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1 # rgToolFactoryMultIn.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 # January 2015
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15
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11 # unified all setups by passing the script on the cl rather than via a PIPE - no need for treat_bash_special so removed
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12 #
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13
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13 # in the process of building a complex tool
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14 # added ability to choose one of the current toolshed package_r or package_perl or package_python dependencies and source that package
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14
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15 # add that package to tool_dependencies
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16 # Note that once the generated tool is loaded, it will have that package's env.sh loaded automagically so there is no
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17 # --envshpath in the parameters for the generated tool and it uses the system one which will be first on the adjusted path.
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13
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18 #
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19 # sept 2014 added additional params from
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20 # https://bitbucket.org/mvdbeek/dockertoolfactory/src/d4863bcf7b521532c7e8c61b6333840ba5393f73/DockerToolFactory.py?at=default
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21 # passing them is complex
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22 # and they are restricted to NOT contain commas or double quotes to ensure that they can be safely passed together on
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23 # the toolfactory command line as a comma delimited double quoted string for parsing and passing to the script
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24 # see examples on this tool form
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25
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26 # august 2014
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27
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28 # Allows arbitrary number of input files
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29 # NOTE positional parameters are now passed to script
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30 # and output (may be "None") is *before* arbitrary number of inputs
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31 #
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32 # march 2014
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33 # 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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34 # grrrrr - night before a demo
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35 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
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36 #
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37 # added ghostscript and graphicsmagick as dependencies
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38 # 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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39 # errors ensued
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40 #
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41 # august 2013
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42 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
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43 #
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44 # july 2013
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45 # added ability to combine images and individual log files into html output
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46 # just make sure there's a log file foo.log and it will be output
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47 # together with all images named like "foo_*.pdf
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48 # otherwise old format for html
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49 #
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50 # January 2013
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51 # problem pointed out by Carlos Borroto
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52 # added escaping for <>$ - thought I did that ages ago...
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53 #
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54 # August 11 2012
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55 # changed to use shell=False and cl as a sequence
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56
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57 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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58 # It also serves as the wrapper for the new tool.
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59 #
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60 # you paste and run your script
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61 # Only works for simple scripts that read one input from the history.
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62 # Optionally can write one new history dataset,
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63 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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64
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65 # DO NOT install on a public or important site - please.
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66
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67 # installed generated tools are fine if the script is safe.
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68 # They just run normally and their user cannot do anything unusually insecure
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69 # but please, practice safe toolshed.
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70 # Read the fucking code before you install any tool
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71 # especially this one
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72
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73 # After you get the script working on some test data, you can
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74 # optionally generate a toolshed compatible gzip file
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75 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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76 # safe and largely automated installation in a production Galaxy.
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77
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78 # If you opt for an HTML output, you get all the script outputs arranged
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79 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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80 # Ugly but really inexpensive.
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81 #
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82 # Patches appreciated please.
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83 #
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84 #
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85 # long route to June 2012 product
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86 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
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87 # derived from an integrated script model
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88 # called rgBaseScriptWrapper.py
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89 # Note to the unwary:
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90 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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91 # There is nothing stopping a malicious user doing whatever they choose
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92 # Extremely dangerous!!
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93 # Totally insecure. So, trusted users only
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94 #
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95 # preferred model is a developer using their throw away workstation instance - ie a private site.
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96 # 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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97 #
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98
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99 import sys
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100 import shutil
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101 import subprocess
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102 import os
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103 import time
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104 import tempfile
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105 import optparse
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106 import tarfile
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107 import re
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108 import shutil
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109 import math
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110
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111 progname = os.path.split(sys.argv[0])[1]
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112 myversion = 'V001.1 March 2014'
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113 verbose = False
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114 debug = False
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115 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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116
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117 # 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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118 # tool xml
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119
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120 def timenow():
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121 """return current time as a string
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122 """
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123 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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124
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125 def quote_non_numeric(s):
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126 """return a prequoted string for non-numerics
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127 useful for perl and Rscript parameter passing?
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128 """
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129 try:
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130 res = float(s)
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131 return s
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132 except ValueError:
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133 return '"%s"' % s
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134
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135 html_escape_table = {
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136 "&": "&",
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137 ">": ">",
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138 "<": "<",
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139 "$": "\$"
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140 }
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141
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142 def html_escape(text):
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143 """Produce entities within text."""
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144 return "".join(html_escape_table.get(c,c) for c in text)
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145
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146
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147 def html_unescape(text):
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148 """Revert entities within text."""
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149 t = text.replace('&','&').replace('>','>').replace('<','<').replace('\$','$')
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150 return t
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151
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152 def cmd_exists(cmd):
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153 return subprocess.call("type " + cmd, shell=True,
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154 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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155
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156 def parse_citations(citations_text):
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157 """
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158 """
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159 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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160 citation_tuples = []
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161 for citation in citations:
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162 if citation.startswith("doi"):
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163 citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
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164 else:
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165 citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
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166 return citation_tuples
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167
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168 def shell_source(script):
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169 """need a way to source a Galaxy tool interpreter env.sh to point at the right dependency package
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170 This based on the idea in http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html
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171 Note that we have to finesse any wierdly quoted newlines in automagic exports using nulls (env -0) as newlines"""
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172 pipe = subprocess.Popen("env -i ; . %s ; env -0" % script, stdout=subprocess.PIPE, shell=True)
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173 output = pipe.communicate()[0]
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174 outl = output.split('\0')
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175 outl = [x for x in outl if len(x.split("=")) == 2]
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176 newenv = dict((line.split("=", 1) for line in outl))
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177 os.environ.update(newenv)
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178
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179 class ScriptRunner:
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180 """class is a wrapper for an arbitrary script
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181 note funky templating. this should all be done proper.
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182 Problem is, this kludge developed quite naturally and seems to work ok with
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183 little overhead...
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184
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185 """
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186
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187
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188 def __init__(self,opts=None):
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189 """
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190 cleanup inputs, setup some outputs
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191
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192 """
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193
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194 self.toolhtmldepinterpskel = """<?xml version="1.0"?>
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195 <tool_dependency>
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196 <package name="ghostscript" version="9.10">
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197 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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198 </package>
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199 <package name="graphicsmagick" version="1.3.18">
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200 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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201 </package>
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202 <package name="%(interpreter_name)s" version="%(interpreter_version)s">
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203 <repository name="%(interpreter_pack)s" owner="%(interpreter_owner)s" prior_installation_required="True" />
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204 </package>
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205
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206 <readme>
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207 %(readme)s
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208 This file was autogenerated by the Galaxy Tool Factory 2
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209 </readme>
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210 </tool_dependency>
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211 """
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212
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213 self.toolhtmldepskel = """<?xml version="1.0"?>
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214 <tool_dependency>
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215 <package name="ghostscript" version="9.10">
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216 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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217 </package>
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218 <package name="graphicsmagick" version="1.3.18">
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219 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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220 </package>
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221 <readme>
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222 %(readme)s
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223 This file was autogenerated by the Galaxy Tool Factory 2
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224 </readme>
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225 </tool_dependency>
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226 """
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227
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228 self.emptytoolhtmldepskel = """<?xml version="1.0"?>
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229 <tool_dependency>
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230 <readme>
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231 %(readme)s
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232 This file was autogenerated by the Galaxy Tool Factory 2
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233 </readme>
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234 </tool_dependency>
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235 """
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236
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237 self.protorequirements = """<requirements>
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238 <requirement type="package" version="9.10">ghostscript</requirement>
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239 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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240 </requirements>"""
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241
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242 self.protorequirements_interpreter = """<requirements>
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243 <requirement type="package" version="9.10">ghostscript</requirement>
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244 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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245 <requirement type="package" version="%(interpreter_version)s">%(interpreter_name)s</requirement>
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246 </requirements>"""
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247
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248
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249 self.newCommand="""
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250 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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251 --tool_name "%(toolname)s"
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252 %(command_inputs)s
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253 %(command_outputs)s
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254 """
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255
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256 self.tooltestsTabOnly = """
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257 <test>
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258 %(test1Inputs)s
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259 <param name="job_name" value="test1"/>
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260 <param name="runMe" value="$runMe"/>
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261 <output name="output1="%(test1Output)s" ftype="tabular"/>
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262 %(additionalParams)s
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263 </test>
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264 """
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265
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266 self.tooltestsHTMLOnly = """
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267 <test>
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268 %(test1Inputs)s
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269 <param name="job_name" value="test1"/>
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270 <param name="runMe" value="$runMe"/>
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271 %(additionalParams)s
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272 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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273 </test>
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274 """
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275
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276 self.tooltestsBoth = """
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277 <test>
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278 %(test1Inputs)s
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279 <param name="job_name" value="test1"/>
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280 <param name="runMe" value="$runMe"/>
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281 %(additionalParams)s
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282 <output name="output1" file="%(test1Output)s" ftype="tabular" />
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283 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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284 </test>
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285 """
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286
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287 self.newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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288 %(tooldesc)s
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289 %(requirements)s
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290 <command interpreter="python">
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291 %(command)s
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292 </command>
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293 <inputs>
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294 %(inputs)s
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295 %(additionalInputs)s
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296 </inputs>
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297 <outputs>
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298 %(outputs)s
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299 </outputs>
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300 <configfiles>
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301 <configfile name="runMe">
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302 %(script)s
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303 </configfile>
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304 </configfiles>
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305 <tests>
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306 %(tooltests)s
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307 </tests>
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308 <help>
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309
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310 %(help)s
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311
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312 This tool was autogenerated from a user provided script using the Galaxy Tool Factory 2
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313 https://toolshed.g2.bx.psu.edu/view/fubar/tool_factory_2
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314 </help>
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315 <citations>
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316 %(citations)s
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317 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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318 </citations>
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319 </tool>"""
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320
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321 self.useGM = cmd_exists('gm')
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322 self.useIM = cmd_exists('convert')
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323 self.useGS = cmd_exists('gs')
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324 self.temp_warned = False # we want only one warning if $TMP not set
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325 if opts.output_dir: # simplify for the tool tarball
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326 os.chdir(opts.output_dir)
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327 self.thumbformat = 'png'
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328 self.opts = opts
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329 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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330 self.toolid = self.toolname
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331 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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332 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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333 self.xmlfile = '%s.xml' % self.toolname
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334 rx = open(self.opts.script_path,'r').readlines()
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335 rx = [x.rstrip() for x in rx] # remove pesky dos line endings if needed
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336 self.script = '\n'.join(rx)
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337 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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338 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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339 tscript.write(self.script)
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340 tscript.close()
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341 self.indentedScript = " %s" % '\n'.join([' %s' % html_escape(x) for x in rx]) # for restructured text in help
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342 self.escapedScript = "%s" % '\n'.join([' %s' % html_escape(x) for x in rx])
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343 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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344 if opts.output_dir: # may not want these complexities
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345 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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346 art = '%s.%s' % (self.toolname,opts.interpreter)
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347 artpath = os.path.join(self.opts.output_dir,art) # need full path
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348 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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349 artifact.write(self.script)
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350 artifact.close()
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351 self.cl = []
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352 self.html = []
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353 self.test1Inputs = [] # now a list
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354 a = self.cl.append
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355 a(opts.interpreter)
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356 a(self.sfile)
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357 # if multiple inputs - positional or need to distinguish them with cl params
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358 if opts.input_tab:
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359 tests = []
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360 for i,intab in enumerate(opts.input_tab): # if multiple, make tests
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361 if intab.find(',') <> -1:
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362 (gpath,uname) = intab.split(',')
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363 else:
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364 gpath = uname = intab
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365 tests.append(os.path.basename(gpath))
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366 self.test1Inputs = '<param name="input_tab" value="%s" />' % (','.join(tests))
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367 else:
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368 self.test1Inputs = ''
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369 # we always pass path,name pairs in using python optparse append
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370 # but the command line has to be different
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371 self.infile_paths = ''
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372 self.infile_names = ''
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373 if self.opts.input_tab:
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374 self.infile_paths = ','.join([x.split(',')[0].strip() for x in self.opts.input_tab])
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375 self.infile_names = ','.join([x.split(',')[1].strip() for x in self.opts.input_tab])
|
|
|
376 if self.opts.interpreter == 'python':
|
|
|
377 # yes, this is how additional parameters are always passed in python - to the TF itself and to
|
|
|
378 # scripts to avoid having unknown parameter names (yes, they can be parsed but...) on the command line
|
|
|
379 if self.opts.input_tab:
|
|
|
380 a('--INPATHS "%s"' % (self.infile_paths))
|
|
|
381 a('--INNAMES "%s"' % (self.infile_names))
|
|
|
382 if self.opts.output_tab:
|
|
|
383 a('--OUTPATH "%s"' % self.opts.output_tab)
|
|
|
384 for p in opts.additional_parameters:
|
|
|
385 p = p.replace('"','')
|
|
|
386 psplit = p.split(',')
|
|
|
387 param = html_unescape(psplit[0])
|
|
|
388 value = html_unescape(psplit[1])
|
|
|
389 a('%s="%s"' % (param,value))
|
|
|
390 if (self.opts.interpreter == 'Rscript'):
|
|
15
|
391 # pass params on command line as expressions which the script evaluates - see sample
|
|
13
|
392 if self.opts.input_tab:
|
|
|
393 a('INPATHS="%s"' % self.infile_paths)
|
|
|
394 a('INNAMES="%s"' % self.infile_names)
|
|
|
395 if self.opts.output_tab:
|
|
|
396 a('OUTPATH="%s"' % self.opts.output_tab)
|
|
|
397 for p in opts.additional_parameters:
|
|
|
398 p = p.replace('"','')
|
|
|
399 psplit = p.split(',')
|
|
|
400 param = html_unescape(psplit[0])
|
|
|
401 value = html_unescape(psplit[1])
|
|
15
|
402 a('%s=%s' % (param,quote_non_numeric(value)))
|
|
13
|
403 if (self.opts.interpreter == 'perl'):
|
|
15
|
404 # pass positional params on command line - perl script needs to discombobulate the path/name lists
|
|
13
|
405 if self.opts.input_tab:
|
|
|
406 a('%s' % self.infile_paths)
|
|
|
407 a('%s' % self.infile_names)
|
|
|
408 if self.opts.output_tab:
|
|
|
409 a('%s' % self.opts.output_tab)
|
|
|
410 for p in opts.additional_parameters:
|
|
15
|
411 # followed by any additional name=value parameter pairs
|
|
13
|
412 p = p.replace('"','')
|
|
|
413 psplit = p.split(',')
|
|
|
414 param = html_unescape(psplit[0])
|
|
|
415 value = html_unescape(psplit[1])
|
|
15
|
416 a('%s=%s' % (param,quote_non_numeric(value)))
|
|
13
|
417 if self.opts.interpreter == 'sh' or self.opts.interpreter == 'bash':
|
|
|
418 # more is better - now move all params into environment AND drop on to command line.
|
|
|
419 self.cl.insert(0,'env')
|
|
|
420 if self.opts.input_tab:
|
|
|
421 self.cl.insert(1,'INPATHS=%s' % (self.infile_paths))
|
|
|
422 self.cl.insert(2,'INNAMES=%s' % (self.infile_names))
|
|
|
423 if self.opts.output_tab:
|
|
|
424 self.cl.insert(3,'OUTPATH=%s' % (self.opts.output_tab))
|
|
|
425 a('OUTPATH=%s' % (self.opts.output_tab))
|
|
|
426 # sets those environment variables for the script
|
|
|
427 # additional params appear in CL - yes, it's confusing
|
|
|
428 for i,p in enumerate(opts.additional_parameters):
|
|
|
429 psplit = p.split(',')
|
|
|
430 param = html_unescape(psplit[0])
|
|
|
431 value = html_unescape(psplit[1])
|
|
15
|
432 a('%s=%s' % (param,quote_non_numeric(value)))
|
|
|
433 self.cl.insert(4+i,'%s=%s' % (param,quote_non_numeric(value)))
|
|
|
434 self.interpreter_owner = 'SYSTEM'
|
|
|
435 self.interpreter_pack = 'SYSTEM'
|
|
|
436 self.interpreter_name = 'SYSTEM'
|
|
|
437 self.interpreter_version = 'SYSTEM'
|
|
|
438 self.interpreter_revision = 'SYSTEM'
|
|
13
|
439 if opts.envshpath <> 'system': # need to parse out details for our tool_dependency
|
|
14
|
440 try: # fragile - depends on common naming convention as at jan 2015 = package_[interp]_v0_v1_v2... = version v0.v1.v2.. is in play
|
|
15
|
441 # this ONLY happens at tool generation by an admin - the generated tool always uses the default of system so path is from local env.sh
|
|
13
|
442 packdetails = opts.envshpath.split(os.path.sep)[-4:-1] # eg ['fubar', 'package_r_3_1_1', '63cdb9b2234c']
|
|
|
443 self.interpreter_owner = packdetails[0]
|
|
|
444 self.interpreter_pack = packdetails[1]
|
|
|
445 self.interpreter_name = packdetails[1].split('_')[1].upper()
|
|
|
446 self.interpreter_revision = packdetails[2]
|
|
14
|
447 self.interpreter_version = '.'.join(packdetails[1].split('_')[2:])
|
|
13
|
448 except:
|
|
|
449 pass
|
|
|
450 self.outFormats = opts.output_format
|
|
|
451 self.inputFormats = opts.input_formats
|
|
|
452 self.test1Output = '%s_test1_output.xls' % self.toolname
|
|
|
453 self.test1HTML = '%s_test1_output.html' % self.toolname
|
|
|
454
|
|
|
455 def makeXML(self):
|
|
|
456 """
|
|
|
457 Create a Galaxy xml tool wrapper for the new script as a string to write out
|
|
|
458 fixme - use templating or something less fugly than this example of what we produce
|
|
|
459
|
|
|
460 <tool id="reverse" name="reverse" version="0.01">
|
|
|
461 <description>a tabular file</description>
|
|
|
462 <command interpreter="python">
|
|
|
463 reverse.py --script_path "$runMe" --interpreter "python"
|
|
|
464 --tool_name "reverse" --input_tab "$input1" --output_tab "$output1"
|
|
|
465 </command>
|
|
|
466 <inputs>
|
|
|
467 <param name="input1" type="data" format="tabular" label="Select one or more input files from your history"/>
|
|
|
468 <param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
|
|
|
469 </inputs>
|
|
|
470 <outputs>
|
|
|
471 <data format="tabular" name="output1q" label="${job_name}"/>
|
|
|
472
|
|
|
473 </outputs>
|
|
|
474 <help>
|
|
|
475
|
|
|
476 **What it Does**
|
|
|
477
|
|
|
478 Reverse the columns in a tabular file
|
|
|
479
|
|
|
480 </help>
|
|
|
481 <configfiles>
|
|
|
482 <configfile name="runMe">
|
|
|
483
|
|
|
484 # reverse order of columns in a tabular file
|
|
|
485 import sys
|
|
|
486 inp = sys.argv[1]
|
|
|
487 outp = sys.argv[2]
|
|
|
488 i = open(inp,'r')
|
|
|
489 o = open(outp,'w')
|
|
|
490 for row in i:
|
|
|
491 rs = row.rstrip().split('\t')
|
|
|
492 rs.reverse()
|
|
|
493 o.write('\t'.join(rs))
|
|
|
494 o.write('\n')
|
|
|
495 i.close()
|
|
|
496 o.close()
|
|
|
497
|
|
|
498
|
|
|
499 </configfile>
|
|
|
500 </configfiles>
|
|
|
501 </tool>
|
|
|
502
|
|
|
503 """
|
|
|
504
|
|
|
505 # these templates need a dict with the right keys to match the parameters - outputs, help, code...
|
|
|
506
|
|
|
507 xdict = {}
|
|
|
508 xdict['additionalParams'] = ''
|
|
|
509 xdict['additionalInputs'] = ''
|
|
|
510 if self.opts.additional_parameters:
|
|
|
511 if self.opts.edit_additional_parameters: # add to new tool form with default value set to original value
|
|
|
512 xdict['additionalInputs'] = '\n'.join(['<param name="%s" value="%s" label="%s" help="%s" type="%s"/>' % \
|
|
|
513 (x.split(',')[0],html_escape(x.split(',')[1]),html_escape(x.split(',')[2]),html_escape(x.split(',')[3]), x.split(',')[4]) for x in self.opts.additional_parameters])
|
|
|
514 xdict['additionalParams'] = '\n'.join(['<param name="%s" value="%s" />' % (x.split(',')[0],html_escape(x.split(',')[1])) for x in self.opts.additional_parameters])
|
|
|
515 xdict['interpreter_owner'] = self.interpreter_owner
|
|
|
516 xdict['interpreter_version'] = self.interpreter_version
|
|
|
517 xdict['interpreter_pack'] = self.interpreter_pack
|
|
|
518 xdict['interpreter_name'] = self.interpreter_name
|
|
|
519 xdict['requirements'] = ''
|
|
|
520 if self.opts.include_dependencies == "yes":
|
|
|
521 if self.opts.envshpath <> 'system':
|
|
|
522 xdict['requirements'] = self.protorequirements_interpreter % xdict
|
|
|
523 else:
|
|
|
524 xdict['requirements'] = self.protorequirements
|
|
|
525 xdict['tool_version'] = self.opts.tool_version
|
|
|
526 xdict['test1HTML'] = self.test1HTML
|
|
|
527 xdict['test1Output'] = self.test1Output
|
|
|
528 xdict['test1Inputs'] = self.test1Inputs
|
|
|
529 if self.opts.make_HTML and self.opts.output_tab:
|
|
|
530 xdict['tooltests'] = self.tooltestsBoth % xdict
|
|
|
531 elif self.opts.make_HTML:
|
|
|
532 xdict['tooltests'] = self.tooltestsHTMLOnly % xdict
|
|
|
533 else:
|
|
|
534 xdict['tooltests'] = self.tooltestsTabOnly % xdict
|
|
|
535 xdict['script'] = self.escapedScript
|
|
|
536 # configfile is least painful way to embed script to avoid external dependencies
|
|
|
537 # but requires escaping of <, > and $ to avoid Mako parsing
|
|
|
538 if self.opts.help_text:
|
|
|
539 helptext = open(self.opts.help_text,'r').readlines()
|
|
|
540 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
|
|
|
541 xdict['help'] = ''.join([x for x in helptext])
|
|
|
542 else:
|
|
|
543 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
|
|
|
544 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
|
|
|
545 coda.append('\n')
|
|
|
546 coda.append(self.indentedScript)
|
|
|
547 coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
|
|
|
548 coda.append('See %s for details of that project' % (toolFactoryURL))
|
|
|
549 coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
|
|
|
550 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
|
|
|
551 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
|
|
|
552 if self.opts.tool_desc:
|
|
|
553 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
|
|
|
554 else:
|
|
|
555 xdict['tooldesc'] = ''
|
|
|
556 xdict['command_outputs'] = ''
|
|
|
557 xdict['outputs'] = ''
|
|
|
558 if self.opts.input_tab:
|
|
|
559 cins = ['\n',]
|
|
|
560 cins.append('--input_formats %s' % self.opts.input_formats)
|
|
|
561 cins.append('#for intab in $input1:')
|
|
|
562 cins.append('--input_tab "${intab},${intab.name}"')
|
|
|
563 cins.append('#end for\n')
|
|
|
564 xdict['command_inputs'] = '\n'.join(cins)
|
|
|
565 xdict['inputs'] = '''<param name="input_tab" multiple="true" type="data" format="%s" label="Select one or more %s input files from your history"
|
|
|
566 help="Multiple inputs may be selected assuming the script can deal with them..."/> \n''' % (self.inputFormats,self.inputFormats)
|
|
|
567 else:
|
|
|
568 xdict['command_inputs'] = '' # assume no input - eg a random data generator
|
|
|
569 xdict['inputs'] = ''
|
|
|
570 if (len(self.opts.additional_parameters) > 0):
|
|
|
571 cins = ['\n',]
|
|
|
572 for params in self.opts.additional_parameters:
|
|
|
573 psplit = params.split(',') # name,value...
|
|
|
574 psplit[3] = html_escape(psplit[3])
|
|
|
575 if self.opts.edit_additional_parameters:
|
|
|
576 psplit[1] = '$%s' % psplit[0] # replace with form value
|
|
|
577 else:
|
|
|
578 psplit[1] = html_escape(psplit[1]) # leave prespecified value
|
|
|
579 cins.append('--additional_parameters """%s"""' % ','.join(psplit))
|
|
|
580 xdict['command_inputs'] = '%s\n%s' % (xdict['command_inputs'],'\n'.join(cins))
|
|
|
581 xdict['inputs'] += '<param name="job_name" type="text" size="60" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
|
|
|
582 xdict['toolname'] = self.toolname
|
|
|
583 xdict['toolid'] = self.toolid
|
|
|
584 xdict['interpreter'] = self.opts.interpreter
|
|
|
585 xdict['scriptname'] = self.sfile
|
|
|
586 if self.opts.make_HTML:
|
|
|
587 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
|
|
|
588 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
|
|
|
589 else:
|
|
|
590 xdict['command_outputs'] += ' --output_dir "./"'
|
|
|
591 if self.opts.output_tab:
|
|
|
592 xdict['command_outputs'] += ' --output_tab "$output1"'
|
|
|
593 xdict['outputs'] += ' <data format="%s" name="output1" label="${job_name}"/>\n' % self.outFormats
|
|
|
594 xdict['command'] = self.newCommand % xdict
|
|
|
595 if self.opts.citations:
|
|
|
596 citationstext = open(self.opts.citations,'r').read()
|
|
|
597 citation_tuples = parse_citations(citationstext)
|
|
|
598 citations_xml = ""
|
|
|
599 for citation_type, citation_content in citation_tuples:
|
|
|
600 citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
|
|
|
601 citations_xml += citation_xml
|
|
|
602 xdict['citations'] = citations_xml
|
|
|
603 else:
|
|
|
604 xdict['citations'] = ""
|
|
|
605 xmls = self.newXML % xdict
|
|
|
606 xf = open(self.xmlfile,'w')
|
|
|
607 xf.write(xmls)
|
|
|
608 xf.write('\n')
|
|
|
609 xf.close()
|
|
|
610 # ready for the tarball
|
|
|
611
|
|
|
612
|
|
|
613 def makeTooltar(self):
|
|
|
614 """
|
|
|
615 a tool is a gz tarball with eg
|
|
|
616 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
617 """
|
|
|
618 retval = self.run()
|
|
|
619 if retval:
|
|
|
620 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
|
|
|
621 sys.exit(1)
|
|
|
622 tdir = self.toolname
|
|
|
623 os.mkdir(tdir)
|
|
|
624 self.makeXML()
|
|
|
625 if self.opts.help_text:
|
|
|
626 hlp = open(self.opts.help_text,'r').read()
|
|
|
627 else:
|
|
|
628 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
|
|
|
629 readme_dict = {'readme':hlp,'interpreter':self.opts.interpreter,'interpreter_version':self.interpreter_version,'interpreter_name':self.interpreter_name,
|
|
14
|
630 'interpreter_owner':self.interpreter_owner,'interpreter_pack':self.interpreter_pack}
|
|
13
|
631 if self.opts.include_dependencies == "yes":
|
|
|
632 if self.opts.envshpath == 'system':
|
|
|
633 tooldepcontent = self.toolhtmldepskel % readme_dict
|
|
|
634 else:
|
|
|
635 tooldepcontent = self.toolhtmldepinterpskel % readme_dict
|
|
|
636 else:
|
|
15
|
637 tooldepcontent = self.emptytoolhtmldepskel % readme_dict
|
|
13
|
638 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
|
|
|
639 depf.write(tooldepcontent)
|
|
|
640 depf.write('\n')
|
|
|
641 depf.close()
|
|
14
|
642 testdir = os.path.join(tdir,'test-data')
|
|
|
643 os.mkdir(testdir) # make tests directory
|
|
|
644 for i,intab in enumerate(self.opts.input_tab):
|
|
|
645 si = self.opts.input_tab[i]
|
|
|
646 if si.find(',') <> -1:
|
|
|
647 s = si.split(',')[0]
|
|
|
648 si = s
|
|
|
649 dest = os.path.join(testdir,os.path.basename(si))
|
|
|
650 if si <> dest:
|
|
|
651 shutil.copyfile(si,dest)
|
|
|
652 if self.opts.output_tab:
|
|
|
653 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
|
|
|
654 if self.opts.make_HTML:
|
|
|
655 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
|
|
|
656 if self.opts.output_dir:
|
|
|
657 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
|
|
13
|
658 outpif = '%s.py' % self.toolname # new name
|
|
|
659 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
|
|
|
660 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
|
|
|
661 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
|
|
|
662 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
|
|
|
663 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
|
|
|
664 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
|
|
|
665 notes += pi
|
|
|
666 outpi = open(outpiname,'w')
|
|
|
667 outpi.write(''.join(notes))
|
|
|
668 outpi.write('\n')
|
|
|
669 outpi.close()
|
|
|
670 stname = os.path.join(tdir,self.sfile)
|
|
|
671 if not os.path.exists(stname):
|
|
|
672 shutil.copyfile(self.sfile, stname)
|
|
|
673 xtname = os.path.join(tdir,self.xmlfile)
|
|
|
674 if not os.path.exists(xtname):
|
|
|
675 shutil.copyfile(self.xmlfile,xtname)
|
|
|
676 tarpath = "%s.tar.gz" % self.toolname
|
|
|
677 tar = tarfile.open(tarpath, "w:gz")
|
|
|
678 tar.add(tdir,arcname='%s' % self.toolname)
|
|
|
679 tar.close()
|
|
|
680 shutil.copyfile(tarpath,self.opts.new_tool)
|
|
|
681 shutil.rmtree(tdir)
|
|
|
682 ## TODO: replace with optional direct upload to local toolshed?
|
|
|
683 return retval
|
|
|
684
|
|
|
685
|
|
|
686 def compressPDF(self,inpdf=None,thumbformat='png'):
|
|
|
687 """need absolute path to pdf
|
|
|
688 note that GS gets confoozled if no $TMP or $TEMP
|
|
|
689 so we set it
|
|
|
690 """
|
|
|
691 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
|
|
|
692 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
|
|
|
693 sto = open(hlog,'a')
|
|
|
694 our_env = os.environ.copy()
|
|
|
695 our_tmp = our_env.get('TMP',None)
|
|
|
696 if not our_tmp:
|
|
|
697 our_tmp = our_env.get('TEMP',None)
|
|
|
698 if not (our_tmp and os.path.exists(our_tmp)):
|
|
|
699 newtmp = os.path.join(self.opts.output_dir,'tmp')
|
|
|
700 try:
|
|
|
701 os.mkdir(newtmp)
|
|
|
702 except:
|
|
|
703 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
|
|
|
704 our_env['TEMP'] = newtmp
|
|
|
705 if not self.temp_warned:
|
|
|
706 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
|
|
|
707 self.temp_warned = True
|
|
|
708 outpdf = '%s_compressed' % inpdf
|
|
|
709 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
|
|
|
710 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
711 retval1 = x.wait()
|
|
|
712 sto.close()
|
|
|
713 if retval1 == 0:
|
|
|
714 os.unlink(inpdf)
|
|
|
715 shutil.move(outpdf,inpdf)
|
|
|
716 os.unlink(hlog)
|
|
|
717 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
|
|
|
718 sto = open(hlog,'w')
|
|
|
719 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
|
|
|
720 if self.useGM:
|
|
|
721 cl2 = ['gm', 'convert', inpdf, outpng]
|
|
|
722 else: # assume imagemagick
|
|
|
723 cl2 = ['convert', inpdf, outpng]
|
|
|
724 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
725 retval2 = x.wait()
|
|
|
726 sto.close()
|
|
|
727 if retval2 == 0:
|
|
|
728 os.unlink(hlog)
|
|
|
729 retval = retval1 or retval2
|
|
|
730 return retval
|
|
|
731
|
|
|
732
|
|
|
733 def getfSize(self,fpath,outpath):
|
|
|
734 """
|
|
|
735 format a nice file size string
|
|
|
736 """
|
|
|
737 size = ''
|
|
|
738 fp = os.path.join(outpath,fpath)
|
|
|
739 if os.path.isfile(fp):
|
|
|
740 size = '0 B'
|
|
|
741 n = float(os.path.getsize(fp))
|
|
|
742 if n > 2**20:
|
|
|
743 size = '%1.1f MB' % (n/2**20)
|
|
|
744 elif n > 2**10:
|
|
|
745 size = '%1.1f KB' % (n/2**10)
|
|
|
746 elif n > 0:
|
|
|
747 size = '%d B' % (int(n))
|
|
|
748 return size
|
|
|
749
|
|
|
750 def makeHtml(self):
|
|
|
751 """ Create an HTML file content to list all the artifacts found in the output_dir
|
|
|
752 """
|
|
|
753
|
|
|
754 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
|
755 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
|
756 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
|
757 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
|
|
|
758 <title></title>
|
|
|
759 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
|
|
760 </head>
|
|
|
761 <body>
|
|
|
762 <div class="toolFormBody">
|
|
|
763 """
|
|
|
764 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/>"""
|
|
|
765 galhtmlpostfix = """</div></body></html>\n"""
|
|
|
766
|
|
|
767 flist = os.listdir(self.opts.output_dir)
|
|
|
768 flist = [x for x in flist if x <> 'Rplots.pdf']
|
|
|
769 flist.sort()
|
|
|
770 html = []
|
|
|
771 html.append(galhtmlprefix % progname)
|
|
|
772 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
|
|
|
773 fhtml = []
|
|
|
774 if len(flist) > 0:
|
|
|
775 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
|
|
|
776 logfiles.sort()
|
|
|
777 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
|
|
|
778 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
|
|
|
779 pdflist = []
|
|
|
780 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
|
|
|
781 for rownum,fname in enumerate(flist):
|
|
|
782 dname,e = os.path.splitext(fname)
|
|
|
783 sfsize = self.getfSize(fname,self.opts.output_dir)
|
|
|
784 if e.lower() == '.pdf' : # compress and make a thumbnail
|
|
|
785 thumb = '%s.%s' % (dname,self.thumbformat)
|
|
|
786 pdff = os.path.join(self.opts.output_dir,fname)
|
|
|
787 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
|
|
|
788 if retval == 0:
|
|
|
789 pdflist.append((fname,thumb))
|
|
|
790 else:
|
|
|
791 pdflist.append((fname,fname))
|
|
|
792 if (rownum+1) % 2 == 0:
|
|
|
793 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
794 else:
|
|
|
795 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
796 for logfname in logfiles: # expect at least tlog - if more
|
|
|
797 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
|
|
|
798 sectionname = 'All tool run'
|
|
|
799 if (len(logfiles) > 1):
|
|
|
800 sectionname = 'Other'
|
|
|
801 ourpdfs = pdflist
|
|
|
802 else:
|
|
|
803 realname = os.path.basename(logfname)
|
|
|
804 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
|
|
|
805 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
|
|
|
806 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
|
|
|
807 nacross = 1
|
|
|
808 npdf = len(ourpdfs)
|
|
|
809
|
|
|
810 if npdf > 0:
|
|
|
811 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
|
|
|
812 if int(nacross)**2 != npdf:
|
|
|
813 nacross += 1
|
|
|
814 nacross = int(nacross)
|
|
|
815 width = min(400,int(1200/nacross))
|
|
|
816 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
|
|
|
817 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
|
|
|
818 ntogo = nacross # counter for table row padding with empty cells
|
|
|
819 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
|
|
|
820 for i,paths in enumerate(ourpdfs):
|
|
|
821 fname,thumb = paths
|
|
|
822 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
|
|
|
823 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
|
|
|
824 if ((i+1) % nacross == 0):
|
|
|
825 s += '</tr>\n'
|
|
|
826 ntogo = 0
|
|
|
827 if i < (npdf - 1): # more to come
|
|
|
828 s += '<tr>'
|
|
|
829 ntogo = nacross
|
|
|
830 else:
|
|
|
831 ntogo -= 1
|
|
|
832 html.append(s)
|
|
|
833 if html[-1].strip().endswith('</tr>'):
|
|
|
834 html.append('</table></div>\n')
|
|
|
835 else:
|
|
|
836 if ntogo > 0: # pad
|
|
|
837 html.append('<td> </td>'*ntogo)
|
|
|
838 html.append('</tr></table></div>\n')
|
|
|
839 logt = open(logfname,'r').readlines()
|
|
|
840 logtext = [x for x in logt if x.strip() > '']
|
|
|
841 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
|
|
|
842 if len(logtext) > 1:
|
|
|
843 html.append('\n<pre>\n')
|
|
|
844 html += logtext
|
|
|
845 html.append('\n</pre>\n')
|
|
|
846 else:
|
|
|
847 html.append('%s is empty<br/>' % logfname)
|
|
|
848 if len(fhtml) > 0:
|
|
|
849 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')
|
|
|
850 fhtml.append('</table></div><br/>')
|
|
|
851 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
|
|
|
852 html += fhtml # add all non-pdf files to the end of the display
|
|
|
853 else:
|
|
|
854 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
|
|
|
855 html.append(galhtmlpostfix)
|
|
|
856 htmlf = file(self.opts.output_html,'w')
|
|
|
857 htmlf.write('\n'.join(html))
|
|
|
858 htmlf.write('\n')
|
|
|
859 htmlf.close()
|
|
|
860 self.html = html
|
|
|
861
|
|
|
862
|
|
|
863
|
|
|
864 def run(self):
|
|
|
865 """
|
|
15
|
866 Some devteam tools have this defensive stderr read so I'm keeping with the faith
|
|
|
867 Feel free to update.
|
|
13
|
868 """
|
|
|
869 if self.opts.envshpath <> 'system':
|
|
|
870 shell_source(self.opts.envshpath)
|
|
15
|
871 # this only happens at tool generation - the generated tool relies on the dependencies all being set up
|
|
|
872 # at toolshed installation by sourcing local env.sh
|
|
|
873 if self.opts.output_dir:
|
|
|
874 ste = open(self.elog,'wb')
|
|
|
875 sto = open(self.tlog,'wb')
|
|
|
876 s = ' '.join(self.cl)
|
|
|
877 sto.write('## Executing Toolfactory generated command line = %s\n' % s)
|
|
|
878 sto.flush()
|
|
|
879 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,cwd=self.opts.output_dir)
|
|
13
|
880 retval = p.wait()
|
|
15
|
881 sto.close()
|
|
|
882 ste.close()
|
|
|
883 tmp_stderr = open( self.elog, 'rb' )
|
|
|
884 err = ''
|
|
|
885 buffsize = 1048576
|
|
|
886 try:
|
|
|
887 while True:
|
|
|
888 err += tmp_stderr.read( buffsize )
|
|
|
889 if not err or len( stderr ) % buffsize != 0:
|
|
|
890 break
|
|
|
891 except OverflowError:
|
|
|
892 pass
|
|
|
893 tmp_stderr.close()
|
|
|
894 else:
|
|
|
895 p = subprocess.Popen(self.cl,shell=False)
|
|
|
896 retval = p.wait()
|
|
13
|
897 if self.opts.output_dir:
|
|
15
|
898 if retval <> 0 and err: # problem
|
|
|
899 print >> sys.stderr,err
|
|
13
|
900 if self.opts.make_HTML:
|
|
|
901 self.makeHtml()
|
|
|
902 return retval
|
|
15
|
903
|
|
13
|
904
|
|
|
905
|
|
|
906 def main():
|
|
|
907 u = """
|
|
|
908 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
909 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
910 </command>
|
|
|
911 """
|
|
|
912 op = optparse.OptionParser()
|
|
|
913 a = op.add_option
|
|
|
914 a('--script_path',default=None)
|
|
|
915 a('--tool_name',default=None)
|
|
|
916 a('--interpreter',default=None)
|
|
|
917 a('--output_dir',default='./')
|
|
|
918 a('--output_html',default=None)
|
|
|
919 a('--input_tab',default=[], action="append") # these are "galaxypath,metadataname" pairs
|
|
|
920 a("--input_formats",default="tabular")
|
|
|
921 a('--output_tab',default=None)
|
|
|
922 a('--output_format',default='tabular')
|
|
|
923 a('--user_email',default='Unknown')
|
|
|
924 a('--bad_user',default=None)
|
|
|
925 a('--make_Tool',default=None)
|
|
|
926 a('--make_HTML',default=None)
|
|
|
927 a('--help_text',default=None)
|
|
|
928 a('--tool_desc',default=None)
|
|
|
929 a('--new_tool',default=None)
|
|
|
930 a('--tool_version',default=None)
|
|
|
931 a('--include_dependencies',default="yes")
|
|
|
932 a('--citations',default=None)
|
|
|
933 a('--additional_parameters', dest='additional_parameters', action='append', default=[])
|
|
|
934 a('--edit_additional_parameters', action="store_true", default=False)
|
|
|
935 a('--envshpath',default="system")
|
|
|
936 opts, args = op.parse_args()
|
|
|
937 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)
|
|
|
938 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
|
|
|
939 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
|
|
|
940 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
|
|
|
941 if opts.output_dir:
|
|
|
942 try:
|
|
|
943 os.makedirs(opts.output_dir)
|
|
|
944 except:
|
|
|
945 pass
|
|
|
946 opts.input_tab = [x.replace('"','').replace("'",'') for x in opts.input_tab]
|
|
|
947 for i,x in enumerate(opts.additional_parameters): # remove quotes we need to deal with spaces in CL params
|
|
|
948 opts.additional_parameters[i] = opts.additional_parameters[i].replace('"','')
|
|
|
949 r = ScriptRunner(opts)
|
|
|
950 if opts.make_Tool:
|
|
|
951 retcode = r.makeTooltar()
|
|
|
952 else:
|
|
|
953 retcode = r.run()
|
|
|
954 os.unlink(r.sfile)
|
|
|
955 if retcode:
|
|
|
956 sys.exit(retcode) # indicate failure to job runner
|
|
|
957
|
|
|
958
|
|
|
959 if __name__ == "__main__":
|
|
|
960 main()
|
|
|
961
|
|
|
962
|
