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1 #!/usr/bin/env python
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30
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2 # rgToolFactory.py
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3 # see https://github.com/fubar2/toolfactory
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4 #
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5 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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6 #
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7 # all rights reserved
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8 # Licensed under the LGPL
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9 # suggestions for improvement and bug fixes welcome at https://github.com/fubar2/toolfactory
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10 #
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11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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12 # Decided to
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13 # 1. Fix the toolfactory so it works - done for simplest case
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14 # 2. Fix planemo so the toolfactory function works
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15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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16 #
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17 # removed all the old complications including making the new tool use this same script
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18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
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19 # No support for automatic HTML file creation from arbitrary outputs
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39
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20 # essential problem is to create two command lines - one for the tool xml and a different
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21 # one to run the executable with the supplied test data and settings
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22 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
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23
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30
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24
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36
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25
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26 import argparse
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27 import logging
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28 import os
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29 import re
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30 import shutil
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30
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31 import subprocess
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36
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32 import sys
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33 import tarfile
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34 import tempfile
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30
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35 import time
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36
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36
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30
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37 import galaxyxml.tool as gxt
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38 import galaxyxml.tool.parameters as gxtp
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38
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39
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36
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40 import lxml
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30
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41
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36
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42 myversion = "V2.1 July 2020"
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30
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43 verbose = True
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44 debug = True
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45 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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46 ourdelim = "~~~"
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47
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48 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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49 # ~~~$input_help"
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50 IPATHPOS = 0
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51 ICLPOS = 1
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52 IFMTPOS = 2
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53 ILABPOS = 3
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54 IHELPOS = 4
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55 IOCLPOS = 5
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56
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57 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL
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58 ONAMEPOS = 0
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59 OFMTPOS = 1
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60 OCLPOS = 2
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61 OOCLPOS = 3
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62
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63 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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64 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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65 ANAMEPOS = 0
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66 AVALPOS = 1
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67 ALABPOS = 2
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68 AHELPPOS = 3
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69 ATYPEPOS = 4
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70 ACLPOS = 5
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71 AOVERPOS = 6
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72 AOCLPOS = 7
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73
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74
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75 foo = len(lxml.__version__)
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76 # fug you, flake8. Say my name!
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77
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78 def timenow():
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79 """return current time as a string
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80 """
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81 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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82
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83
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84 def quote_non_numeric(s):
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85 """return a prequoted string for non-numerics
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86 useful for perl and Rscript parameter passing?
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87 """
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88 try:
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89 _ = float(s)
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90 return s
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91 except ValueError:
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92 return '"%s"' % s
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93
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94
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95 html_escape_table = {"&": "&", ">": ">", "<": "<", "$": r"\$"}
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96
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97
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98 def html_escape(text):
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99 """Produce entities within text."""
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100 return "".join(html_escape_table.get(c, c) for c in text)
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101
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102
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103 def html_unescape(text):
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104 """Revert entities within text. Multiple character targets so use replace"""
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105 t = text.replace("&", "&")
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106 t = t.replace(">", ">")
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107 t = t.replace("<", "<")
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108 t = t.replace("\\$", "$")
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109 return t
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110
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111
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112 def parse_citations(citations_text):
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113 """
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114 """
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115 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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116 citation_tuples = []
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117 for citation in citations:
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118 if citation.startswith("doi"):
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119 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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120 else:
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121 citation_tuples.append(
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122 ("bibtex", citation[len("bibtex") :].strip())
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123 )
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124 return citation_tuples
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125
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126
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127 class ScriptRunner:
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128 """Wrapper for an arbitrary script
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129 uses galaxyxml
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130
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131 """
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132
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133 def __init__(self, args=None):
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134 """
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135 prepare command line cl for running the tool here
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136 and prepare elements needed for galaxyxml tool generation
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137 """
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138
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139 self.infiles = [x.split(ourdelim) for x in args.input_files]
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140 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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141 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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142 self.args = args
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143 self.cleanuppar()
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144 self.lastclredirect = None
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145 self.lastxclredirect = None
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146 self.cl = []
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147 self.xmlcl = []
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148 self.is_positional = self.args.parampass == "positional"
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149 aCL = self.cl.append
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150 assert args.parampass in [
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151 "0",
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152 "argparse",
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153 "positional",
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154 ], 'Parameter passing in args.parampass must be "0","positional" or "argparse"'
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155 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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156 self.tool_id = self.tool_name
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157 if self.args.interpreter_name:
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158 exe = "$runMe"
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159 else:
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160 exe = self.args.exe_package
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161 assert (
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162 exe is not None
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163 ), "No interpeter or executable passed in - nothing to run so cannot build"
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164 self.tool = gxt.Tool(
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165 self.args.tool_name,
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166 self.tool_id,
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167 self.args.tool_version,
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168 self.args.tool_desc,
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169 exe,
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170 )
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171 self.tinputs = gxtp.Inputs()
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172 self.toutputs = gxtp.Outputs()
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173 self.testparam = []
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174 if (
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175 self.args.runmode == "Executable" or self.args.runmode == "system"
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176 ): # binary - no need
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177 aCL(self.args.exe_package) # this little CL will just run
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178 else:
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179 self.prepScript()
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180 self.elog = "%s_error_log.txt" % self.tool_name
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181 self.tlog = "%s_runner_log.txt" % self.tool_name
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182
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183 if self.args.parampass == "0":
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184 self.clsimple()
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185 else:
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186 clsuffix = []
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187 xclsuffix = []
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188 for i, p in enumerate(self.infiles):
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189 if p[IOCLPOS] == "STDIN":
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190 appendme = [
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191 p[IOCLPOS],
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192 p[ICLPOS],
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193 p[IPATHPOS],
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194 "< %s" % p[IPATHPOS],
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195 ]
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196 xappendme = [
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197 p[IOCLPOS],
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198 p[ICLPOS],
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199 p[IPATHPOS],
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200 "< $%s" % p[ICLPOS],
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201 ]
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202 else:
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203 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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204 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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205 clsuffix.append(appendme)
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206 xclsuffix.append(xappendme)
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207 # print('##infile i=%d, appendme=%s' % (i,appendme))
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208 for i, p in enumerate(self.outfiles):
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209 if p[OOCLPOS] == "STDOUT":
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210 self.lastclredirect = [">", p[ONAMEPOS]]
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211 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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212 else:
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213 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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214 xclsuffix.append(
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215 [p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""]
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216 )
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217 for p in self.addpar:
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218 clsuffix.append(
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219 [p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]]
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220 )
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221 xclsuffix.append(
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222 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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223 )
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224 clsuffix.sort()
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225 xclsuffix.sort()
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226 self.xclsuffix = xclsuffix
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227 self.clsuffix = clsuffix
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228 if self.args.parampass == "positional":
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229 self.clpositional()
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230 else:
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231 self.clargparse()
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232
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233 def prepScript(self):
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234 aCL = self.cl.append
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235 rx = open(self.args.script_path, "r").readlines()
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236 rx = [x.rstrip() for x in rx]
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237 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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238 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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239 self.script = "\n".join(rx)
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240 fhandle, self.sfile = tempfile.mkstemp(
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241 prefix=self.tool_name, suffix="_%s" % (self.args.interpreter_name)
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242 )
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243 tscript = open(self.sfile, "w")
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244 tscript.write(self.script)
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245 tscript.close()
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246 self.indentedScript = " %s" % "\n".join(
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247 [" %s" % html_escape(x) for x in rx]
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248 )
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249 self.escapedScript = "%s" % "\n".join(
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250 [" %s" % html_escape(x) for x in rx]
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251 )
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252 art = "%s.%s" % (self.tool_name, self.args.interpreter_name)
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253 artifact = open(art, "wb")
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254 if self.args.interpreter_name == "python":
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255 artifact.write(bytes("#!/usr/bin/env python\n", "utf8"))
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256 artifact.write(bytes(self.script, "utf8"))
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257 artifact.close()
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258 aCL(self.args.interpreter_name)
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259 aCL(self.sfile)
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260
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261 def cleanuppar(self):
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262 """ positional parameters are complicated by their numeric ordinal"""
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263 for i, p in enumerate(self.infiles):
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264 if self.args.parampass == "positional":
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265 assert p[ICLPOS].isdigit(), (
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266 "Positional parameters must be ordinal integers - got %s for %s"
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267 % (p[ICLPOS], p[ILABPOS])
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268 )
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269 p.append(p[ICLPOS])
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270 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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271 scl = "input%d" % (i + 1)
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272 p[ICLPOS] = scl
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273 self.infiles[i] = p
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274 for i, p in enumerate(
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275 self.outfiles
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276 ): # trying to automagically gather using extensions
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277 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
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278 assert p[OCLPOS].isdigit(), (
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279 "Positional parameters must be ordinal integers - got %s for %s"
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280 % (p[OCLPOS], p[ONAMEPOS])
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281 )
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282 p.append(p[OCLPOS])
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283 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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284 scl = p[ONAMEPOS]
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285 p[OCLPOS] = scl
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286 self.outfiles[i] = p
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287 for i, p in enumerate(self.addpar):
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288 if self.args.parampass == "positional":
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289 assert p[ACLPOS].isdigit(), (
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290 "Positional parameters must be ordinal integers - got %s for %s"
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291 % (p[ACLPOS], p[ANAMEPOS])
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292 )
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293 p.append(p[ACLPOS])
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294 if p[ACLPOS].isdigit():
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295 scl = "input%s" % p[ACLPOS]
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296 p[ACLPOS] = scl
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297 self.addpar[i] = p
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298
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299 def clsimple(self):
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300 """ no parameters - uses < and > for i/o
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301 """
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302 aCL = self.cl.append
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303 aCL("<")
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304 aCL(self.infiles[0][IPATHPOS])
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305 aCL(">")
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306 aCL(self.outfiles[0][OCLPOS])
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307 aXCL = self.xmlcl.append
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308 aXCL("<")
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309 aXCL("$%s" % self.infiles[0][ICLPOS])
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310 aXCL(">")
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311 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
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312
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313 def clpositional(self):
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314 # inputs in order then params
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315 aCL = self.cl.append
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316 for (o_v, k, v, koverride) in self.clsuffix:
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317 if " " in v:
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318 aCL("%s" % v)
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319 else:
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320 aCL(v)
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321 aXCL = self.xmlcl.append
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322 for (o_v, k, v, koverride) in self.xclsuffix:
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323 aXCL(v)
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324 if self.lastxclredirect:
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325 aXCL(self.lastxclredirect[0])
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326 aXCL(self.lastxclredirect[1])
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327
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328 def clargparse(self):
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329 """ argparse style
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330 """
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331 aCL = self.cl.append
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332 aXCL = self.xmlcl.append
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333 # inputs then params in argparse named form
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334 for (o_v, k, v, koverride) in self.xclsuffix:
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335 if koverride > "":
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336 k = koverride
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337 elif len(k.strip()) == 1:
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338 k = "-%s" % k
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34
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339 else:
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340 k = "--%s" % k
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341 aXCL(k)
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342 aXCL(v)
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38
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343 for (o_v, k, v, koverride) in self.clsuffix:
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344 if koverride > "":
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345 k = koverride
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346 elif len(k.strip()) == 1:
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347 k = "-%s" % k
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348 else:
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349 k = "--%s" % k
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350 aCL(k)
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351 aCL(v)
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352
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36
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353 def getNdash(self, newname):
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354 if self.is_positional:
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355 ndash = 0
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356 else:
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357 ndash = 2
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358 if len(newname) < 2:
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359 ndash = 1
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360 return ndash
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30
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361
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36
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362 def doXMLparam(self):
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363 """flake8 made me do this..."""
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364 for p in self.outfiles:
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365 newname, newfmt, newcl, oldcl = p
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366 ndash = self.getNdash(newcl)
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367 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
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368 aparm.positional = self.is_positional
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369 if self.is_positional:
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370 if oldcl == "STDOUT":
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371 aparm.positional = 9999999
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372 aparm.command_line_override = "> $%s" % newcl
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373 else:
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374 aparm.positional = int(oldcl)
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375 aparm.command_line_override = "$%s" % newcl
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376 self.toutputs.append(aparm)
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38
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377 tp = gxtp.TestOutput(
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378 name=newcl, value="%s_sample" % newcl, format=newfmt
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379 )
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36
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380 self.testparam.append(tp)
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381 for p in self.infiles:
|
|
|
382 newname = p[ICLPOS]
|
|
|
383 newfmt = p[IFMTPOS]
|
|
|
384 ndash = self.getNdash(newname)
|
|
|
385 if not len(p[ILABPOS]) > 0:
|
|
|
386 alab = p[ICLPOS]
|
|
|
387 else:
|
|
|
388 alab = p[ILABPOS]
|
|
|
389 aninput = gxtp.DataParam(
|
|
|
390 newname,
|
|
|
391 optional=False,
|
|
|
392 label=alab,
|
|
|
393 help=p[IHELPOS],
|
|
|
394 format=newfmt,
|
|
|
395 multiple=False,
|
|
|
396 num_dashes=ndash,
|
|
|
397 )
|
|
|
398 aninput.positional = self.is_positional
|
|
|
399 self.tinputs.append(aninput)
|
|
|
400 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
401 self.testparam.append(tparm)
|
|
|
402 for p in self.addpar:
|
|
38
|
403 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
|
|
36
|
404 if not len(newlabel) > 0:
|
|
|
405 newlabel = newname
|
|
|
406 ndash = self.getNdash(newname)
|
|
|
407 if newtype == "text":
|
|
|
408 aparm = gxtp.TextParam(
|
|
|
409 newname,
|
|
|
410 label=newlabel,
|
|
|
411 help=newhelp,
|
|
|
412 value=newval,
|
|
|
413 num_dashes=ndash,
|
|
|
414 )
|
|
|
415 elif newtype == "integer":
|
|
|
416 aparm = gxtp.IntegerParam(
|
|
|
417 newname,
|
|
|
418 label=newname,
|
|
|
419 help=newhelp,
|
|
|
420 value=newval,
|
|
|
421 num_dashes=ndash,
|
|
|
422 )
|
|
|
423 elif newtype == "float":
|
|
|
424 aparm = gxtp.FloatParam(
|
|
|
425 newname,
|
|
|
426 label=newname,
|
|
|
427 help=newhelp,
|
|
|
428 value=newval,
|
|
|
429 num_dashes=ndash,
|
|
|
430 )
|
|
|
431 else:
|
|
|
432 raise ValueError(
|
|
|
433 'Unrecognised parameter type "%s" for\
|
|
|
434 additional parameter %s in makeXML'
|
|
|
435 % (newtype, newname)
|
|
|
436 )
|
|
|
437 aparm.positional = self.is_positional
|
|
|
438 if self.is_positional:
|
|
|
439 aninput.positional = int(oldcl)
|
|
|
440 self.tinputs.append(aparm)
|
|
|
441 self.tparm = gxtp.TestParam(newname, value=newval)
|
|
|
442 self.testparam.append(tparm)
|
|
|
443
|
|
|
444 def doNoXMLparam(self):
|
|
|
445 alab = self.infiles[0][ILABPOS]
|
|
|
446 if len(alab) == 0:
|
|
|
447 alab = self.infiles[0][ICLPOS]
|
|
|
448 max1s = (
|
|
|
449 "Maximum one input if parampass is 0 - more than one input files supplied - %s"
|
|
|
450 % str(self.infiles)
|
|
|
451 )
|
|
|
452 assert len(self.infiles) == 1, max1s
|
|
|
453 newname = self.infiles[0][ICLPOS]
|
|
|
454 aninput = gxtp.DataParam(
|
|
|
455 newname,
|
|
|
456 optional=False,
|
|
|
457 label=alab,
|
|
|
458 help=self.infiles[0][IHELPOS],
|
|
|
459 format=self.infiles[0][IFMTPOS],
|
|
|
460 multiple=False,
|
|
|
461 num_dashes=0,
|
|
|
462 )
|
|
|
463 aninput.command_line_override = "< $%s" % newname
|
|
|
464 aninput.positional = self.is_positional
|
|
|
465 self.tinputs.append(aninput)
|
|
|
466 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
467 self.testparam.append(tp)
|
|
|
468 newname = self.outfiles[0][OCLPOS]
|
|
|
469 newfmt = self.outfiles[0][OFMTPOS]
|
|
|
470 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
|
|
|
471 anout.command_line_override = "> $%s" % newname
|
|
|
472 anout.positional = self.is_positional
|
|
|
473 self.toutputs.append(anout)
|
|
38
|
474 tp = gxtp.TestOutput(
|
|
|
475 name=newname, value="%s_sample" % newname, format=newfmt
|
|
|
476 )
|
|
36
|
477 self.testparam.append(tp)
|
|
30
|
478
|
|
|
479 def makeXML(self):
|
|
|
480 """
|
|
|
481 Create a Galaxy xml tool wrapper for the new script
|
|
|
482 Uses galaxyhtml
|
|
|
483 Hmmm. How to get the command line into correct order...
|
|
|
484 """
|
|
36
|
485 self.tool.command_line_override = self.xmlcl
|
|
30
|
486 if self.args.interpreter_name:
|
|
38
|
487 self.tool.interpreter = self.args.interpreter_name
|
|
30
|
488 if self.args.help_text:
|
|
36
|
489 helptext = open(self.args.help_text, "r").readlines()
|
|
30
|
490 helptext = [html_escape(x) for x in helptext]
|
|
36
|
491 self.tool.help = "".join([x for x in helptext])
|
|
30
|
492 else:
|
|
36
|
493 self.tool.help = (
|
|
|
494 "Please ask the tool author (%s) for help \
|
|
|
495 as none was supplied at tool generation\n"
|
|
|
496 % (self.args.user_email)
|
|
|
497 )
|
|
|
498 self.tool.version_command = None # do not want
|
|
30
|
499 requirements = gxtp.Requirements()
|
|
36
|
500
|
|
30
|
501 if self.args.interpreter_name:
|
|
36
|
502 if self.args.interpreter_name == "python":
|
|
|
503 requirements.append(
|
|
38
|
504 gxtp.Requirement(
|
|
|
505 "package", "python", self.args.interpreter_version
|
|
|
506 )
|
|
36
|
507 )
|
|
|
508 elif self.args.interpreter_name not in ["bash", "sh"]:
|
|
|
509 requirements.append(
|
|
|
510 gxtp.Requirement(
|
|
|
511 "package",
|
|
|
512 self.args.interpreter_name,
|
|
|
513 self.args.interpreter_version,
|
|
|
514 )
|
|
|
515 )
|
|
30
|
516 else:
|
|
|
517 if self.args.exe_package and self.args.parampass != "system":
|
|
36
|
518 requirements.append(
|
|
|
519 gxtp.Requirement(
|
|
38
|
520 "package",
|
|
|
521 self.args.exe_package,
|
|
|
522 self.args.exe_package_version,
|
|
36
|
523 )
|
|
|
524 )
|
|
|
525 self.tool.requirements = requirements
|
|
|
526 if self.args.parampass == "0":
|
|
38
|
527 self.doNoXMLparam()
|
|
30
|
528 else:
|
|
38
|
529 self.doXMLparam()
|
|
36
|
530 self.tool.outputs = self.toutputs
|
|
|
531 self.tool.inputs = self.tinputs
|
|
|
532 if self.args.runmode not in ["Executable", "system"]:
|
|
30
|
533 configfiles = gxtp.Configfiles()
|
|
|
534 configfiles.append(gxtp.Configfile(name="runMe", text=self.script))
|
|
36
|
535 self.tool.configfiles = configfiles
|
|
30
|
536 tests = gxtp.Tests()
|
|
|
537 test_a = gxtp.Test()
|
|
36
|
538 for tp in self.testparam:
|
|
30
|
539 test_a.append(tp)
|
|
|
540 tests.append(test_a)
|
|
36
|
541 self.tool.tests = tests
|
|
|
542 self.tool.add_comment(
|
|
|
543 "Created by %s at %s using the Galaxy Tool Factory."
|
|
|
544 % (self.args.user_email, timenow())
|
|
|
545 )
|
|
|
546 self.tool.add_comment("Source in git at: %s" % (toolFactoryURL))
|
|
|
547 self.tool.add_comment(
|
|
39
|
548 "Cite: Creating re-usable tools from scripts doi: \
|
|
|
549 10.1093/bioinformatics/bts573"
|
|
36
|
550 )
|
|
|
551 exml = self.tool.export()
|
|
38
|
552 xf = open('%s.xml' % self.tool_name, "w")
|
|
30
|
553 xf.write(exml)
|
|
36
|
554 xf.write("\n")
|
|
30
|
555 xf.close()
|
|
|
556 # ready for the tarball
|
|
|
557
|
|
|
558 def makeTooltar(self):
|
|
|
559 """
|
|
|
560 a tool is a gz tarball with eg
|
|
|
561 /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
|
|
|
562 NOTE names for test inputs and outputs are munged here so must
|
|
|
563 correspond to actual input and output names used on the generated cl
|
|
|
564 """
|
|
|
565 retval = self.run()
|
|
|
566 if retval:
|
|
38
|
567 sys.stderr.write(
|
|
|
568 "## Run failed. Cannot build yet. Please fix and retry"
|
|
|
569 )
|
|
30
|
570 sys.exit(1)
|
|
36
|
571 tdir = "tfout"
|
|
30
|
572 if not os.path.exists(tdir):
|
|
|
573 os.mkdir(tdir)
|
|
|
574 self.makeXML()
|
|
36
|
575 testdir = os.path.join(tdir, "test-data")
|
|
30
|
576 if not os.path.exists(testdir):
|
|
|
577 os.mkdir(testdir) # make tests directory
|
|
|
578 for p in self.infiles:
|
|
|
579 pth = p[IPATHPOS]
|
|
36
|
580 dest = os.path.join(testdir, "%s_sample" % p[ICLPOS])
|
|
30
|
581 shutil.copyfile(pth, dest)
|
|
|
582 for p in self.outfiles:
|
|
|
583 pth = p[OCLPOS]
|
|
36
|
584 if p[OOCLPOS] == "STDOUT" or self.args.parampass == "0":
|
|
30
|
585 pth = p[ONAMEPOS]
|
|
36
|
586 dest = os.path.join(testdir, "%s_sample" % p[ONAMEPOS])
|
|
30
|
587 shutil.copyfile(pth, dest)
|
|
|
588 dest = os.path.join(tdir, p[ONAMEPOS])
|
|
36
|
589 shutil.copyfile(pth, dest)
|
|
30
|
590 else:
|
|
|
591 pth = p[OCLPOS]
|
|
36
|
592 dest = os.path.join(testdir, "%s_sample" % p[OCLPOS])
|
|
30
|
593 shutil.copyfile(pth, dest)
|
|
|
594 dest = os.path.join(tdir, p[OCLPOS])
|
|
36
|
595 shutil.copyfile(pth, dest)
|
|
30
|
596
|
|
|
597 if os.path.exists(self.tlog) and os.stat(self.tlog).st_size > 0:
|
|
38
|
598 shutil.copyfile(self.tlog, os.path.join(testdir, "test1_log_outfiletxt"))
|
|
36
|
599 if self.args.runmode not in ["Executable", "system"]:
|
|
|
600 stname = os.path.join(tdir, "%s" % (self.sfile))
|
|
30
|
601 if not os.path.exists(stname):
|
|
|
602 shutil.copyfile(self.sfile, stname)
|
|
38
|
603 xreal = '%s.xml' % self.tool_name
|
|
|
604 xout = os.path.join(tdir,xreal)
|
|
|
605 shutil.copyfile(xreal, xout)
|
|
36
|
606 tarpath = "toolfactory_%s.tgz" % self.tool_name
|
|
|
607 tf = tarfile.open(tarpath, "w:gz")
|
|
|
608 tf.add(name=tdir, arcname=self.tool_name)
|
|
30
|
609 tf.close()
|
|
|
610 shutil.copyfile(tarpath, self.args.new_tool)
|
|
38
|
611 shutil.copyfile(xreal,"tool_xml.txt")
|
|
|
612 repdir = "TF_run_report_tempdir"
|
|
|
613 if not os.path.exists(repdir):
|
|
|
614 os.mkdir(repdir)
|
|
|
615 repoutnames = [x[OCLPOS] for x in self.outfiles]
|
|
|
616 with os.scandir('.') as outs:
|
|
|
617 for entry in outs:
|
|
|
618 if entry.name.endswith('.tgz') or not entry.is_file():
|
|
|
619 continue
|
|
|
620 if entry.name in repoutnames:
|
|
|
621 shutil.copyfile(entry.name,os.path.join(repdir,entry.name))
|
|
|
622 elif entry.name == "%s.xml" % self.tool_name:
|
|
|
623 shutil.copyfile(entry.name,os.path.join(repdir,"new_tool_xml"))
|
|
30
|
624 return retval
|
|
|
625
|
|
|
626 def run(self):
|
|
|
627 """
|
|
|
628 Some devteam tools have this defensive stderr read so I'm keeping with the faith
|
|
|
629 Feel free to update.
|
|
|
630 """
|
|
36
|
631 s = "run cl=%s" % str(self.cl)
|
|
|
632
|
|
30
|
633 logging.debug(s)
|
|
36
|
634 scl = " ".join(self.cl)
|
|
30
|
635 err = None
|
|
36
|
636 if self.args.parampass != "0":
|
|
|
637 ste = open(self.elog, "wb")
|
|
30
|
638 if self.lastclredirect:
|
|
38
|
639 sto = open(
|
|
|
640 self.lastclredirect[1], "wb"
|
|
|
641 ) # is name of an output file
|
|
30
|
642 else:
|
|
36
|
643 sto = open(self.tlog, "wb")
|
|
30
|
644 sto.write(
|
|
36
|
645 bytes(
|
|
38
|
646 "## Executing Toolfactory generated command line = %s\n"
|
|
|
647 % scl,
|
|
36
|
648 "utf8",
|
|
|
649 )
|
|
|
650 )
|
|
30
|
651 sto.flush()
|
|
36
|
652 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
|
|
30
|
653 sto.close()
|
|
|
654 ste.close()
|
|
36
|
655 tmp_stderr = open(self.elog, "rb")
|
|
|
656 err = ""
|
|
30
|
657 buffsize = 1048576
|
|
|
658 try:
|
|
|
659 while True:
|
|
|
660 err += str(tmp_stderr.read(buffsize))
|
|
|
661 if not err or len(err) % buffsize != 0:
|
|
|
662 break
|
|
|
663 except OverflowError:
|
|
|
664 pass
|
|
|
665 tmp_stderr.close()
|
|
|
666 retval = p.returncode
|
|
|
667 else: # work around special case of simple scripts that take stdin and write to stdout
|
|
36
|
668 sti = open(self.infiles[0][IPATHPOS], "rb")
|
|
|
669 sto = open(self.outfiles[0][ONAMEPOS], "wb")
|
|
30
|
670 # must use shell to redirect
|
|
|
671 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
|
|
|
672 retval = p.returncode
|
|
|
673 sto.close()
|
|
|
674 sti.close()
|
|
|
675 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
|
|
|
676 os.unlink(self.tlog)
|
|
|
677 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
|
|
|
678 os.unlink(self.elog)
|
|
|
679 if p.returncode != 0 and err: # problem
|
|
|
680 sys.stderr.write(err)
|
|
36
|
681 logging.debug("run done")
|
|
30
|
682 return retval
|
|
|
683
|
|
|
684
|
|
|
685 def main():
|
|
|
686 """
|
|
|
687 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
|
|
|
688 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
|
|
|
689 </command>
|
|
|
690 """
|
|
|
691 parser = argparse.ArgumentParser()
|
|
|
692 a = parser.add_argument
|
|
36
|
693 a("--script_path", default="")
|
|
|
694 a("--tool_name", default=None)
|
|
|
695 a("--interpreter_name", default=None)
|
|
|
696 a("--interpreter_version", default=None)
|
|
|
697 a("--exe_package", default=None)
|
|
|
698 a("--exe_package_version", default=None)
|
|
|
699 a("--input_files", default=[], action="append")
|
|
|
700 a("--output_files", default=[], action="append")
|
|
|
701 a("--user_email", default="Unknown")
|
|
|
702 a("--bad_user", default=None)
|
|
|
703 a("--make_Tool", default=None)
|
|
|
704 a("--help_text", default=None)
|
|
|
705 a("--tool_desc", default=None)
|
|
|
706 a("--tool_version", default=None)
|
|
|
707 a("--citations", default=None)
|
|
|
708 a("--additional_parameters", action="append", default=[])
|
|
|
709 a("--edit_additional_parameters", action="store_true", default=False)
|
|
|
710 a("--parampass", default="positional")
|
|
|
711 a("--tfout", default="./tfout")
|
|
|
712 a("--new_tool", default="new_tool")
|
|
|
713 a("--runmode", default=None)
|
|
30
|
714 args = parser.parse_args()
|
|
36
|
715 assert not args.bad_user, (
|
|
|
716 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file'
|
|
|
717 % (args.bad_user, args.bad_user)
|
|
|
718 )
|
|
38
|
719 assert (
|
|
|
720 args.tool_name
|
|
|
721 ), "## Tool Factory expects a tool name - eg --tool_name=DESeq"
|
|
36
|
722 assert (
|
|
|
723 args.interpreter_name or args.exe_package
|
|
|
724 ), "## Tool Factory wrapper expects an interpreter or an executable package"
|
|
|
725 assert args.exe_package or (
|
|
|
726 len(args.script_path) > 0 and os.path.isfile(args.script_path)
|
|
|
727 ), "## Tool Factory wrapper expects a script path - eg --script_path=foo.R if no executable"
|
|
38
|
728 args.input_files = [
|
|
|
729 x.replace('"', "").replace("'", "") for x in args.input_files
|
|
|
730 ]
|
|
30
|
731 # remove quotes we need to deal with spaces in CL params
|
|
|
732 for i, x in enumerate(args.additional_parameters):
|
|
38
|
733 args.additional_parameters[i] = args.additional_parameters[i].replace(
|
|
|
734 '"', ""
|
|
|
735 )
|
|
30
|
736 r = ScriptRunner(args)
|
|
|
737 if args.make_Tool:
|
|
|
738 retcode = r.makeTooltar()
|
|
|
739 else:
|
|
|
740 retcode = r.run()
|
|
|
741 if retcode:
|
|
|
742 sys.exit(retcode) # indicate failure to job runner
|
|
|
743
|
|
|
744
|
|
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745 if __name__ == "__main__":
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746 main()
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