06:00:21 -0400
parents a898ba82496e
children 43ab59672f78
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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 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
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12 #
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13 # added ghostscript and graphicsmagick as dependencies
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14 # 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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15 # errors ensued
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16 #
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17 # august 2013
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18 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
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19 #
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20 # july 2013
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21 # added ability to combine images and individual log files into html output
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22 # just make sure there's a log file foo.log and it will be output
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23 # together with all images named like "foo_*.pdf
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24 # otherwise old format for html
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25 #
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26 # January 2013
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27 # problem pointed out by Carlos Borroto
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28 # added escaping for <>$ - thought I did that ages ago...
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29 #
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30 # August 11 2012
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31 # changed to use shell=False and cl as a sequence
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32
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33 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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34 # It also serves as the wrapper for the new tool.
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35 #
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36 # you paste and run your script
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37 # Only works for simple scripts that read one input from the history.
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38 # Optionally can write one new history dataset,
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39 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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40
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41 # DO NOT install on a public or important site - please.
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42
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43 # installed generated tools are fine if the script is safe.
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44 # They just run normally and their user cannot do anything unusually insecure
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45 # but please, practice safe toolshed.
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46 # Read the fucking code before you install any tool
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47 # especially this one
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48
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49 # After you get the script working on some test data, you can
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50 # optionally generate a toolshed compatible gzip file
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51 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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52 # safe and largely automated installation in a production Galaxy.
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53
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54 # If you opt for an HTML output, you get all the script outputs arranged
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55 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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56 # Ugly but really inexpensive.
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57 #
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58 # Patches appreciated please.
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59 #
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60 #
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61 # long route to June 2012 product
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62 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
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63 # derived from an integrated script model
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64 # called rgBaseScriptWrapper.py
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65 # Note to the unwary:
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66 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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67 # There is nothing stopping a malicious user doing whatever they choose
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68 # Extremely dangerous!!
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69 # Totally insecure. So, trusted users only
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70 #
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71 # preferred model is a developer using their throw away workstation instance - ie a private site.
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72 # 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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73 #
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74
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75 import sys
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76 import shutil
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77 import subprocess
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78 import os
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79 import time
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80 import tempfile
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81 import optparse
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82 import tarfile
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83 import re
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84 import shutil
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85 import math
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86
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87 progname = os.path.split(sys.argv[0])[1]
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88 myversion = 'V001.1 March 2014'
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89 verbose = False
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90 debug = False
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91 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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92
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93 # if we do html we need these dependencies
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94 toolhtmldep = """<?xml version="1.0"?>
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95 <tool_dependency>
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96 <package name="ghostscript" version="9.10">
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97 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
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98 </package>
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99 <package name="graphicsmagick" version="1.3.18">
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100 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" />
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101 </package>
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102 <readme>
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103 %s
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104 </readme>
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105 </tool_dependency>
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106 """
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107
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108 def timenow():
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109 """return current time as a string
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110 """
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111 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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112
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113 html_escape_table = {
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114 "&": "&amp;",
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115 ">": "&gt;",
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116 "<": "&lt;",
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117 "$": "\$"
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118 }
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119
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120 def html_escape(text):
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121 """Produce entities within text."""
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122 return "".join(html_escape_table.get(c,c) for c in text)
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123
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124 def cmd_exists(cmd):
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125 return subprocess.call("type " + cmd, shell=True,
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126 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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127
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128
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129 class ScriptRunner:
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130 """class is a wrapper for an arbitrary script
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131 """
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132
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133 def __init__(self,opts=None,treatbashSpecial=True):
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134 """
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135 cleanup inputs, setup some outputs
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136
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137 """
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138 self.useGM = cmd_exists('gm')
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139 self.useIM = cmd_exists('convert')
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140 self.useGS = cmd_exists('gs')
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141 self.temp_warned = False # we want only one warning if $TMP not set
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142 self.treatbashSpecial = treatbashSpecial
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143 if opts.output_dir: # simplify for the tool tarball
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144 os.chdir(opts.output_dir)
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145 self.thumbformat = 'png'
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146 self.opts = opts
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147 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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148 self.toolid = self.toolname
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149 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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150 self.pyfile = self.myname # crude but efficient - the cruft won't hurt muchself.tooldepfile)
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151 self.xmlfile = '%s.xml' % self.toolname
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152 s = open(self.opts.script_path,'r').readlines()
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153 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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154 self.script = '\n'.join(s)
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155 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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156 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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157 tscript.write(self.script)
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158 tscript.close()
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159 self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
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160 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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161 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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162 if opts.output_dir: # may not want these complexities
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163 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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164 art = '%s.%s' % (self.toolname,opts.interpreter)
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165 artpath = os.path.join(self.opts.output_dir,art) # need full path
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166 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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167 artifact.write(self.script)
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168 artifact.close()
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169 self.cl = []
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170 self.html = []
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171 a = self.cl.append
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172 a(opts.interpreter)
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173 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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174 a(self.sfile)
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175 else:
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176 a('-') # stdin
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177 a(opts.input_tab)
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178 a(opts.output_tab)
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179 self.outFormats = 'tabular' # TODO make this an option at tool generation time
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180 self.inputFormats = 'tabular' # TODO make this an option at tool generation time
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181 self.test1Input = '%s_test1_input.xls' % self.toolname
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182 self.test1Output = '%s_test1_output.xls' % self.toolname
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183 self.test1HTML = '%s_test1_output.html' % self.toolname
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184
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185 def makeXML(self):
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186 """
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187 Create a Galaxy xml tool wrapper for the new script as a string to write out
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188 fixme - use templating or something less fugly than this example of what we produce
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189
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190 <tool id="reverse" name="reverse" version="0.01">
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191 <description>a tabular file</description>
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192 <command interpreter="python">
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193 reverse.py --script_path "$runMe" --interpreter "python"
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194 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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195 </command>
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196 <inputs>
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197 <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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198
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199 </inputs>
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200 <outputs>
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201 <data format="tabular" name="tab_file" label="${job_name}"/>
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202
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203 </outputs>
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204 <help>
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205
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206 **What it Does**
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207
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208 Reverse the columns in a tabular file
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209
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210 </help>
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211 <configfiles>
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212 <configfile name="runMe">
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213
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214 # reverse order of columns in a tabular file
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215 import sys
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216 inp = sys.argv[1]
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217 outp = sys.argv[2]
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218 i = open(inp,'r')
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219 o = open(outp,'w')
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220 for row in i:
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221 rs = row.rstrip().split('\t')
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222 rs.reverse()
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223 o.write('\t'.join(rs))
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224 o.write('\n')
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225 i.close()
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226 o.close()
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227
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228
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229 </configfile>
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230 </configfiles>
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231 </tool>
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232
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233 """
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234 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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235 %(tooldesc)s
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236 %(command)s
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237 <inputs>
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238 %(inputs)s
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239 </inputs>
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240 <outputs>
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241 %(outputs)s
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242 </outputs>
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243 <configfiles>
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244 <configfile name="runMe">
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245 %(script)s
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246 </configfile>
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247 </configfiles>
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248 %(tooltests)s
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249 <help>
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250 %(help)s
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251 </help>
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252 </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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704ccaade924 Uploaded
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253
7
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254 newCommand="""<command interpreter="python">
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255 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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256 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s
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257 </command>""" # may NOT be an input or htmlout
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258 tooltestsTabOnly = """<tests><test>
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259 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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260 <param name="job_name" value="test1"/>
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261 <param name="runMe" value="$runMe"/>
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262 <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
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263 </test></tests>"""
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264 tooltestsHTMLOnly = """<tests><test>
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265 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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266 <param name="job_name" value="test1"/>
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267 <param name="runMe" value="$runMe"/>
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268 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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269 </test></tests>"""
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270 tooltestsBoth = """<tests><test>
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271 <param name="input1" value="%(test1Input)s" ftype="tabular"/>
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272 <param name="job_name" value="test1"/>
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273 <param name="runMe" value="$runMe"/>
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274 <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
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275 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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276 </test></tests>"""
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277 xdict = {}
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278 xdict['tool_version'] = self.opts.tool_version
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279 xdict['test1Input'] = self.test1Input
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280 xdict['test1HTML'] = self.test1HTML
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281 xdict['test1Output'] = self.test1Output
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282 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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283 xdict['tooltests'] = tooltestsBoth % xdict
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284 elif self.opts.make_HTML:
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285 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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286 else:
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287 xdict['tooltests'] = tooltestsTabOnly % xdict
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288 xdict['script'] = self.escapedScript
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289 # configfile is least painful way to embed script to avoid external dependencies
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290 # but requires escaping of <, > and $ to avoid Mako parsing
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291 if self.opts.help_text:
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292 xdict['help'] = open(self.opts.help_text,'r').read()
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293 else:
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294 xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
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295 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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296 coda.append(self.indentedScript)
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297 coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
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298 coda.append('See %s for details of that project' % (toolFactoryURL))
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299 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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300 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
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301 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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302 if self.opts.tool_desc:
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303 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
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304 else:
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305 xdict['tooldesc'] = ''
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306 xdict['command_outputs'] = ''
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307 xdict['outputs'] = ''
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308 if self.opts.input_tab <> 'None':
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309 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
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310 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
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311 else:
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312 xdict['command_inputs'] = '' # assume no input - eg a random data generator
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313 xdict['inputs'] = ''
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314 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
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315 xdict['toolname'] = self.toolname
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316 xdict['toolid'] = self.toolid
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317 xdict['interpreter'] = self.opts.interpreter
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318 xdict['scriptname'] = self.sfile
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319 if self.opts.make_HTML:
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320 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
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321 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
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322 if self.opts.output_tab <> 'None':
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323 xdict['command_outputs'] += ' --output_tab "$tab_file"'
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324 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
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325 xdict['command'] = newCommand % xdict
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326 xmls = newXML % xdict
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327 xf = open(self.xmlfile,'w')
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328 xf.write(xmls)
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329 xf.write('\n')
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330 xf.close()
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331 # ready for the tarball
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332
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333
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334 def makeTooltar(self):
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335 """
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336 a tool is a gz tarball with eg
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337 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
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338 """
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339 retval = self.run()
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340 if retval:
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341 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
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342 sys.exit(1)
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343 tdir = self.toolname
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344 os.mkdir(tdir)
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345 self.makeXML()
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346 if self.opts.make_HTML:
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diff changeset
347 if self.opts.help_text:
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348 hlp = open(self.opts.help_text,'r').read()
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349 else:
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diff changeset
350 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
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351 tooldeps = toolhtmldep % hlp
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352 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
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353 depf.write(hlp)
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354 depf.write('\n')
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diff changeset
355 depf.close()
7
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356 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
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357 testdir = os.path.join(tdir,'test-data')
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358 os.mkdir(testdir) # make tests directory
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359 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
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360 if self.opts.output_tab <> 'None':
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361 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
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362 if self.opts.make_HTML:
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363 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
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364 if self.opts.output_dir:
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365 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
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366 outpif = '%s.py' % self.toolname # new name
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367 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
7
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368 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
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369 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
7
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370 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
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371 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
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372 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
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373 notes += pi
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374 outpi = open(outpiname,'w')
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375 outpi.write(''.join(notes))
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diff changeset
376 outpi.write('\n')
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377 outpi.close()
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378 stname = os.path.join(tdir,self.sfile)
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379 if not os.path.exists(stname):
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380 shutil.copyfile(self.sfile, stname)
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381 xtname = os.path.join(tdir,self.xmlfile)
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diff changeset
382 if not os.path.exists(xtname):
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383 shutil.copyfile(self.xmlfile,xtname)
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384 tarpath = "%s.gz" % self.toolname
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385 tar = tarfile.open(tarpath, "w:gz")
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386 tar.add(tdir,arcname=self.toolname)
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387 tar.close()
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388 shutil.copyfile(tarpath,self.opts.new_tool)
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389 shutil.rmtree(tdir)
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diff changeset
390 ## TODO: replace with optional direct upload to local toolshed?
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391 return retval
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diff changeset
392
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393
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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394 def compressPDF(self,inpdf=None,thumbformat='png'):
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diff changeset
395 """need absolute path to pdf
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396 note that GS gets confoozled if no $TMP or $TEMP
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diff changeset
397 so we set it
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398 """
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399 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
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400 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
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diff changeset
401 sto = open(hlog,'a')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
402 our_env = os.environ.copy()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
403 our_tmp = our_env.get('TMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
404 if not our_tmp:
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diff changeset
405 our_tmp = our_env.get('TEMP',None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
406 if not (our_tmp and os.path.exists(our_tmp)):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
407 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
408 try:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
409 os.mkdir(newtmp)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
410 except:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
411 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
412 our_env['TEMP'] = newtmp
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
413 if not self.temp_warned:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
414 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
415 self.temp_warned = True
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
416 outpdf = '%s_compressed' % inpdf
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diff changeset
417 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
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diff changeset
418 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
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diff changeset
419 retval1 = x.wait()
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diff changeset
420 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
421 if retval1 == 0:
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diff changeset
422 os.unlink(inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
423 shutil.move(outpdf,inpdf)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
424 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
425 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
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diff changeset
426 sto = open(hlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
427 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
428 if self.useGM:
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diff changeset
429 cl2 = ['gm', 'convert', inpdf, outpng]
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diff changeset
430 else: # assume imagemagick
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diff changeset
431 cl2 = ['convert', inpdf, outpng]
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diff changeset
432 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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diff changeset
433 retval2 = x.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
434 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
435 if retval2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
436 os.unlink(hlog)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
437 retval = retval1 or retval2
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
438 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
439
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
440
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
441 def getfSize(self,fpath,outpath):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
442 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
443 format a nice file size string
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
444 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
445 size = ''
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
446 fp = os.path.join(outpath,fpath)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
447 if os.path.isfile(fp):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
448 size = '0 B'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
449 n = float(os.path.getsize(fp))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
450 if n > 2**20:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
451 size = '%1.1f MB' % (n/2**20)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
452 elif n > 2**10:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
453 size = '%1.1f KB' % (n/2**10)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
454 elif n > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
455 size = '%d B' % (int(n))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
456 return size
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
457
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
458 def makeHtml(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
459 """ 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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parents:
diff changeset
460 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
461
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
462 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
463 <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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parents:
diff changeset
464 <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
465 <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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parents:
diff changeset
466 <title></title>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
467 <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
468 </head>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
469 <body>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
470 <div class="toolFormBody">
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 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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parents:
diff changeset
473 galhtmlpostfix = """</div></body></html>\n"""
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
474
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
475 flist = os.listdir(self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
476 flist = [x for x in flist if x <> 'Rplots.pdf']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
477 flist.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
478 html = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
479 html.append(galhtmlprefix % progname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
480 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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parents:
diff changeset
481 fhtml = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
482 if len(flist) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
483 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
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parents:
diff changeset
484 logfiles.sort()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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diff changeset
485 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
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diff changeset
486 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
487 pdflist = []
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
488 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
489 for rownum,fname in enumerate(flist):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
490 dname,e = os.path.splitext(fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
491 sfsize = self.getfSize(fname,self.opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
492 if e.lower() == '.pdf' : # compress and make a thumbnail
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
493 thumb = '%s.%s' % (dname,self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
494 pdff = os.path.join(self.opts.output_dir,fname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
495 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
496 if retval == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
497 pdflist.append((fname,thumb))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
498 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
499 pdflist.append((fname,fname))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
500 if (rownum+1) % 2 == 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
501 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
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parents:
diff changeset
502 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
503 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
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parents:
diff changeset
504 for logfname in logfiles: # expect at least tlog - if more
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
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parents:
diff changeset
505 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
506 sectionname = 'All tool run'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
507 if (len(logfiles) > 1):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
508 sectionname = 'Other'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
509 ourpdfs = pdflist
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
510 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
511 realname = os.path.basename(logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
512 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
513 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
514 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
515 nacross = 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
516 npdf = len(ourpdfs)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
517
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
518 if npdf > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
519 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
520 if int(nacross)**2 != npdf:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
521 nacross += 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
522 nacross = int(nacross)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
523 width = min(400,int(1200/nacross))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
524 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
525 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
526 ntogo = nacross # counter for table row padding with empty cells
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
527 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
528 for i,paths in enumerate(ourpdfs):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
529 fname,thumb = paths
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
530 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
531 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
532 if ((i+1) % nacross == 0):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
533 s += '</tr>\n'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
534 ntogo = 0
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
535 if i < (npdf - 1): # more to come
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
536 s += '<tr>'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
537 ntogo = nacross
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
538 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
539 ntogo -= 1
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
540 html.append(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
541 if html[-1].strip().endswith('</tr>'):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
542 html.append('</table></div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
543 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
544 if ntogo > 0: # pad
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
545 html.append('<td>&nbsp;</td>'*ntogo)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
546 html.append('</tr></table></div>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
547 logt = open(logfname,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
548 logtext = [x for x in logt if x.strip() > '']
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
549 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
550 if len(logtext) > 1:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
551 html.append('\n<pre>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
552 html += logtext
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
553 html.append('\n</pre>\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
554 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
555 html.append('%s is empty<br/>' % logfname)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
556 if len(fhtml) > 0:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
557 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
558 fhtml.append('</table></div><br/>')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
559 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
560 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
561 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
562 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
563 html.append(galhtmlpostfix)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
564 htmlf = file(self.opts.output_html,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
565 htmlf.write('\n'.join(html))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
566 htmlf.write('\n')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
567 htmlf.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
568 self.html = html
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
569
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
570
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
571 def run(self):
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
572 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
573 scripts must be small enough not to fill the pipe!
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
574 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
575 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
576 retval = self.runBash()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
577 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
578 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
579 ste = open(self.elog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
580 sto = open(self.tlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
581 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
582 sto.flush()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
583 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
584 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
585 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
586 p.stdin.write(self.script)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
587 p.stdin.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
588 retval = p.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
589 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
590 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
591 ste.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
592 err = open(self.elog,'r').readlines()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
593 if retval <> 0 and err: # problem
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
594 print >> sys.stderr,err
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
595 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
596 self.makeHtml()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
597 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
598
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
599 def runBash(self):
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 cannot use - for bash so use self.sfile
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
602 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
603 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
604 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
605 sto = open(self.tlog,'w')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
606 sto.write(s)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
607 sto.flush()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
608 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
609 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
610 p = subprocess.Popen(self.cl,shell=False)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
611 retval = p.wait()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
612 if self.opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
613 sto.close()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
614 if self.opts.make_HTML:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
615 self.makeHtml()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
616 return retval
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
617
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
618
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
619 def main():
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
620 u = """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
621 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
622 <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
623 </command>
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
624 """
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
625 op = optparse.OptionParser()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
626 a = op.add_option
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
627 a('--script_path',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
628 a('--tool_name',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
629 a('--interpreter',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
630 a('--output_dir',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
631 a('--output_html',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
632 a('--input_tab',default="None")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
633 a('--output_tab',default="None")
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
634 a('--user_email',default='Unknown')
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
635 a('--bad_user',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
636 a('--make_Tool',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
637 a('--make_HTML',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
638 a('--help_text',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
639 a('--tool_desc',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
640 a('--new_tool',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
641 a('--tool_version',default=None)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
642 opts, args = op.parse_args()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
643 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
644 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
645 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
646 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
647 if opts.output_dir:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
648 try:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
649 os.makedirs(opts.output_dir)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
650 except:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
651 pass
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
652 r = ScriptRunner(opts)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
653 if opts.make_Tool:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
654 retcode = r.makeTooltar()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
655 else:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
656 retcode = r.run()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
657 os.unlink(r.sfile)
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
658 if retcode:
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
659 sys.exit(retcode) # indicate failure to job runner
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
660
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
661
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
662 if __name__ == "__main__":
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
663 main()
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
664
1fcf3fda325f major fixes with GS and graphicsmagick dependencies included
fubar
parents:
diff changeset
665