annotate toolfactory/rgToolFactory2.py @ 105:373e1f9cb609 draft

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author fubar
date Fri, 27 Nov 2020 23:17:10 +0000
parents 05cb28bf2bbc
children 6de08f44e551
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1 # replace with shebang for biocontainer
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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 # well well. sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
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24 # does the needful. Use GALAXY_TEST_SAVE /foo to save outputs - only the tar.gz - not the rest sadly
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25 # GALAXY_TEST_NO_CLEANUP GALAXY_TEST_TMP_DIR=wherever
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26 # planemo test --engine docker_galaxy --test_data ./test-data/ --docker_extra_volume ./test-data rgToolFactory2.xml
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27
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28 import argparse
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29 import copy
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30 import datetime
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31 import grp
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32 import json
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33 import logging
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34 import os
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35 import re
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36 import shutil
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37 import subprocess
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38 import sys
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39 import tarfile
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40 import tempfile
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41 import time
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42
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44 from bioblend import ConnectionError
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45 from bioblend import toolshed
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46
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47 import docker
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48
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49 import galaxyxml.tool as gxt
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50 import galaxyxml.tool.parameters as gxtp
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51
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52 import lxml
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53
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54 import yaml
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55
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56 myversion = "V2.1 July 2020"
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57 verbose = True
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58 debug = True
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59 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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60 ourdelim = "~~~"
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61 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
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62 STDIOXML = """<stdio>
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63 <exit_code range="100:" level="debug" description="shite happens" />
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64 </stdio>"""
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65
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66 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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67 # ~~~$input_help"
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68 IPATHPOS = 0
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69 ICLPOS = 1
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70 IFMTPOS = 2
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71 ILABPOS = 3
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72 IHELPOS = 4
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73 IOCLPOS = 5
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74
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75 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
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76 ONAMEPOS = 0
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77 OFMTPOS = 1
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78 OCLPOS = 2
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79 OTESTPOS = 3
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80 OOCLPOS = 4
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83 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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84 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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85 ANAMEPOS = 0
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86 AVALPOS = 1
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87 ALABPOS = 2
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88 AHELPPOS = 3
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89 ATYPEPOS = 4
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90 ACLPOS = 5
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91 AOVERPOS = 6
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92 AOCLPOS = 7
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95 foo = len(lxml.__version__)
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96 # fug you, flake8. Say my name!
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97 FAKEEXE = "~~~REMOVE~~~ME~~~"
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98 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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99 # with override.
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102 def timenow():
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103 """return current time as a string"""
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104 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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107 def quote_non_numeric(s):
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108 """return a prequoted string for non-numerics
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109 useful for perl and Rscript parameter passing?
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110 """
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111 try:
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112 _ = float(s)
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113 return s
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114 except ValueError:
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115 return '"%s"' % s
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116
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117
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118 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
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119
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120
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121 def html_escape(text):
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122 """Produce entities within text."""
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123 return "".join(html_escape_table.get(c, c) for c in text)
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124
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125
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126 def html_unescape(text):
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127 """Revert entities within text. Multiple character targets so use replace"""
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128 t = text.replace("&amp;", "&")
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129 t = t.replace("&gt;", ">")
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130 t = t.replace("&lt;", "<")
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131 t = t.replace("\\$", "$")
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132 return t
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134
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135 def parse_citations(citations_text):
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136 """"""
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137 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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138 citation_tuples = []
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139 for citation in citations:
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140 if citation.startswith("doi"):
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141 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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142 else:
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143 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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144 return citation_tuples
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145
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147 class ScriptRunner:
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148 """Wrapper for an arbitrary script
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149 uses galaxyxml
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150
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151 """
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152
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153 def __init__(self, args=None):
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154 """
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155 prepare command line cl for running the tool here
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156 and prepare elements needed for galaxyxml tool generation
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157 """
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158 self.ourcwd = os.getcwd()
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159 self.ourenv = copy.deepcopy(os.environ)
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160 self.infiles = [x.split(ourdelim) for x in args.input_files]
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161 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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162 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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163 self.args = args
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164 self.cleanuppar()
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165 self.lastclredirect = None
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166 self.lastxclredirect = None
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167 self.cl = []
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168 self.xmlcl = []
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169 self.is_positional = self.args.parampass == "positional"
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170 if self.args.sysexe:
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171 self.executeme = self.args.sysexe
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172 else:
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173 if self.args.packages:
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174 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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175 else:
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176 self.executeme = None
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177 aCL = self.cl.append
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178 aXCL = self.xmlcl.append
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179 assert args.parampass in [
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180 "0",
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181 "argparse",
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182 "positional",
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183 ], 'args.parampass must be "0","positional" or "argparse"'
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184 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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185 self.tool_id = self.tool_name
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186 self.newtool = gxt.Tool(
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187 self.tool_name,
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188 self.tool_id,
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189 self.args.tool_version,
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190 self.args.tool_desc,
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191 FAKEEXE,
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192 )
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193 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
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194 self.tooloutdir = "./tfout"
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195 self.repdir = "./TF_run_report_tempdir"
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196 self.testdir = os.path.join(self.tooloutdir, "test-data")
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197 if not os.path.exists(self.tooloutdir):
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198 os.mkdir(self.tooloutdir)
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199 if not os.path.exists(self.testdir):
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200 os.mkdir(self.testdir) # make tests directory
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201 if not os.path.exists(self.repdir):
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202 os.mkdir(self.repdir)
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203 self.tinputs = gxtp.Inputs()
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204 self.toutputs = gxtp.Outputs()
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205 self.testparam = []
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206 if self.args.script_path:
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207 self.prepScript()
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208 if self.args.command_override:
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209 scos = open(self.args.command_override, "r").readlines()
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210 self.command_override = [x.rstrip() for x in scos]
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211 else:
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212 self.command_override = None
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213 if self.args.test_override:
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214 stos = open(self.args.test_override, "r").readlines()
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215 self.test_override = [x.rstrip() for x in stos]
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216 else:
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217 self.test_override = None
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218 if self.args.cl_prefix: # DIY CL start
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219 clp = self.args.cl_prefix.split(" ")
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220 for c in clp:
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221 aCL(c)
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222 aXCL(c)
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223 else:
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224 if self.args.script_path:
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225 aCL(self.executeme)
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226 aCL(self.sfile)
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227 aXCL(self.executeme)
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228 aXCL("$runme")
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229 else:
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230 aCL(self.executeme) # this little CL will just run
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231 aXCL(self.executeme)
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232 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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233 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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234
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235 if self.args.parampass == "0":
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236 self.clsimple()
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237 else:
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238 clsuffix = []
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239 xclsuffix = []
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240 for i, p in enumerate(self.infiles):
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241 if p[IOCLPOS] == "STDIN":
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242 appendme = [
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243 p[IOCLPOS],
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244 p[ICLPOS],
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245 p[IPATHPOS],
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246 "< %s" % p[IPATHPOS],
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247 ]
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248 xappendme = [
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249 p[IOCLPOS],
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250 p[ICLPOS],
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251 p[IPATHPOS],
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252 "< $%s" % p[ICLPOS],
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253 ]
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254 else:
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255 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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256 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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257 clsuffix.append(appendme)
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258 xclsuffix.append(xappendme)
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259 for i, p in enumerate(self.outfiles):
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260 if p[OOCLPOS] == "STDOUT":
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261 self.lastclredirect = [">", p[ONAMEPOS]]
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262 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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263 else:
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264 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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265 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
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266 for p in self.addpar:
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267 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
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268 xclsuffix.append(
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269 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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270 )
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271 clsuffix.sort()
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272 xclsuffix.sort()
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273 self.xclsuffix = xclsuffix
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274 self.clsuffix = clsuffix
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275 if self.args.parampass == "positional":
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276 self.clpositional()
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277 else:
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278 self.clargparse()
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279
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280 def prepScript(self):
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281 rx = open(self.args.script_path, "r").readlines()
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282 rx = [x.rstrip() for x in rx]
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283 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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284 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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285 self.script = "\n".join(rx)
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286 fhandle, self.sfile = tempfile.mkstemp(
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287 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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288 )
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289 tscript = open(self.sfile, "w")
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290 tscript.write(self.script)
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291 tscript.close()
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292 self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx])
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293 self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
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294 art = "%s.%s" % (self.tool_name, self.executeme)
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295 artifact = open(art, "wb")
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296 artifact.write(bytes(self.script, "utf8"))
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297 artifact.close()
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298
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299 def cleanuppar(self):
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300 """ positional parameters are complicated by their numeric ordinal"""
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301 for i, p in enumerate(self.infiles):
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302 if self.args.parampass == "positional":
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303 assert p[
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304 ICLPOS
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305 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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diff changeset
306 p[ICLPOS],
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diff changeset
307 p[ILABPOS],
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308 )
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309 p.append(p[ICLPOS])
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310 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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311 scl = "input%d" % (i + 1)
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312 p[ICLPOS] = scl
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313 self.infiles[i] = p
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314 for i, p in enumerate(
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315 self.outfiles
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316 ): # trying to automagically gather using extensions
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317 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
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diff changeset
318 assert p[
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diff changeset
319 OCLPOS
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diff changeset
320 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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diff changeset
321 p[OCLPOS],
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322 p[ONAMEPOS],
48
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323 )
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324 p.append(p[OCLPOS])
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325 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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326 scl = p[ONAMEPOS]
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327 p[OCLPOS] = scl
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328 self.outfiles[i] = p
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329 for i, p in enumerate(self.addpar):
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330 if self.args.parampass == "positional":
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331 assert p[
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332 ACLPOS
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333 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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334 p[ACLPOS],
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parents: 74
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335 p[ANAMEPOS],
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336 )
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337 p.append(p[ACLPOS])
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parents:
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338 if p[ACLPOS].isdigit():
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parents:
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339 scl = "input%s" % p[ACLPOS]
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340 p[ACLPOS] = scl
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341 self.addpar[i] = p
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342
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343 def clsimple(self):
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344 """no parameters - uses < and > for i/o"""
48
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parents:
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345 aCL = self.cl.append
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346 aXCL = self.xmlcl.append
62
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parents: 57
diff changeset
347
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348 if len(self.infiles) > 0:
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349 aCL("<")
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350 aCL(self.infiles[0][IPATHPOS])
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351 aXCL("<")
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352 aXCL("$%s" % self.infiles[0][ICLPOS])
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353 if len(self.outfiles) > 0:
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parents: 57
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354 aCL(">")
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355 aCL(self.outfiles[0][OCLPOS])
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356 aXCL(">")
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357 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
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parents:
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358
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359 def clpositional(self):
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parents:
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360 # inputs in order then params
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361 aCL = self.cl.append
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parents:
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362 for (o_v, k, v, koverride) in self.clsuffix:
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parents:
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363 if " " in v:
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parents:
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364 aCL("%s" % v)
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parents:
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365 else:
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parents:
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366 aCL(v)
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parents:
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367 aXCL = self.xmlcl.append
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368 for (o_v, k, v, koverride) in self.xclsuffix:
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369 aXCL(v)
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parents:
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370 if self.lastxclredirect:
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parents:
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371 aXCL(self.lastxclredirect[0])
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372 aXCL(self.lastxclredirect[1])
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373
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374 def clargparse(self):
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diff changeset
375 """argparse style"""
48
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parents:
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376 aCL = self.cl.append
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377 aXCL = self.xmlcl.append
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378 # inputs then params in argparse named form
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379 for (o_v, k, v, koverride) in self.xclsuffix:
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parents:
diff changeset
380 if koverride > "":
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parents:
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381 k = koverride
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parents:
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382 elif len(k.strip()) == 1:
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383 k = "-%s" % k
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parents:
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384 else:
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385 k = "--%s" % k
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parents:
diff changeset
386 aXCL(k)
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fubar
parents:
diff changeset
387 aXCL(v)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
388 for (o_v, k, v, koverride) in self.clsuffix:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
389 if koverride > "":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
390 k = koverride
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391 elif len(k.strip()) == 1:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392 k = "-%s" % k
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fubar
parents:
diff changeset
393 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
394 k = "--%s" % k
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 aCL(k)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396 aCL(v)
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fubar
parents:
diff changeset
397
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 def getNdash(self, newname):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 ndash = 0
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 ndash = 2
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 if len(newname) < 2:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 ndash = 1
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 return ndash
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 def doXMLparam(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408 """flake8 made me do this..."""
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
409 for p in self.outfiles:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
410 newname, newfmt, newcl, test, oldcl = p
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
411 ndash = self.getNdash(newcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
412 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
413 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
414 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
415 if oldcl == "STDOUT":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
416 aparm.positional = 9999999
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
417 aparm.command_line_override = "> $%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
418 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
419 aparm.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
420 aparm.command_line_override = "$%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
421 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
422 usetest = None
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
423 ld = None
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
424 if test > "":
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
425 if test.startswith("diff"):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
426 usetest = "diff"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
427 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
428 ld = int(test.split(":")[1])
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
429 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
430 usetest = test
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
431 tp = gxtp.TestOutput(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
432 name=newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
433 value="%s_sample" % newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
434 format=newfmt,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
435 compare=usetest,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
436 lines_diff=ld,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
437 delta=None,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
438 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 self.testparam.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 for p in self.addpar:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
486 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
488 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
489 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
490 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
491 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
492 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
493 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
494 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
495 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
496 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
497 if self.is_positional:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
498 aparm.positional = int(oldcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
499 self.tinputs.append(aparm)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
500 tparm = gxtp.TestParam(newname, value=newval)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
501 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
502
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
503 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
504 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
505 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
506 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
507 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
508 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
509 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
510 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
511 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
512 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
513 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
514 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
515 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
516 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
517 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
518 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
519 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
520 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
521 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
522 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
523 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
524 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
525 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
526 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
527 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
528 self.testparam.append(tp)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
529 if len(self.outfiles) > 0:
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
530 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
531 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
532 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
533 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
534 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
535 self.toutputs.append(anout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
536 tp = gxtp.TestOutput(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
537 name=newname, value="%s_sample" % newname, format=newfmt
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
538 )
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
539 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
540
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
541 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
542 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
543 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
544 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
545 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
546 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
547 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
548 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
549 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
550 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
551 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
552 helptext = open(self.args.help_text, "r").readlines()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
553 safertext = [html_escape(x) for x in helptext]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
554 if False and self.args.script_path:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
555 scrp = self.script.split("\n")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
556 scrpt = [" %s" % x for x in scrp] # try to stop templating
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
557 scrpt.insert(0, "```\n")
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
558 if len(scrpt) > 300:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
559 safertext = (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
560 safertext + scrpt[:100] + \
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
561 [">500 lines - stuff deleted", "......"] + scrpt[-100:]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
562 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
563 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
564 safertext = safertext + scrpt
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
565 safertext.append("\n```")
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
566 self.newtool.help = "\n".join([x for x in safertext])
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
567 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
568 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
569 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
570 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
571 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
572 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
573 self.newtool.version_command = None # do not want
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
574 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
575 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
576 for d in self.args.packages.split(","):
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
577 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
578 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
579 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
580 packg = d
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
581 ver = ""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
582 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
583 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
584 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
585 self.newtool.requirements = requirements
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
586 if self.args.parampass == "0":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
587 self.doNoXMLparam()
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fubar
parents:
diff changeset
588 else:
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parents:
diff changeset
589 self.doXMLparam()
50
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fubar
parents: 49
diff changeset
590 self.newtool.outputs = self.toutputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
591 self.newtool.inputs = self.tinputs
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fubar
parents: 49
diff changeset
592 if self.args.script_path:
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
593 configfiles = gxtp.Configfiles()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
594 configfiles.append(gxtp.Configfile(name="runme", text=self.script))
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
595 self.newtool.configfiles = configfiles
48
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fubar
parents:
diff changeset
596 tests = gxtp.Tests()
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fubar
parents:
diff changeset
597 test_a = gxtp.Test()
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fubar
parents:
diff changeset
598 for tp in self.testparam:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
599 test_a.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
600 tests.append(test_a)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
601 self.newtool.tests = tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
602 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
603 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
604 % (self.args.user_email, timenow())
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
605 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
606 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
607 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
608 "Cite: Creating re-usable tools from scripts doi: \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
609 10.1093/bioinformatics/bts573"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
610 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
611 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
612 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
613 if (
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parents: 49
diff changeset
614 self.test_override
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parents: 49
diff changeset
615 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
616 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
617 part2 = exml.split("</tests>")[1]
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fubar
parents: 49
diff changeset
618 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
619 exml = fixed
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
620 exml = exml.replace('range="1:"', 'range="1000:"')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
621 xf = open("%s.xml" % self.tool_name, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
622 xf.write(exml)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
623 xf.write("\n")
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fubar
parents:
diff changeset
624 xf.close()
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fubar
parents:
diff changeset
625 # ready for the tarball
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
626
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fubar
parents:
diff changeset
627 def run(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
628 """
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
629 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
630 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
631 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
632 automagically selected
48
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fubar
parents:
diff changeset
633 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
634 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
635 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
636 if self.args.parampass != "0":
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
637 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
638 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
639 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
640 ste = open(self.elog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
641 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
642 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
643 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
644 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
645 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
646 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
647 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
648 sto.write(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
649 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
650 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
651 sto.flush()
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
652 subp = subprocess.run(self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
653 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
654 ste.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
655 retval = subp.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
656 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
657 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
658 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
659 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
660 sti = sys.stdin
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
661 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
662 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
663 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
664 sto = sys.stdout
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
665 subp = subprocess.run(self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
666 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
667 retval = subp.returncode
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
668 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
669 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
670 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
671 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
672 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
673 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
674 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
675 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
676 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
677 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
678
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
679
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
680 def copy_to_container(self, src, dest, container):
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
681 """ Recreate the src directory tree at dest - full path included
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
682 """
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
683 idir = os.getcwd()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
684 workdir = os.path.dirname(src)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
685 os.chdir(workdir)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
686 _, tfname = tempfile.mkstemp(suffix=".tar")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
687 tar = tarfile.open(tfname, mode='w')
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
688 srcb = os.path.basename(src)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
689 tar.add(srcb)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
690 tar.close()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
691 data = open(tfname, 'rb').read()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
692 container.put_archive(dest, data)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
693 os.unlink(tfname)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
694 os.chdir(idir)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
695
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
696
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
697 def copy_from_container(self, src, dest, container):
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
698 """ recreate the src directory tree at dest using docker sdk
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
699 """
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
700 os.makedirs(dest,exist_ok=True)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
701 _, tfname = tempfile.mkstemp(suffix=".tar")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
702 tf = open(tfname,'wb')
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
703 bits, stat = container.get_archive(src)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
704 for chunk in bits:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
705 tf.write(chunk)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
706 tf.close()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
707 tar = tarfile.open(tfname,'r')
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
708 tar.extractall(dest)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
709 tar.close()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
710 os.unlink(tfname)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
711
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
712
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
713
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
714
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
715 def planemo_biodocker_test(self):
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
716 """planemo currently leaks dependencies if used in the same container and gets unhappy after a
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
717 first successful run. https://github.com/galaxyproject/planemo/issues/1078#issuecomment-731476930
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
718
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
719 Docker biocontainer has planemo with caches filled to save repeated downloads
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
720
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
721
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
722 """
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
723 def prun(container,tout,cl,user="biodocker"):
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
724 rlog = container.exec_run(cl,user=user)
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
725 slogl = str(rlog).split('\\n')
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
726 slog = '\n'.join(slogl)
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
727 tout.write(f"## got rlog {slog} from {cl}\n")
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
728
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
729 dgroup = grp.getgrnam('docker')[2]
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
730 if os.path.exists(self.tlog):
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
731 tout = open(self.tlog, "a")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
732 else:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
733 tout = open(self.tlog, "w")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
734 planemoimage = "quay.io/fubar2/planemo-biocontainer"
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
735 xreal = "%s.xml" % self.tool_name
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
736 repname = f"{self.tool_name}_planemo_test_report.html"
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
737 ptestrep_path = os.path.join(self.repdir,repname)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
738 tool_name = self.tool_name
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
739 client = docker.from_env()
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
740 tvol = client.volumes.create()
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
741 tvolname = tvol.name
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
742 destdir = "/toolfactory/ptest"
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
743 imrep = os.path.join(destdir,repname)
105
373e1f9cb609 Uploaded
fubar
parents: 104
diff changeset
744 # need to keep the container running so sleep a while - we stop and destroy it when we are done
373e1f9cb609 Uploaded
fubar
parents: 104
diff changeset
745 container = client.containers.run(planemoimage,'sleep 30m', detach=True, user="biodocker",
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
746 network="host", volumes={f"{tvolname}": {'bind': '/toolfactory', 'mode': 'rw'}})
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
747 cl = f"groupmod -g {dgroup} docker"
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
748 prun(container, tout, cl, user="root")
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
749 cl = f"mkdir -p {destdir}"
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
750 prun(container, tout, cl, user="root")
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
751 cl = f"rm -rf {destdir}/*"
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
752 prun(container, tout, cl, user="root")
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
753 ptestpath = os.path.join(destdir,'tfout',xreal)
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
754 self.copy_to_container(self.tooloutdir,destdir,container)
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
755 cl ='chmod -R a+rwx /toolfactory'
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
756 prun(container, tout, cl, user="root")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
757 rlog = container.exec_run(f"ls -la {destdir}")
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
758 ptestcl = f"planemo test --update_test_data --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
759 try:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
760 rlog = container.exec_run(ptestcl)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
761 except:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
762 e = sys.exc_info()[0]
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
763 tout.write(f"#### error: {e} from {ptestcl}\n")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
764 # fails - used to generate test outputs
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
765 cl = f"planemo test --test_output {imrep} --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
766 try:
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
767 prun(container,tout,cl)
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
768 except:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
769 pass
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
770 testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp",dir=".")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
771 self.copy_from_container(destdir,testouts,container)
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
772 src = os.path.join(testouts,'ptest')
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
773 if os.path.isdir(src):
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
774 shutil.copytree(src, '.', dirs_exist_ok=True)
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
775 src = repname
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
776 if os.path.isfile(repname):
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
777 shutil.copyfile(src,ptestrep_path)
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
778 else:
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
779 tout.write(f"No output from run to shutil.copytree in {src}\n")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
780 tout.close()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
781 container.stop()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
782 container.remove()
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
783 tvol.remove()
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
784 #shutil.rmtree(testouts)
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
785
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
786 def shedLoad(self):
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
787 """
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
788 {'deleted': False,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
789 'description': 'Tools for manipulating data',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
790 'id': '175812cd7caaf439',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
791 'model_class': 'Category',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
792 'name': 'Text Manipulation',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
793 'url': '/api/categories/175812cd7caaf439'}]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
794
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
795
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
796 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
797 if os.path.exists(self.tlog):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
798 sto = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
799 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
800 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
801
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
802 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
803 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
804 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
805 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
806 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
807 rids = [x.get("id", "?") for x in repos]
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
808 sto.write(f"############names={rnames} rids={rids}\n")
100
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
809 sto.write(f"############names={repos}\n")
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
810 tfcat = "ToolFactory generated tools"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
811 if self.tool_name not in rnames:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
812 tscat = ts.categories.get_categories()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
813 cnames = [x.get("name", "?").strip() for x in tscat]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
814 cids = [x.get("id", "?") for x in tscat]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
815 catID = None
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
816 if tfcat.strip() in cnames:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
817 ci = cnames.index(tfcat)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
818 catID = cids[ci]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
819 res = ts.repositories.create_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
820 name=self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
821 synopsis="Synopsis:%s" % self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
822 description=self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
823 type="unrestricted",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
824 remote_repository_url=self.args.toolshed_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
825 homepage_url=None,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
826 category_ids=catID,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
827 )
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
828 tid = res.get("id", None)
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
829 sto.write(f"##########create res={res}\n")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
830 else:
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
831 i = rnames.index(self.tool_name)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
832 tid = rids[i]
100
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
833 try:
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
834 res = ts.repositories.update_repository(
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
835 id=tid, tar_ball_path=self.newtarpath, commit_message=None)
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
836 sto.write(f"#####update res={res}\n")
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
837 except ConnectionError:
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
838 sto.write("Probably no change to repository - bioblend shed upload failed\n")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
839 sto.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
840
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
841 def eph_galaxy_load(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
842 """load the new tool from the local toolshed after planemo uploads it"""
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
843 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
844 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
845 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
846 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
847 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
848 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
849 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
850 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
851 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
852 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
853 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
854 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
855 "--name",
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
856 self.tool_name,
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
857 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
858 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
859 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
860 self.args.toolshed_url,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
861 "--section_label",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
862 "ToolFactory",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
863 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
864 tout.write("running\n%s\n" % " ".join(cll))
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
865 subp = subprocess.run(cll, env=self.ourenv, cwd=self.ourcwd, shell=False, stderr=tout, stdout=tout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
866 tout.write(
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
867 "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
868 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
869 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
870 return subp.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
871
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
872 def planemo_shedLoad(self):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
873 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
874 planemo shed_create --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
875 planemo shed_init --name=<name>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
876 --owner=<shed_username>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
877 --description=<short description>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
878 [--remote_repository_url=<URL to .shed.yml on github>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
879 [--homepage_url=<Homepage for tool.>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
880 [--long_description=<long description>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
881 [--category=<category name>]*
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
882
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
883
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
884 planemo shed_update --check_diff --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
885 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
886 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
887 tout = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
888 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
889 tout = open(self.tlog, "w")
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
890 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
891 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
892 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
893 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
894 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
895 rids = [x.get("id", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
896 #cat = "ToolFactory generated tools"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
897 if self.tool_name not in rnames:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
898 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
899 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
900 "shed_create",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
901 "--shed_target",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
902 "local",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
903 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
904 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
905 "--name",
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
906 self.tool_name,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
907 "--shed_key",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
908 self.args.toolshed_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
909 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
910 try:
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
911 subp = subprocess.run(
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
912 cll, env=self.ourenv, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
913 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
914 except:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
915 pass
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
916 if subp.returncode != 0:
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
917 tout.write("Repository %s exists\n" % self.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
918 else:
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
919 tout.write("initiated %s\n" % self.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
920 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
921 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
922 "shed_upload",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
923 "--shed_target",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
924 "local",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
925 "--owner",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
926 "fubar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
927 "--name",
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
928 self.tool_name,
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
929 "--shed_key",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
930 self.args.toolshed_api_key,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
931 "--tar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
932 self.newtarpath,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
933 ]
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
934 subp = subprocess.run(cll, env=self.ourenv, cwd=self.ourcwd, shell=False, stdout=tout, stderr=tout)
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
935 tout.write("Ran %s got %d\n" % (" ".join(cll),subp.returncode))
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
936 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
937 return subp.returncode
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
938
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
939 def eph_test(self, genoutputs=True):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
940 """problem getting jobid - ephemeris upload is the job before the one we want - but depends on how many inputs
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
941 """
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
942 if os.path.exists(self.tlog):
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
943 tout = open(self.tlog, "a")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
944 else:
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
945 tout = open(self.tlog, "w")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
946 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
947 "shed-tools",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
948 "test",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
949 "-g",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
950 self.args.galaxy_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
951 "-a",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
952 self.args.galaxy_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
953 "--name",
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
954 self.tool_name,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
955 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
956 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
957 ]
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
958 if genoutputs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
959 dummy, tfile = tempfile.mkstemp()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
960 subp = subprocess.run(
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
961 cll, env=self.ourenv, cwd=self.ourcwd, shell=False, stderr=dummy, stdout=dummy
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
962 )
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
963
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
964 with open('tool_test_output.json','rb') as f:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
965 s = json.loads(f.read())
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
966 print('read %s' % s)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
967 cl = s['tests'][0]['data']['job']['command_line'].split()
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
968 n = cl.index('--script_path')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
969 jobdir = cl[n+1]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
970 jobdir = jobdir.replace('"','')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
971 jobdir = jobdir.split('/configs')[0]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
972 print('jobdir=%s' % jobdir)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
973
46db8143adb7 Uploaded
fubar
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diff changeset
974 #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\"
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
975 src = os.path.join(jobdir,'working',self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
976 if os.path.exists(src):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
977 dest = os.path.join(self.testdir, self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
978 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
979 else:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
980 tout.write('No toolshed archive found after first ephemeris test - not a good sign')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
981 ephouts = os.path.join(jobdir,'working','tfout','test-data')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
982 with os.scandir(ephouts) as outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
983 for entry in outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
984 if not entry.is_file():
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
985 continue
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
986 dest = os.path.join(self.tooloutdir, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
987 src = os.path.join(ephouts, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
988 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
989 else:
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
990 subp = subprocess.run(
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
991 cll, env=self.ourenv, cwd=self.ourcwd, shell=False, stderr=tout, stdout=tout)
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
992 tout.write("eph_test Ran %s got %d" % (" ".join(cll), subp.returncode))
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
993 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
994 return subp.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
995
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
996 def planemo_test_biocontainer(self, genoutputs=True):
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
997 """planemo is a requirement so is available for testing but testing in a biocontainer
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
998 requires some fiddling to use the hacked galaxy-central .venv
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
999
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1000 Planemo runs:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1001 python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1002 /export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1003 --with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1004 --structured-data-file
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1005 /export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1006
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1007
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1008 for the planemo-biocontainer,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1009 planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1010
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1011 """
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1012 xreal = "%s.xml" % self.tool_name
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1013 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1014 if os.path.exists(self.tlog):
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1015 tout = open(self.tlog, "a")
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1016 else:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1017 tout = open(self.tlog, "w")
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1018 if genoutputs:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1019 dummy, tfile = tempfile.mkstemp()
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1020 cll = [
95
6d122fd54cd0 Uploaded
fubar
parents: 91
diff changeset
1021 ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1022 "planemo",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1023 "test",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1024 "--test_data", self.testdir,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1025 "--test_output", tool_test_path,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1026 "--skip_venv",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1027 "--galaxy_root",
91
7176af503cdd Uploaded
fubar
parents: 87
diff changeset
1028 self.args.galaxy_root,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1029 "--update_test_data",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1030 xreal,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1031 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1032 subp = subprocess.run(
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1033 cll,
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
1034 env=self.ourenv,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1035 shell=False,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1036 cwd=self.tooloutdir,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1037 stderr=dummy,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1038 stdout=dummy,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1039 )
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1040
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1041 else:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1042 cll = [
95
6d122fd54cd0 Uploaded
fubar
parents: 91
diff changeset
1043 ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1044 "planemo",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1045 "test",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1046 "--test_data", os.path.self.testdir,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1047 "--test_output", os.path.tool_test_path,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1048 "--skip_venv",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1049 "--galaxy_root",
91
7176af503cdd Uploaded
fubar
parents: 87
diff changeset
1050 self.args.galaxy_root,
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1051 xreal,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1052 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1053 subp = subprocess.run(
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
1054 cll, env=self.ourenv, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1055 )
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1056 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1057 return subp.returncode
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1058
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1059
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1060 def writeShedyml(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1061 """for planemo"""
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1062 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1063 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1064 yamlf = open(yfname, "w")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1065 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1066 "name": self.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1067 "owner": yuser,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1068 "type": "unrestricted",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1069 "description": self.args.tool_desc,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1070 "synopsis": self.args.tool_desc,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1071 "category": "TF Generated Tools",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1072 }
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1073 yaml.dump(odict, yamlf, allow_unicode=True)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1074 yamlf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1075
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1076 def makeTool(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1077 """write xmls and input samples into place"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1078 self.makeXML()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1079 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1080 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1081 if not os.path.exists(stname):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1082 shutil.copyfile(self.sfile, stname)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1083 xreal = "%s.xml" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1084 xout = os.path.join(self.tooloutdir, xreal)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1085 shutil.copyfile(xreal, xout)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1086 for p in self.infiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1087 pth = p[IPATHPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1088 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1089 shutil.copyfile(pth, dest)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1090
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1091 def makeToolTar(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1092 """move outputs into test-data and prepare the tarball"""
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
1093 excludeme = "_planemo_test_report.html"
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1094
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1095 def exclude_function(tarinfo):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1096 filename = tarinfo.name
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1097 return (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1098 None
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
1099 if filename.endswith(excludeme)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1100 else tarinfo
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1101 )
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1102
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1103 for p in self.outfiles:
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
1104 oname = p[ONAMEPOS]
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1105 tdest = os.path.join(self.testdir, "%s_sample" % oname)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1106 if not os.path.isfile(tdest):
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1107 src = os.path.join(self.testdir,oname)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1108 if os.path.isfile(src):
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1109 shutil.copyfile(src, tdest)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1110 dest = os.path.join(self.repdir, "%s.sample" % (oname))
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1111 shutil.copyfile(src, dest)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1112 else:
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1113 print(
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1114 "### problem - output file %s not found in testdir %s"
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1115 % (tdest, self.testdir)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
1116 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1117 tf = tarfile.open(self.newtarpath, "w:gz")
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1118 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1119 tf.close()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1120 shutil.copyfile(self.newtarpath, self.args.new_tool)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1121
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1122 def moveRunOutputs(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1123 """need to move planemo or run outputs into toolfactory collection"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1124 with os.scandir(self.tooloutdir) as outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1125 for entry in outs:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1126 if not entry.is_file():
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1127 continue
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1128 if "." in entry.name:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1129 nayme, ext = os.path.splitext(entry.name)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1130 if ext in ['.yml','.xml','.json','.yaml']:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1131 ext = f'{ext}.txt'
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1132 else:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1133 ext = ".txt"
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1134 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1135 dest = os.path.join(self.repdir, ofn)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1136 src = os.path.join(self.tooloutdir, entry.name)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1137 shutil.copyfile(src, dest)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1138 with os.scandir(self.testdir) as outs:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1139 for entry in outs:
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
1140 if (not entry.is_file()) or entry.name.endswith('_sample') or entry.name.endswith("_planemo_test_report.html"):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1141 continue
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1142 if "." in entry.name:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1143 nayme, ext = os.path.splitext(entry.name)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1144 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1145 ext = ".txt"
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1146 newname = f"{entry.name}{ext}"
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1147 dest = os.path.join(self.repdir, newname)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1148 src = os.path.join(self.testdir, entry.name)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1149 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1150
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1151
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
1152
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1153 def main():
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1154 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1155 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
1156 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1157 --tool_name "foo" --interpreter "Rscript"
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1158 </command>
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1159 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1160 parser = argparse.ArgumentParser()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1161 a = parser.add_argument
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1162 a("--script_path", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1163 a("--history_test", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1164 a("--cl_prefix", default=None)
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1165 a("--sysexe", default=None)
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1166 a("--packages", default=None)
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1167 a("--tool_name", default="newtool")
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1168 a("--tool_dir", default=None)
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1169 a("--input_files", default=[], action="append")
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1170 a("--output_files", default=[], action="append")
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1171 a("--user_email", default="Unknown")
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1172 a("--bad_user", default=None)
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1173 a("--make_Tool", default="runonly")
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1174 a("--help_text", default=None)
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1175 a("--tool_desc", default=None)
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1176 a("--tool_version", default=None)
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1177 a("--citations", default=None)
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1178 a("--command_override", default=None)
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1179 a("--test_override", default=None)
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1180 a("--additional_parameters", action="append", default=[])
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1181 a("--edit_additional_parameters", action="store_true", default=False)
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1182 a("--parampass", default="positional")
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1183 a("--tfout", default="./tfout")
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1184 a("--new_tool", default="new_tool")
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1185 a("--galaxy_url", default="http://localhost:8080")
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1186 a(
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1187 "--toolshed_url", default="http://localhost:9009")
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1188 # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails
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1189 a("--toolshed_api_key", default="fakekey")
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1190 a("--galaxy_api_key", default="fakekey")
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1191 a("--galaxy_root", default="/galaxy-central")
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1192 a("--galaxy_venv", default="/galaxy_venv")
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1193 args = parser.parse_args()
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1194 assert not args.bad_user, (
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1195 '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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1196 % (args.bad_user, args.bad_user)
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1197 )
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1198 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
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1199 assert (
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1200 args.sysexe or args.packages
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1201 ), "## Tool Factory wrapper expects an interpreter or an executable package"
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1202 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
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1203 # remove quotes we need to deal with spaces in CL params
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1204 for i, x in enumerate(args.additional_parameters):
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1205 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
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1206 r = ScriptRunner(args)
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1207 r.writeShedyml()
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1208 r.makeTool()
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1209 if args.make_Tool == "generate":
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1210 retcode = r.run() # for testing toolfactory itself
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1211 r.moveRunOutputs()
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1212 r.makeToolTar()
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1213 else:
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1214 r.planemo_biodocker_test() # test to make outputs and then test
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1215 r.moveRunOutputs()
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1216 r.makeToolTar()
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1217 if args.make_Tool == "gentestinstall":
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1218 r.shedLoad()
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1219 r.eph_galaxy_load()
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1220
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1221
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1222 if __name__ == "__main__":
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1223 main()