annotate toolfactory/rgToolFactory2.py @ 67:2cb06a59d84b draft

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author fubar
date Thu, 12 Nov 2020 09:24:59 +0000
parents bc1977b1f7b5
children afa3da660ae3
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1 # rgToolFactory.py
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2 # see https://github.com/fubar2/toolfactory
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at
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9 # 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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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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24
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25 import argparse
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26 import copy
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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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31 import subprocess
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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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35 import time
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36
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37 from bioblend import galaxy
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38 from bioblend import toolshed
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39
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40 import galaxyxml.tool as gxt
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41 import galaxyxml.tool.parameters as gxtp
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42
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43 import lxml
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44
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45 import yaml
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46
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47 myversion = "V2.1 July 2020"
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48 verbose = True
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49 debug = True
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50 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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51 ourdelim = "~~~"
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52 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
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53 STDIOXML = """<stdio>
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54 <exit_code range="100:" level="debug" description="shite happens" />
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55 </stdio>"""
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56
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57 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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58 # ~~~$input_help"
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59 IPATHPOS = 0
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60 ICLPOS = 1
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61 IFMTPOS = 2
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62 ILABPOS = 3
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63 IHELPOS = 4
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64 IOCLPOS = 5
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65
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66 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
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67 ONAMEPOS = 0
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68 OFMTPOS = 1
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69 OCLPOS = 2
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70 OTESTPOS = 3
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71 OOCLPOS = 4
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74 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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75 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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76 ANAMEPOS = 0
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77 AVALPOS = 1
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78 ALABPOS = 2
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79 AHELPPOS = 3
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80 ATYPEPOS = 4
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81 ACLPOS = 5
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82 AOVERPOS = 6
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83 AOCLPOS = 7
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86 foo = len(lxml.__version__)
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87 # fug you, flake8. Say my name!
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88 FAKEEXE = "~~~REMOVE~~~ME~~~"
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89 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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90 # with override.
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93 def timenow():
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94 """return current time as a string
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95 """
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96 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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99 def quote_non_numeric(s):
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100 """return a prequoted string for non-numerics
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101 useful for perl and Rscript parameter passing?
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102 """
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103 try:
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104 _ = float(s)
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105 return s
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106 except ValueError:
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107 return '"%s"' % s
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110 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
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111
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112
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113 def html_escape(text):
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114 """Produce entities within text."""
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115 return "".join(html_escape_table.get(c, c) for c in text)
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116
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117
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118 def html_unescape(text):
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119 """Revert entities within text. Multiple character targets so use replace"""
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120 t = text.replace("&amp;", "&")
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121 t = t.replace("&gt;", ">")
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122 t = t.replace("&lt;", "<")
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123 t = t.replace("\\$", "$")
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124 return t
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125
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126
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127 def parse_citations(citations_text):
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128 """
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129 """
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130 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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131 citation_tuples = []
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132 for citation in citations:
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133 if citation.startswith("doi"):
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134 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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135 else:
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136 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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137 return citation_tuples
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138
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139
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140 class ScriptRunner:
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141 """Wrapper for an arbitrary script
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142 uses galaxyxml
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143
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144 """
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145
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146 def __init__(self, args=None):
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147 """
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148 prepare command line cl for running the tool here
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149 and prepare elements needed for galaxyxml tool generation
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150 """
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151 self.infiles = [x.split(ourdelim) for x in args.input_files]
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152 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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153 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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154 self.args = args
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155 self.cleanuppar()
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156 self.lastclredirect = None
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157 self.lastxclredirect = None
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158 self.cl = []
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159 self.xmlcl = []
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160 self.is_positional = self.args.parampass == "positional"
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161 if self.args.sysexe:
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162 self.executeme = self.args.sysexe
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163 else:
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164 if self.args.packages:
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165 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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166 else:
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167 self.executeme = None
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168 aCL = self.cl.append
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169 aXCL = self.xmlcl.append
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170 assert args.parampass in [
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171 "0",
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172 "argparse",
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173 "positional",
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174 ], 'args.parampass must be "0","positional" or "argparse"'
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175 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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176 self.tool_id = self.tool_name
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177 self.newtool = gxt.Tool(
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178 self.args.tool_name,
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179 self.tool_id,
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180 self.args.tool_version,
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181 self.args.tool_desc,
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182 FAKEEXE,
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183 )
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184 self.tooloutdir = "tfout"
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185 self.repdir = "TF_run_report_tempdir"
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186 self.testdir = os.path.join(self.tooloutdir, "test-data")
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187 if not os.path.exists(self.tooloutdir):
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188 os.mkdir(self.tooloutdir)
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189 if not os.path.exists(self.testdir):
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190 os.mkdir(self.testdir) # make tests directory
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191 if not os.path.exists(self.repdir):
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192 os.mkdir(self.repdir)
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193 self.tinputs = gxtp.Inputs()
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194 self.toutputs = gxtp.Outputs()
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195 self.testparam = []
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196 if self.args.script_path:
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197 self.prepScript()
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198 if self.args.command_override:
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199 scos = open(self.args.command_override, "r").readlines()
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200 self.command_override = [x.rstrip() for x in scos]
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201 else:
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202 self.command_override = None
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203 if self.args.test_override:
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204 stos = open(self.args.test_override, "r").readlines()
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205 self.test_override = [x.rstrip() for x in stos]
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206 else:
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diff changeset
207 self.test_override = None
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208 if self.args.cl_prefix: # DIY CL start
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209 clp = self.args.cl_prefix.split(" ")
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210 for c in clp:
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diff changeset
211 aCL(c)
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diff changeset
212 aXCL(c)
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213 else:
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214 if self.args.script_path:
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215 aCL(self.executeme)
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216 aCL(self.sfile)
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217 aXCL(self.executeme)
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218 aXCL("$runme")
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219 else:
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220 aCL(self.executeme) # this little CL will just run
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221 aXCL(self.executeme)
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222 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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diff changeset
223 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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224
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225 if self.args.parampass == "0":
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226 self.clsimple()
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227 else:
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228 clsuffix = []
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229 xclsuffix = []
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230 for i, p in enumerate(self.infiles):
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231 if p[IOCLPOS] == "STDIN":
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232 appendme = [
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233 p[IOCLPOS],
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234 p[ICLPOS],
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235 p[IPATHPOS],
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parents:
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236 "< %s" % p[IPATHPOS],
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237 ]
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238 xappendme = [
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239 p[IOCLPOS],
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240 p[ICLPOS],
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241 p[IPATHPOS],
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parents:
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242 "< $%s" % p[ICLPOS],
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243 ]
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244 else:
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245 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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246 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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247 clsuffix.append(appendme)
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248 xclsuffix.append(xappendme)
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249 for i, p in enumerate(self.outfiles):
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250 if p[OOCLPOS] == "STDOUT":
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251 self.lastclredirect = [">", p[ONAMEPOS]]
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252 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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253 else:
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254 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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255 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
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256 for p in self.addpar:
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257 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
48
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258 xclsuffix.append(
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259 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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260 )
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261 clsuffix.sort()
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262 xclsuffix.sort()
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263 self.xclsuffix = xclsuffix
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264 self.clsuffix = clsuffix
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265 if self.args.parampass == "positional":
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266 self.clpositional()
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267 else:
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268 self.clargparse()
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269
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270 def prepScript(self):
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271 rx = open(self.args.script_path, "r").readlines()
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272 rx = [x.rstrip() for x in rx]
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273 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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274 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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275 self.script = "\n".join(rx)
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276 fhandle, self.sfile = tempfile.mkstemp(
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277 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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278 )
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279 tscript = open(self.sfile, "w")
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280 tscript.write(self.script)
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281 tscript.close()
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282 self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx])
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283 self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
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284 art = "%s.%s" % (self.tool_name, self.executeme)
48
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285 artifact = open(art, "wb")
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286 artifact.write(bytes(self.script, "utf8"))
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287 artifact.close()
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288
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289 def cleanuppar(self):
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parents:
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290 """ positional parameters are complicated by their numeric ordinal"""
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291 for i, p in enumerate(self.infiles):
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parents:
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292 if self.args.parampass == "positional":
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293 assert p[ICLPOS].isdigit(), (
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parents:
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294 "Positional parameters must be ordinal integers - got %s for %s"
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parents:
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295 % (p[ICLPOS], p[ILABPOS])
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296 )
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297 p.append(p[ICLPOS])
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298 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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299 scl = "input%d" % (i + 1)
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parents:
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300 p[ICLPOS] = scl
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parents:
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301 self.infiles[i] = p
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parents:
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302 for i, p in enumerate(
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parents:
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303 self.outfiles
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parents:
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304 ): # trying to automagically gather using extensions
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parents:
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305 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
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parents:
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306 assert p[OCLPOS].isdigit(), (
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fubar
parents:
diff changeset
307 "Positional parameters must be ordinal integers - got %s for %s"
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parents:
diff changeset
308 % (p[OCLPOS], p[ONAMEPOS])
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parents:
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309 )
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310 p.append(p[OCLPOS])
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parents:
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311 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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parents:
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312 scl = p[ONAMEPOS]
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parents:
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313 p[OCLPOS] = scl
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parents:
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314 self.outfiles[i] = p
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parents:
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315 for i, p in enumerate(self.addpar):
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parents:
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316 if self.args.parampass == "positional":
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parents:
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317 assert p[ACLPOS].isdigit(), (
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parents:
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318 "Positional parameters must be ordinal integers - got %s for %s"
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parents:
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319 % (p[ACLPOS], p[ANAMEPOS])
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parents:
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320 )
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parents:
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321 p.append(p[ACLPOS])
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parents:
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322 if p[ACLPOS].isdigit():
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parents:
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323 scl = "input%s" % p[ACLPOS]
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fubar
parents:
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324 p[ACLPOS] = scl
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parents:
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325 self.addpar[i] = p
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parents:
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326
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parents:
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327 def clsimple(self):
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parents:
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328 """ no parameters - uses < and > for i/o
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parents:
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329 """
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parents:
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330 aCL = self.cl.append
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parents:
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331 aXCL = self.xmlcl.append
62
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parents: 57
diff changeset
332
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parents: 57
diff changeset
333 if len(self.infiles) > 0:
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parents: 57
diff changeset
334 aCL("<")
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parents: 57
diff changeset
335 aCL(self.infiles[0][IPATHPOS])
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parents: 57
diff changeset
336 aXCL("<")
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parents: 57
diff changeset
337 aXCL("$%s" % self.infiles[0][ICLPOS])
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parents: 57
diff changeset
338 if len(self.outfiles) > 0:
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parents: 57
diff changeset
339 aCL(">")
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fubar
parents: 57
diff changeset
340 aCL(self.outfiles[0][OCLPOS])
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parents: 57
diff changeset
341 aXCL(">")
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fubar
parents: 57
diff changeset
342 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
48
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fubar
parents:
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343
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parents:
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344 def clpositional(self):
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parents:
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345 # inputs in order then params
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parents:
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346 aCL = self.cl.append
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parents:
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347 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
348 if " " in v:
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fubar
parents:
diff changeset
349 aCL("%s" % v)
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fubar
parents:
diff changeset
350 else:
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fubar
parents:
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351 aCL(v)
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parents:
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352 aXCL = self.xmlcl.append
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fubar
parents:
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353 for (o_v, k, v, koverride) in self.xclsuffix:
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fubar
parents:
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354 aXCL(v)
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fubar
parents:
diff changeset
355 if self.lastxclredirect:
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fubar
parents:
diff changeset
356 aXCL(self.lastxclredirect[0])
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fubar
parents:
diff changeset
357 aXCL(self.lastxclredirect[1])
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parents:
diff changeset
358
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fubar
parents:
diff changeset
359 def clargparse(self):
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parents:
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360 """ argparse style
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fubar
parents:
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361 """
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parents:
diff changeset
362 aCL = self.cl.append
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parents:
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363 aXCL = self.xmlcl.append
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parents:
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364 # inputs then params in argparse named form
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parents:
diff changeset
365 for (o_v, k, v, koverride) in self.xclsuffix:
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fubar
parents:
diff changeset
366 if koverride > "":
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fubar
parents:
diff changeset
367 k = koverride
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fubar
parents:
diff changeset
368 elif len(k.strip()) == 1:
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parents:
diff changeset
369 k = "-%s" % k
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fubar
parents:
diff changeset
370 else:
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fubar
parents:
diff changeset
371 k = "--%s" % k
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fubar
parents:
diff changeset
372 aXCL(k)
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fubar
parents:
diff changeset
373 aXCL(v)
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fubar
parents:
diff changeset
374 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
375 if koverride > "":
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fubar
parents:
diff changeset
376 k = koverride
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fubar
parents:
diff changeset
377 elif len(k.strip()) == 1:
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fubar
parents:
diff changeset
378 k = "-%s" % k
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fubar
parents:
diff changeset
379 else:
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fubar
parents:
diff changeset
380 k = "--%s" % k
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fubar
parents:
diff changeset
381 aCL(k)
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fubar
parents:
diff changeset
382 aCL(v)
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fubar
parents:
diff changeset
383
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fubar
parents:
diff changeset
384 def getNdash(self, newname):
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fubar
parents:
diff changeset
385 if self.is_positional:
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fubar
parents:
diff changeset
386 ndash = 0
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fubar
parents:
diff changeset
387 else:
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fubar
parents:
diff changeset
388 ndash = 2
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fubar
parents:
diff changeset
389 if len(newname) < 2:
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fubar
parents:
diff changeset
390 ndash = 1
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391 return ndash
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
393 def doXMLparam(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
394 """flake8 made me do this..."""
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 for p in self.outfiles:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
396 newname, newfmt, newcl, test, oldcl = p
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397 ndash = self.getNdash(newcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 if oldcl == "STDOUT":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 aparm.positional = 9999999
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 aparm.command_line_override = "> $%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 aparm.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406 aparm.command_line_override = "$%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
408 usetest = None
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
409 ld = None
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
410 if test > "":
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
411 if test.startswith("diff"):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
412 usetest = "diff"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
413 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
414 ld = int(test.split(":")[1])
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
415 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
416 usetest = test
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
417 tp = gxtp.TestOutput(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
418 name=newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
419 value="%s_sample" % newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
420 format=newfmt,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
421 compare=usetest,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
422 lines_diff=ld,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
423 delta=None,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
424 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
425 self.testparam.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
426 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
427 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
428 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
429 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
430 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
431 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
432 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
434 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
435 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
436 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
438 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 for p in self.addpar:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 if self.is_positional:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
484 aparm.positional = int(oldcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 self.tinputs.append(aparm)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
486 tparm = gxtp.TestParam(newname, value=newval)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
488
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
489 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
490 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
491 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
492 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
493 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
494 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
495 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
496 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
497 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
498 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
499 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
500 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
501 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
502 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
503 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
504 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
505 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
506 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
507 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
508 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
509 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
510 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
511 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
512 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
513 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
514 self.testparam.append(tp)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
515 if len(self.outfiles) > 0:
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
516 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
517 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
518 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
519 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
520 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
521 self.toutputs.append(anout)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
522 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
523 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
524
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
525 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
526 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
527 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
528 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
529 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
530 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
531 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
532 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
533 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
534 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
535 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
536 helptext = open(self.args.help_text, "r").readlines()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
537 safertext = [html_escape(x) for x in helptext]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
538 if False and self.args.script_path:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
539 scrp = self.script.split('\n')
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
540 scrpt = [' %s' % x for x in scrp] # try to stop templating
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
541 scrpt.insert(0,"```\n")
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
542 if len(scrpt) > 300:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
543 safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
544 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
545 safertext = safertext + scrpt
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
546 safertext.append("\n```")
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
547 self.newtool.help = "\n".join([x for x in safertext])
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
548 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
549 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
550 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
551 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
552 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
553 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
554 self.newtool.version_command = None # do not want
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
555 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
556 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
557 for d in self.args.packages.split(","):
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
558 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
559 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
560 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
561 packg = d
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
562 ver = ""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
563 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
564 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
565 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
566 self.newtool.requirements = requirements
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
567 if self.args.parampass == "0":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
568 self.doNoXMLparam()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
569 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
570 self.doXMLparam()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
571 self.newtool.outputs = self.toutputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
572 self.newtool.inputs = self.tinputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
573 if self.args.script_path:
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
574 configfiles = gxtp.Configfiles()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
575 configfiles.append(gxtp.Configfile(name="runme", text=self.script))
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
576 self.newtool.configfiles = configfiles
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
577 tests = gxtp.Tests()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
578 test_a = gxtp.Test()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
579 for tp in self.testparam:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
580 test_a.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
581 tests.append(test_a)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
582 self.newtool.tests = tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
583 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
584 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
585 % (self.args.user_email, timenow())
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
586 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
587 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
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fubar
parents: 49
diff changeset
588 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
589 "Cite: Creating re-usable tools from scripts doi: \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
590 10.1093/bioinformatics/bts573"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
591 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
592 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
593 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
594 if (
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
595 self.test_override
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
596 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
597 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
598 part2 = exml.split("</tests>")[1]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
599 fixed = "%s\n%s\n%s" % (part1, self.test_override, part2)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
600 exml = fixed
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
601 exml = exml.replace('range="1:"', 'range="1000:"')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
602 xf = open("%s.xml" % self.tool_name, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
603 xf.write(exml)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
604 xf.write("\n")
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fubar
parents:
diff changeset
605 xf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
606 # ready for the tarball
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
607
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fubar
parents:
diff changeset
608 def run(self):
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fubar
parents:
diff changeset
609 """
50
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fubar
parents: 49
diff changeset
610 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
611 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
612 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
613 automagically selected
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
614 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
615 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
616 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
617 if self.args.parampass != "0":
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
618 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
619 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
620 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
621 ste = open(self.elog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
622 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
623 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
624 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
625 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
626 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
627 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
628 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
629 sto.write(
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
630 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
631 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
632 sto.flush()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
633 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
634 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
635 ste.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
636 retval = p.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
637 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
638 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
639 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
640 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
641 sti = sys.stdin
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
642 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
643 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
644 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
645 sto = sys.stdout
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
646 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
647 sto.write(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
648 "## Executing Toolfactory generated command line = %s\n" % scl
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
649 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
650 retval = p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
651 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
652 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
653 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
654 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
655 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
656 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
657 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
658 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
659 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
660 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
661
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
662
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
663 def shedLoad(self):
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
664 """
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
665 {'deleted': False,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
666 'description': 'Tools for manipulating data',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
667 'id': '175812cd7caaf439',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
668 'model_class': 'Category',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
669 'name': 'Text Manipulation',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
670 'url': '/api/categories/175812cd7caaf439'}]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
671
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
672
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
673 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
674 if os.path.exists(self.tlog):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
675 sto = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
676 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
677 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
678
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
679 ts = toolshed.ToolShedInstance(url=self.args.toolshed_url,key=self.args.toolshed_api_key,verify=False)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
680 repos = ts.repositories.get_repositories()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
681 rnames = [x.get('name','?') for x in repos]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
682 rids = [x.get('id','?') for x in repos]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
683 sto.write(f'############names={rnames} rids={rids}')
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
684 cat = 'ToolFactory generated tools'
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
685 if self.args.tool_name not in rnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
686 tscat = ts.categories.get_categories()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
687 cnames = [x.get('name','?') for x in tscat]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
688 cids = [x.get('id','?') for x in tscat]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
689 catID = None
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
690 if cat in cnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
691 ci = cnames.index(cat)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
692 catID = cids[ci]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
693 res = ts.repositories.create_repository(name=self.args.tool_name, synopsis='Synopsis:%s' % self.args.tool_desc, description=self.args.tool_desc,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
694 type='unrestricted', remote_repository_url=self.args.toolshed_url,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
695 homepage_url=None, category_ids=catID)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
696 tid = res.get('id',None)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
697 sto.write(f'##########create res={res}')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
698 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
699 i = rnames.index(self.args.tool_name)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
700 tid = rids[i]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
701 res = ts.repositories.update_repository(id=tid, tar_ball_path=self.newtarpath, commit_message=None)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
702 sto.write(f'#####update res={res}')
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
703 sto.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
704
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
705
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
706 def eph_galaxy_load(self):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
707 """load the new tool from the local toolshed after planemo uploads it
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
708 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
709 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
710 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
711 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
712 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
713 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
714 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
715 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
716 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
717 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
718 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
719 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
720 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
721 "--name",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
722 self.args.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
723 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
724 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
725 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
726 self.args.toolshed_url,
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
727 "--section_label",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
728 "ToolFactory",
51
4b71b252eacb Uploaded
fubar
parents: 50
diff changeset
729
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
730 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
731 tout.write("running\n%s\n" % " ".join(cll))
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
732 p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
733 tout.write("installed %s - got retcode %d\n" % (self.args.tool_name,p.returncode))
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
734 tout.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
735 return p.returncode
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
736
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
737
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
738 def planemo_shedload(self):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
739 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
740 planemo shed_create --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
741 planemo shed_init --name=<name>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
742 --owner=<shed_username>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
743 --description=<short description>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
744 [--remote_repository_url=<URL to .shed.yml on github>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
745 [--homepage_url=<Homepage for tool.>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
746 [--long_description=<long description>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
747 [--category=<category name>]*
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
748
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
749
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
750 planemo shed_update --check_diff --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
751 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
752 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
753 tout = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
754 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
755 tout = open(self.tlog, "w")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
756 ts = toolshed.ToolShedInstance(url=self.args.toolshed_url,key=self.args.toolshed_api_key,verify=False)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
757 repos = ts.repositories.get_repositories()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
758 rnames = [x.get('name','?') for x in repos]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
759 rids = [x.get('id','?') for x in repos]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
760 tout.write(f'############names={rnames} rids={rids}')
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
761 cat = 'ToolFactory generated tools'
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
762 if self.args.tool_name not in rnames:
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
763 cll = ["planemo", "shed_create", "--shed_target", "local",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
764 "--owner","fubar","--name",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
765 self.args.tool_name,"--shed_key",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
766 self.args.toolshed_api_key,]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
767 try:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
768 p = subprocess.run(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
769 cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
770 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
771 except:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
772 pass
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
773 if p.returncode != 0:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
774 tout.write("Repository %s exists" % self.args.tool_name)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
775 else:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
776 tout.write("initiated %s" % self.args.tool_name)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
777 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
778 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
779 "shed_upload",
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diff changeset
780 "--shed_target",
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fubar
parents: 62
diff changeset
781 "local",
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fubar
parents: 62
diff changeset
782 "--owner",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
783 "fubar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
784 "--name",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
785 self.args.tool_name,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
786 "--shed_key",
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fubar
parents: 62
diff changeset
787 self.args.toolshed_api_key,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
788 "--tar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
789 self.newtarpath,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
790 ]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
791 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
792 tout.write("Ran %s got %d" % (" ".join(cll), p.returncode))
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
793 tout.close()
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
794 return p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
795
63
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fubar
parents: 62
diff changeset
796
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fubar
parents: 62
diff changeset
797 def eph_test(self):
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parents: 62
diff changeset
798 """
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fubar
parents: 62
diff changeset
799 """
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fubar
parents: 62
diff changeset
800 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
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parents: 62
diff changeset
801 tout = open(self.tlog, "a")
b3254219d4fb Uploaded
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parents: 62
diff changeset
802 else:
b3254219d4fb Uploaded
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parents: 62
diff changeset
803 tout = open(self.tlog, "w")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
804 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
805 "shed-tools",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
806 "test",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
807 "-g",
b3254219d4fb Uploaded
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parents: 62
diff changeset
808 self.args.galaxy_url,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
809 "-a",
b3254219d4fb Uploaded
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parents: 62
diff changeset
810 self.args.galaxy_api_key,
b3254219d4fb Uploaded
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parents: 62
diff changeset
811 "--name",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
812 self.args.tool_name,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
813 "--owner",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
814 "fubar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
815 ]
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fubar
parents: 62
diff changeset
816 p = subprocess.run(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
817 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
818 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
819 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode))
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
820 tout.close()
b3254219d4fb Uploaded
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parents: 62
diff changeset
821 return p.returncode
b3254219d4fb Uploaded
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parents: 62
diff changeset
822
b3254219d4fb Uploaded
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parents: 62
diff changeset
823 def planemo_test(self, genoutputs=True):
b3254219d4fb Uploaded
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parents: 62
diff changeset
824 """planemo is a requirement so is available for testing
b3254219d4fb Uploaded
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parents: 62
diff changeset
825 and for generating test outputs if command or test overrides are supplied
b3254219d4fb Uploaded
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parents: 62
diff changeset
826 test outputs are sent to repdir for display
67
2cb06a59d84b Uploaded
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parents: 66
diff changeset
827 planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
63
b3254219d4fb Uploaded
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parents: 62
diff changeset
828 """
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parents: 62
diff changeset
829 xreal = "%s.xml" % self.tool_name
b3254219d4fb Uploaded
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parents: 62
diff changeset
830 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
831 tout = open(self.tlog, "a")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
832 else:
b3254219d4fb Uploaded
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parents: 62
diff changeset
833 tout = open(self.tlog, "w")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
834 if genoutputs:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
835 dummy,tfile = tempfile.mkstemp()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
836 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
837 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
838 "test",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
839 "--galaxy_root",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
840 self.args.galaxy_root,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
841 "--update_test_data",
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
842 "--docker",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
843 xreal,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
844 ]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
845 p = subprocess.run(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
846 cll, shell=False, cwd=self.tooloutdir, stderr=dummy, stdout=dummy,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
847 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
848 else:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
849 cll = ["planemo", "test", "--galaxy_root",
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
850 self.args.galaxy_root, "--docker",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
851 xreal,]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
852 p = subprocess.run(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
853 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
854 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
855 tout.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
856 return p.returncode
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
857
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
858
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
859
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
860 def writeShedyml(self):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
861 """for planemo
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
862 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
863 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
864 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
865 yamlf = open(yfname, "w")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
866 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
867 "name": self.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
868 "owner": yuser,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
869 "type": "unrestricted",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
870 "description": self.args.tool_desc,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
871 "synopsis": self.args.tool_desc,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
872 "category": "TF Generated Tools",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
873 }
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
874 yaml.dump(odict, yamlf, allow_unicode=True)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
875 yamlf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
876
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
877 def makeTool(self):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
878 """write xmls and input samples into place
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
879 """
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
880 self.makeXML()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
881 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
882 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
883 if not os.path.exists(stname):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
884 shutil.copyfile(self.sfile, stname)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
885 xreal = "%s.xml" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
886 xout = os.path.join(self.tooloutdir, xreal)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
887 shutil.copyfile(xreal, xout)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
888 for p in self.infiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
889 pth = p[IPATHPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
890 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
891 shutil.copyfile(pth, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
892 dest = os.path.join(self.repdir, "%s.%s" % (p[ICLPOS], p[IFMTPOS]))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
893 shutil.copyfile(pth, dest)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
894
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
895 def makeToolTar(self):
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
896 """ move outputs into test-data and prepare the tarball
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
897 """
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
898 excludeme = "tool_test_output"
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
899 def exclude_function(tarinfo):
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
900 filename = tarinfo.name
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
901 return None if filename.startswith(excludeme) or os.path.splitext(filename)[1].startswith(excludeme) else tarinfo
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
902
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
903 for p in self.outfiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
904 src = p[ONAMEPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
905 if os.path.isfile(src):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
906 dest = os.path.join(self.testdir, "%s_sample" % src)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
907 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
908 dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS]))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
909 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
910 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
911 print(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
912 "### problem - output file %s not found in tooloutdir %s"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
913 % (src, self.tooloutdir)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
914 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
915 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
916 tf = tarfile.open(self.newtarpath, "w:gz")
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
917 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
918 tf.close()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
919 shutil.copyfile(self.newtarpath, self.args.new_tool)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
920
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
921 def moveRunOutputs(self):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
922 """need to move planemo or run outputs into toolfactory collection
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
923 """
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
924 with os.scandir(self.tooloutdir) as outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
925 for entry in outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
926 if not entry.is_file() or entry.name.startswith("."):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
927 continue
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
928 if "." in entry.name:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
929 nayme, ext = os.path.splitext(entry.name)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
930 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
931 ext = ".txt"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
932 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
933 dest = os.path.join(self.repdir, ofn)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
934 src = os.path.join(self.tooloutdir, entry.name)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
935 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
936
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
937
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
938 def main():
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
939 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
940 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
941 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
942 --tool_name "foo" --interpreter "Rscript"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
943 </command>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
944 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
945 parser = argparse.ArgumentParser()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
946 a = parser.add_argument
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
947 a("--script_path", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
948 a("--history_test", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
949 a("--cl_prefix", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
950 a("--sysexe", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
951 a("--packages", default=None)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
952 a("--tool_name", default=None)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
953 a("--input_files", default=[], action="append")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
954 a("--output_files", default=[], action="append")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
955 a("--user_email", default="Unknown")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
956 a("--bad_user", default=None)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
957 a("--make_Tool", default="runonly")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
958 a("--help_text", default=None)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
959 a("--tool_desc", default=None)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
960 a("--tool_version", default=None)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
961 a("--citations", default=None)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
962 a("--command_override", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
963 a("--test_override", default=None)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
964 a("--additional_parameters", action="append", default=[])
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
965 a("--edit_additional_parameters", action="store_true", default=False)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
966 a("--parampass", default="positional")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
967 a("--tfout", default="./tfout")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
968 a("--new_tool", default="new_tool")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
969 a("--galaxy_url", default="http://localhost:8080")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
970 a("--toolshed_url", default="http://localhost:9009") # make sure this is NOT 127.0.0.1 - it won't work if tool_sheds_conf.xml has localhost
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
971 #a("--galaxy_api_key", default="1e62ddad74fe9bf112859f4e9efea48b")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
972 #a("--toolshed_api_key", default="9154c91f2a162bf12fda15764f43846c")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
973
b3254219d4fb Uploaded
fubar
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974 a("--toolshed_api_key", default="fakekey")
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975 a("--galaxy_api_key", default="fakekey")
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976 a("--galaxy_root", default="/galaxy-central")
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977
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978
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979 args = parser.parse_args()
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980 assert not args.bad_user, (
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981 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the Galaxy configuration file'
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982 % (args.bad_user, args.bad_user)
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983 )
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984 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
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985 assert (
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986 args.sysexe or args.packages
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987 ), "## Tool Factory wrapper expects an interpreter or an executable package"
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988 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
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989 # remove quotes we need to deal with spaces in CL params
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990 for i, x in enumerate(args.additional_parameters):
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991 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
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992 r = ScriptRunner(args)
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993 r.writeShedyml()
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994 r.makeTool()
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995 if args.make_Tool == "generate":
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996 retcode = r.run()
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997 r.moveRunOutputs()
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998 r.makeToolTar()
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999 else:
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1000 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR
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1001 r.moveRunOutputs()
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1002 r.makeToolTar()
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1003 retcode = r.planemo_test(genoutputs=False)
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1004 r.moveRunOutputs()
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1005 if args.make_Tool == "gentestinstall":
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1006 retcode = r.planemo_shedload() #r.shedLoad()
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1007 print(f'planemo_shedload returned {retcode}')
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1008 r.eph_galaxy_load()
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1009
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1010
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1011
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1012 if __name__ == "__main__":
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1013 main()