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1 # CloudMapzfhommapping/CloudMapzfhommapping.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
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2 # to make a new Galaxy tool called CloudMapzfhommapping
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3 # User r.poole@ucl.ac.uk at 08/10/2014 18:05:06
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4 # rgToolFactory.py
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5 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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6 #
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7 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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8 #
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9 # all rights reserved
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10 # Licensed under the LGPL
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11 # suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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12 #
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13 # August 2014
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14 # merged John Chilton's citation addition and ideas from Marius van den Beek to enable arbitrary
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15 # data types for input and output - thanks!
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16 #
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17 # march 2014
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18 # 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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19 # grrrrr - night before a demo
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20 # added dependencies to a tool_dependencies.xml if html page generated so generated tool is properly portable
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21 #
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22 # added ghostscript and graphicsmagick as dependencies
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23 # 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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24 # errors ensued
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25 #
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26 # august 2013
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27 # found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
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28 #
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29 # july 2013
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30 # added ability to combine images and individual log files into html output
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31 # just make sure there's a log file foo.log and it will be output
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32 # together with all images named like "foo_*.pdf
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33 # otherwise old format for html
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34 #
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35 # January 2013
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36 # problem pointed out by Carlos Borroto
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37 # added escaping for <>$ - thought I did that ages ago...
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38 #
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39 # August 11 2012
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40 # changed to use shell=False and cl as a sequence
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41
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42 # This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
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43 # It also serves as the wrapper for the new tool.
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44 #
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45 # you paste and run your script
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46 # Only works for simple scripts that read one input from the history.
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47 # Optionally can write one new history dataset,
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48 # and optionally collect any number of outputs into links on an autogenerated HTML page.
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49
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50 # DO NOT install on a public or important site - please.
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51
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52 # installed generated tools are fine if the script is safe.
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53 # They just run normally and their user cannot do anything unusually insecure
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54 # but please, practice safe toolshed.
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55 # Read the fucking code before you install any tool
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56 # especially this one
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57
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58 # After you get the script working on some test data, you can
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59 # optionally generate a toolshed compatible gzip file
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60 # containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
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61 # safe and largely automated installation in a production Galaxy.
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62
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63 # If you opt for an HTML output, you get all the script outputs arranged
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64 # as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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65 # Ugly but really inexpensive.
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66 #
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67 # Patches appreciated please.
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68 #
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69 #
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70 # long route to June 2012 product
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71 # Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
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72 # derived from an integrated script model
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73 # called rgBaseScriptWrapper.py
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74 # Note to the unwary:
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75 # This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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76 # There is nothing stopping a malicious user doing whatever they choose
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77 # Extremely dangerous!!
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78 # Totally insecure. So, trusted users only
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79 #
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80 # preferred model is a developer using their throw away workstation instance - ie a private site.
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81 # 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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82 #
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83
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84 import sys
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85 import shutil
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86 import subprocess
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87 import os
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88 import time
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89 import tempfile
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90 import optparse
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91 import tarfile
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92 import re
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93 import shutil
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94 import math
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95
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96 progname = os.path.split(sys.argv[0])[1]
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97 myversion = 'V001.1 March 2014'
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98 verbose = False
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99 debug = False
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100 toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
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101
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102 # 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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103 # tool xml
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104 toolhtmldepskel = """<?xml version="1.0"?>
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105 <tool_dependency>
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106 <package name="ghostscript" version="9.10">
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107 <repository name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" />
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108 </package>
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109 <package name="graphicsmagick" version="1.3.18">
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110 <repository name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" />
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111 </package>
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112 <readme>
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113 %s
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114 </readme>
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115 </tool_dependency>
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116 """
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117
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118 protorequirements = """<requirements>
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119 <requirement type="package" version="9.10">ghostscript</requirement>
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120 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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121 </requirements>"""
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122
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123 def timenow():
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124 """return current time as a string
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125 """
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126 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
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127
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128 html_escape_table = {
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129 "&": "&",
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130 ">": ">",
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131 "<": "<",
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132 "$": "\$"
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133 }
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134
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135 def html_escape(text):
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136 """Produce entities within text."""
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137 return "".join(html_escape_table.get(c,c) for c in text)
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138
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139 def cmd_exists(cmd):
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140 return subprocess.call("type " + cmd, shell=True,
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141 stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
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142
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143
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144 def parse_citations(citations_text):
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145 """
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146 """
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147 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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148 citation_tuples = []
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149 for citation in citations:
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150 if citation.startswith("doi"):
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151 citation_tuples.append( ("doi", citation[len("doi"):].strip() ) )
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152 else:
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153 citation_tuples.append( ("bibtex", citation[len("bibtex"):].strip() ) )
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154 return citation_tuples
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155
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156
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157 class ScriptRunner:
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158 """class is a wrapper for an arbitrary script
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159 """
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160
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161 def __init__(self,opts=None,treatbashSpecial=True):
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162 """
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163 cleanup inputs, setup some outputs
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164
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165 """
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166 self.useGM = cmd_exists('gm')
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167 self.useIM = cmd_exists('convert')
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168 self.useGS = cmd_exists('gs')
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169 self.temp_warned = False # we want only one warning if $TMP not set
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170 self.treatbashSpecial = treatbashSpecial
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171 if opts.output_dir: # simplify for the tool tarball
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172 os.chdir(opts.output_dir)
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173 self.thumbformat = 'png'
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174 self.opts = opts
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175 self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
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176 self.toolid = self.toolname
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177 self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
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178 self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
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179 self.xmlfile = '%s.xml' % self.toolname
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180 s = open(self.opts.script_path,'r').readlines()
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181 s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
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182 self.script = '\n'.join(s)
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183 fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
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184 tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
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185 tscript.write(self.script)
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186 tscript.close()
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187 self.indentedScript = '\n'.join([' %s' % html_escape(x) for x in s]) # for restructured text in help
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188 self.escapedScript = '\n'.join([html_escape(x) for x in s])
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189 self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
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190 if opts.output_dir: # may not want these complexities
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191 self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
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192 art = '%s.%s' % (self.toolname,opts.interpreter)
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193 artpath = os.path.join(self.opts.output_dir,art) # need full path
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194 artifact = open(artpath,'w') # use self.sfile as script source for Popen
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195 artifact.write(self.script)
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196 artifact.close()
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197 self.cl = []
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198 self.html = []
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199 a = self.cl.append
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200 a(opts.interpreter)
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201 if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
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202 a(self.sfile)
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203 else:
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204 a('-') # stdin
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205 a(opts.input_tab)
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206 a(opts.output_tab)
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207 self.outputFormat = self.opts.output_format
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208 self.inputFormats = self.opts.input_formats
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209 self.test1Input = '%s_test1_input.xls' % self.toolname
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210 self.test1Output = '%s_test1_output.xls' % self.toolname
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211 self.test1HTML = '%s_test1_output.html' % self.toolname
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212
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213 def makeXML(self):
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214 """
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215 Create a Galaxy xml tool wrapper for the new script as a string to write out
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216 fixme - use templating or something less fugly than this example of what we produce
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217
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218 <tool id="reverse" name="reverse" version="0.01">
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219 <description>a tabular file</description>
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220 <command interpreter="python">
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221 reverse.py --script_path "$runMe" --interpreter "python"
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222 --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file"
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223 </command>
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224 <inputs>
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225 <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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226
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227 </inputs>
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228 <outputs>
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229 <data format="tabular" name="tab_file" label="${job_name}"/>
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230
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231 </outputs>
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232 <help>
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233
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234 **What it Does**
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235
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236 Reverse the columns in a tabular file
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237
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238 </help>
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239 <configfiles>
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240 <configfile name="runMe">
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241
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242 # reverse order of columns in a tabular file
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243 import sys
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244 inp = sys.argv[1]
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245 outp = sys.argv[2]
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246 i = open(inp,'r')
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247 o = open(outp,'w')
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248 for row in i:
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249 rs = row.rstrip().split('\t')
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250 rs.reverse()
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251 o.write('\t'.join(rs))
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252 o.write('\n')
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253 i.close()
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254 o.close()
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255
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256
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257 </configfile>
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258 </configfiles>
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259 </tool>
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260
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261 """
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262 newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
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263 %(tooldesc)s
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264 %(requirements)s
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265 <command interpreter="python">
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266 %(command)s
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267 </command>
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268 <inputs>
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269 %(inputs)s
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270 </inputs>
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271 <outputs>
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272 %(outputs)s
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273 </outputs>
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274 <configfiles>
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275 <configfile name="runMe">
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276 %(script)s
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277 </configfile>
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278 </configfiles>
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279
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280 %(tooltests)s
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281
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282 <help>
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283
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284 %(help)s
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285
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286 </help>
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287 <citations>
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288 %(citations)s
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289 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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290 </citations>
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291 </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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292
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293 newCommand="""
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294 %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s"
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295 --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s """
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296 # may NOT be an input or htmlout - appended later
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297 tooltestsTabOnly = """
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298 <tests>
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299 <test>
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300 <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
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301 <param name="job_name" value="test1"/>
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302 <param name="runMe" value="$runMe"/>
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303 <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s"/>
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304 </test>
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305 </tests>
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306 """
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307 tooltestsHTMLOnly = """
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308 <tests>
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309 <test>
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310 <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
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311 <param name="job_name" value="test1"/>
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312 <param name="runMe" value="$runMe"/>
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313 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
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314 </test>
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315 </tests>
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316 """
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317 tooltestsBoth = """<tests>
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318 <test>
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319 <param name="input1" value="%(test1Input)s" ftype="%(inputFormats)s"/>
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320 <param name="job_name" value="test1"/>
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321 <param name="runMe" value="$runMe"/>
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322 <output name="tab_file" file="%(test1Output)s" ftype="%(outputFormat)s" />
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323 <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
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324 </test>
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325 </tests>
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326 """
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327 xdict = {}
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328 xdict['outputFormat'] = self.outputFormat
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329 xdict['inputFormats'] = self.inputFormats
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330 xdict['requirements'] = ''
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331 if self.opts.make_HTML:
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332 if self.opts.include_dependencies == "yes":
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333 xdict['requirements'] = protorequirements
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334 xdict['tool_version'] = self.opts.tool_version
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335 xdict['test1Input'] = self.test1Input
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336 xdict['test1HTML'] = self.test1HTML
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337 xdict['test1Output'] = self.test1Output
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338 if self.opts.make_HTML and self.opts.output_tab <> 'None':
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339 xdict['tooltests'] = tooltestsBoth % xdict
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340 elif self.opts.make_HTML:
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341 xdict['tooltests'] = tooltestsHTMLOnly % xdict
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342 else:
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343 xdict['tooltests'] = tooltestsTabOnly % xdict
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344 xdict['script'] = self.escapedScript
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345 # configfile is least painful way to embed script to avoid external dependencies
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346 # but requires escaping of <, > and $ to avoid Mako parsing
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347 if self.opts.help_text:
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348 helptext = open(self.opts.help_text,'r').readlines()
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349 helptext = [html_escape(x) for x in helptext] # must html escape here too - thanks to Marius van den Beek
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350 xdict['help'] = ''.join([x for x in helptext])
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351 else:
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352 xdict['help'] = 'Please ask the tool author (%s) for help as none was supplied at tool generation\n' % (self.opts.user_email)
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353 if self.opts.citations:
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354 citationstext = open(self.opts.citations,'r').read()
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355 citation_tuples = parse_citations(citationstext)
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356 citations_xml = ""
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357 for citation_type, citation_content in citation_tuples:
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358 citation_xml = """<citation type="%s">%s</citation>""" % (citation_type, html_escape(citation_content))
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359 citations_xml += citation_xml
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360 xdict['citations'] = citations_xml
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361 else:
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362 xdict['citations'] = ""
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363 coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
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364 coda.append('\n')
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365 coda.append(self.indentedScript)
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366 coda.append('\n**Attribution**\nThis Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.\n' % (self.opts.user_email,timenow()))
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367 coda.append('See %s for details of that project' % (toolFactoryURL))
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368 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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369 coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573\n')
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370 xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
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371 if self.opts.tool_desc:
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372 xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
|
|
|
373 else:
|
|
|
374 xdict['tooldesc'] = ''
|
|
|
375 xdict['command_outputs'] = ''
|
|
|
376 xdict['outputs'] = ''
|
|
|
377 if self.opts.input_tab <> 'None':
|
|
|
378 xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
|
|
|
379 xdict['inputs'] = '<param name="input1" type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
|
|
|
380 else:
|
|
|
381 xdict['command_inputs'] = '' # assume no input - eg a random data generator
|
|
|
382 xdict['inputs'] = ''
|
|
|
383 xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
|
|
|
384 xdict['toolname'] = self.toolname
|
|
|
385 xdict['toolid'] = self.toolid
|
|
|
386 xdict['interpreter'] = self.opts.interpreter
|
|
|
387 xdict['scriptname'] = self.sfile
|
|
|
388 if self.opts.make_HTML:
|
|
|
389 xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"'
|
|
|
390 xdict['outputs'] += ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
|
|
|
391 else:
|
|
|
392 xdict['command_outputs'] += ' --output_dir "./"'
|
|
|
393 if self.opts.output_tab <> 'None':
|
|
|
394 xdict['command_outputs'] += ' --output_tab "$tab_file"'
|
|
|
395 xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outputFormat
|
|
|
396 xdict['command'] = newCommand % xdict
|
|
|
397 xmls = newXML % xdict
|
|
|
398 xf = open(self.xmlfile,'w')
|
|
|
399 xf.write(xmls)
|
|
|
400 xf.write('\n')
|
|
|
401 xf.close()
|
|
|
402 # ready for the tarball
|
|
|
403
|
|
|
404
|
|
|
405 def makeTooltar(self):
|
|
|
406 """
|
|
|
407 a tool is a gz tarball with eg
|
|
|
408 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
409 """
|
|
|
410 retval = self.run()
|
|
|
411 if retval:
|
|
|
412 print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
|
|
|
413 sys.exit(1)
|
|
|
414 tdir = self.toolname
|
|
|
415 os.mkdir(tdir)
|
|
|
416 self.makeXML()
|
|
|
417 if self.opts.make_HTML:
|
|
|
418 if self.opts.help_text:
|
|
|
419 hlp = open(self.opts.help_text,'r').read()
|
|
|
420 else:
|
|
|
421 hlp = 'Please ask the tool author for help as none was supplied at tool generation\n'
|
|
|
422 if self.opts.include_dependencies:
|
|
|
423 tooldepcontent = toolhtmldepskel % hlp
|
|
|
424 depf = open(os.path.join(tdir,'tool_dependencies.xml'),'w')
|
|
|
425 depf.write(tooldepcontent)
|
|
|
426 depf.write('\n')
|
|
|
427 depf.close()
|
|
|
428 if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
|
|
|
429 testdir = os.path.join(tdir,'test-data')
|
|
|
430 os.mkdir(testdir) # make tests directory
|
|
|
431 shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
|
|
|
432 if self.opts.output_tab <> 'None':
|
|
|
433 shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
|
|
|
434 if self.opts.make_HTML:
|
|
|
435 shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
|
|
|
436 if self.opts.output_dir:
|
|
|
437 shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
|
|
|
438 outpif = '%s.py' % self.toolname # new name
|
|
|
439 outpiname = os.path.join(tdir,outpif) # path for the tool tarball
|
|
|
440 pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
|
|
|
441 notes = ['# %s - a self annotated version of %s generated by running %s\n' % (outpiname,pyin,pyin),]
|
|
|
442 notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
|
|
|
443 notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
|
|
|
444 pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
|
|
|
445 notes += pi
|
|
|
446 outpi = open(outpiname,'w')
|
|
|
447 outpi.write(''.join(notes))
|
|
|
448 outpi.write('\n')
|
|
|
449 outpi.close()
|
|
|
450 stname = os.path.join(tdir,self.sfile)
|
|
|
451 if not os.path.exists(stname):
|
|
|
452 shutil.copyfile(self.sfile, stname)
|
|
|
453 xtname = os.path.join(tdir,self.xmlfile)
|
|
|
454 if not os.path.exists(xtname):
|
|
|
455 shutil.copyfile(self.xmlfile,xtname)
|
|
|
456 tarpath = "%s.gz" % self.toolname
|
|
|
457 tar = tarfile.open(tarpath, "w:gz")
|
|
|
458 tar.add(tdir,arcname=self.toolname)
|
|
|
459 tar.close()
|
|
|
460 shutil.copyfile(tarpath,self.opts.new_tool)
|
|
|
461 shutil.rmtree(tdir)
|
|
|
462 ## TODO: replace with optional direct upload to local toolshed?
|
|
|
463 return retval
|
|
|
464
|
|
|
465
|
|
|
466 def compressPDF(self,inpdf=None,thumbformat='png'):
|
|
|
467 """need absolute path to pdf
|
|
|
468 note that GS gets confoozled if no $TMP or $TEMP
|
|
|
469 so we set it
|
|
|
470 """
|
|
|
471 assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
|
|
|
472 hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
|
|
|
473 sto = open(hlog,'a')
|
|
|
474 our_env = os.environ.copy()
|
|
|
475 our_tmp = our_env.get('TMP',None)
|
|
|
476 if not our_tmp:
|
|
|
477 our_tmp = our_env.get('TEMP',None)
|
|
|
478 if not (our_tmp and os.path.exists(our_tmp)):
|
|
|
479 newtmp = os.path.join(self.opts.output_dir,'tmp')
|
|
|
480 try:
|
|
|
481 os.mkdir(newtmp)
|
|
|
482 except:
|
|
|
483 sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
|
|
|
484 our_env['TEMP'] = newtmp
|
|
|
485 if not self.temp_warned:
|
|
|
486 sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
|
|
|
487 self.temp_warned = True
|
|
|
488 outpdf = '%s_compressed' % inpdf
|
|
|
489 cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
|
|
|
490 x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
491 retval1 = x.wait()
|
|
|
492 sto.close()
|
|
|
493 if retval1 == 0:
|
|
|
494 os.unlink(inpdf)
|
|
|
495 shutil.move(outpdf,inpdf)
|
|
|
496 os.unlink(hlog)
|
|
|
497 hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
|
|
|
498 sto = open(hlog,'w')
|
|
|
499 outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
|
|
|
500 if self.useGM:
|
|
|
501 cl2 = ['gm', 'convert', inpdf, outpng]
|
|
|
502 else: # assume imagemagick
|
|
|
503 cl2 = ['convert', inpdf, outpng]
|
|
|
504 x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
|
|
|
505 retval2 = x.wait()
|
|
|
506 sto.close()
|
|
|
507 if retval2 == 0:
|
|
|
508 os.unlink(hlog)
|
|
|
509 retval = retval1 or retval2
|
|
|
510 return retval
|
|
|
511
|
|
|
512
|
|
|
513 def getfSize(self,fpath,outpath):
|
|
|
514 """
|
|
|
515 format a nice file size string
|
|
|
516 """
|
|
|
517 size = ''
|
|
|
518 fp = os.path.join(outpath,fpath)
|
|
|
519 if os.path.isfile(fp):
|
|
|
520 size = '0 B'
|
|
|
521 n = float(os.path.getsize(fp))
|
|
|
522 if n > 2**20:
|
|
|
523 size = '%1.1f MB' % (n/2**20)
|
|
|
524 elif n > 2**10:
|
|
|
525 size = '%1.1f KB' % (n/2**10)
|
|
|
526 elif n > 0:
|
|
|
527 size = '%d B' % (int(n))
|
|
|
528 return size
|
|
|
529
|
|
|
530 def makeHtml(self):
|
|
|
531 """ Create an HTML file content to list all the artifacts found in the output_dir
|
|
|
532 """
|
|
|
533
|
|
|
534 galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
|
535 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
|
536 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
|
537 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
|
|
|
538 <title></title>
|
|
|
539 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
|
|
540 </head>
|
|
|
541 <body>
|
|
|
542 <div class="toolFormBody">
|
|
|
543 """
|
|
|
544 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/>"""
|
|
|
545 galhtmlpostfix = """</div></body></html>\n"""
|
|
|
546
|
|
|
547 flist = os.listdir(self.opts.output_dir)
|
|
|
548 flist = [x for x in flist if x <> 'Rplots.pdf']
|
|
|
549 flist.sort()
|
|
|
550 html = []
|
|
|
551 html.append(galhtmlprefix % progname)
|
|
|
552 html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
|
|
|
553 fhtml = []
|
|
|
554 if len(flist) > 0:
|
|
|
555 logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
|
|
|
556 logfiles.sort()
|
|
|
557 logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
|
|
|
558 logfiles.append(os.path.abspath(self.tlog)) # make it the last one
|
|
|
559 pdflist = []
|
|
|
560 npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
|
|
|
561 for rownum,fname in enumerate(flist):
|
|
|
562 dname,e = os.path.splitext(fname)
|
|
|
563 sfsize = self.getfSize(fname,self.opts.output_dir)
|
|
|
564 if e.lower() == '.pdf' : # compress and make a thumbnail
|
|
|
565 thumb = '%s.%s' % (dname,self.thumbformat)
|
|
|
566 pdff = os.path.join(self.opts.output_dir,fname)
|
|
|
567 retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
|
|
|
568 if retval == 0:
|
|
|
569 pdflist.append((fname,thumb))
|
|
|
570 else:
|
|
|
571 pdflist.append((fname,fname))
|
|
|
572 if (rownum+1) % 2 == 0:
|
|
|
573 fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
574 else:
|
|
|
575 fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
|
|
|
576 for logfname in logfiles: # expect at least tlog - if more
|
|
|
577 if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
|
|
|
578 sectionname = 'All tool run'
|
|
|
579 if (len(logfiles) > 1):
|
|
|
580 sectionname = 'Other'
|
|
|
581 ourpdfs = pdflist
|
|
|
582 else:
|
|
|
583 realname = os.path.basename(logfname)
|
|
|
584 sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
|
|
|
585 ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
|
|
|
586 pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
|
|
|
587 nacross = 1
|
|
|
588 npdf = len(ourpdfs)
|
|
|
589
|
|
|
590 if npdf > 0:
|
|
|
591 nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
|
|
|
592 if int(nacross)**2 != npdf:
|
|
|
593 nacross += 1
|
|
|
594 nacross = int(nacross)
|
|
|
595 width = min(400,int(1200/nacross))
|
|
|
596 html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
|
|
|
597 html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
|
|
|
598 ntogo = nacross # counter for table row padding with empty cells
|
|
|
599 html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
|
|
|
600 for i,paths in enumerate(ourpdfs):
|
|
|
601 fname,thumb = paths
|
|
|
602 s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d"
|
|
|
603 alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
|
|
|
604 if ((i+1) % nacross == 0):
|
|
|
605 s += '</tr>\n'
|
|
|
606 ntogo = 0
|
|
|
607 if i < (npdf - 1): # more to come
|
|
|
608 s += '<tr>'
|
|
|
609 ntogo = nacross
|
|
|
610 else:
|
|
|
611 ntogo -= 1
|
|
|
612 html.append(s)
|
|
|
613 if html[-1].strip().endswith('</tr>'):
|
|
|
614 html.append('</table></div>\n')
|
|
|
615 else:
|
|
|
616 if ntogo > 0: # pad
|
|
|
617 html.append('<td> </td>'*ntogo)
|
|
|
618 html.append('</tr></table></div>\n')
|
|
|
619 logt = open(logfname,'r').readlines()
|
|
|
620 logtext = [x for x in logt if x.strip() > '']
|
|
|
621 html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
|
|
|
622 if len(logtext) > 1:
|
|
|
623 html.append('\n<pre>\n')
|
|
|
624 html += logtext
|
|
|
625 html.append('\n</pre>\n')
|
|
|
626 else:
|
|
|
627 html.append('%s is empty<br/>' % logfname)
|
|
|
628 if len(fhtml) > 0:
|
|
|
629 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')
|
|
|
630 fhtml.append('</table></div><br/>')
|
|
|
631 html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
|
|
|
632 html += fhtml # add all non-pdf files to the end of the display
|
|
|
633 else:
|
|
|
634 html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
|
|
|
635 html.append(galhtmlpostfix)
|
|
|
636 htmlf = file(self.opts.output_html,'w')
|
|
|
637 htmlf.write('\n'.join(html))
|
|
|
638 htmlf.write('\n')
|
|
|
639 htmlf.close()
|
|
|
640 self.html = html
|
|
|
641
|
|
|
642
|
|
|
643 def run(self):
|
|
|
644 """
|
|
|
645 scripts must be small enough not to fill the pipe!
|
|
|
646 """
|
|
|
647 if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
|
|
|
648 retval = self.runBash()
|
|
|
649 else:
|
|
|
650 if self.opts.output_dir:
|
|
|
651 ste = open(self.elog,'w')
|
|
|
652 sto = open(self.tlog,'w')
|
|
|
653 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
|
|
|
654 sto.flush()
|
|
|
655 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
|
|
|
656 else:
|
|
|
657 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
|
|
|
658 p.stdin.write(self.script)
|
|
|
659 p.stdin.close()
|
|
|
660 retval = p.wait()
|
|
|
661 if self.opts.output_dir:
|
|
|
662 sto.close()
|
|
|
663 ste.close()
|
|
|
664 err = open(self.elog,'r').readlines()
|
|
|
665 if retval <> 0 and err: # problem
|
|
|
666 print >> sys.stderr,err
|
|
|
667 if self.opts.make_HTML:
|
|
|
668 self.makeHtml()
|
|
|
669 return retval
|
|
|
670
|
|
|
671 def runBash(self):
|
|
|
672 """
|
|
|
673 cannot use - for bash so use self.sfile
|
|
|
674 """
|
|
|
675 if self.opts.output_dir:
|
|
|
676 s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
|
|
|
677 sto = open(self.tlog,'w')
|
|
|
678 sto.write(s)
|
|
|
679 sto.flush()
|
|
|
680 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
|
|
|
681 else:
|
|
|
682 p = subprocess.Popen(self.cl,shell=False)
|
|
|
683 retval = p.wait()
|
|
|
684 if self.opts.output_dir:
|
|
|
685 sto.close()
|
|
|
686 if self.opts.make_HTML:
|
|
|
687 self.makeHtml()
|
|
|
688 return retval
|
|
|
689
|
|
|
690
|
|
|
691 def main():
|
|
|
692 u = """
|
|
|
693 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
694 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
695 </command>
|
|
|
696 """
|
|
|
697 op = optparse.OptionParser()
|
|
|
698 a = op.add_option
|
|
|
699 a('--script_path',default=None)
|
|
|
700 a('--tool_name',default=None)
|
|
|
701 a('--interpreter',default=None)
|
|
|
702 a('--output_dir',default='./')
|
|
|
703 a('--output_html',default=None)
|
|
|
704 a('--input_tab',default="None")
|
|
|
705 a('--input_formats',default="tabular,text")
|
|
|
706 a('--output_tab',default="None")
|
|
|
707 a('--output_format',default="tabular")
|
|
|
708 a('--user_email',default='Unknown')
|
|
|
709 a('--bad_user',default=None)
|
|
|
710 a('--make_Tool',default=None)
|
|
|
711 a('--make_HTML',default=None)
|
|
|
712 a('--help_text',default=None)
|
|
|
713 a('--citations',default=None)
|
|
|
714 a('--tool_desc',default=None)
|
|
|
715 a('--new_tool',default=None)
|
|
|
716 a('--tool_version',default=None)
|
|
|
717 a('--include_dependencies',default=None)
|
|
|
718 opts, args = op.parse_args()
|
|
|
719 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)
|
|
|
720 assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
|
|
|
721 assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
|
|
|
722 assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
|
|
|
723 if opts.output_dir:
|
|
|
724 try:
|
|
|
725 os.makedirs(opts.output_dir)
|
|
|
726 except:
|
|
|
727 pass
|
|
|
728 r = ScriptRunner(opts)
|
|
|
729 if opts.make_Tool:
|
|
|
730 retcode = r.makeTooltar()
|
|
|
731 else:
|
|
|
732 retcode = r.run()
|
|
|
733 os.unlink(r.sfile)
|
|
|
734 if retcode:
|
|
|
735 sys.exit(retcode) # indicate failure to job runner
|
|
|
736
|
|
|
737
|
|
|
738 if __name__ == "__main__":
|
|
|
739 main()
|
|
|
740
|
|
|
741
|
|
|
742
|
