annotate toolfactory/rgToolFactory2.py @ 98:67628c7dc9f3 draft

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author fubar
date Sun, 22 Nov 2020 06:29:33 +0000
parents 515be7318f2b
children d4d88d393285
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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
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27 import argparse
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28 import datetime
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29 import json
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30 import logging
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31 import os
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32 import re
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33 import shutil
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34 import subprocess
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35 import sys
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36 import tarfile
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37 import tempfile
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38 import time
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41 from bioblend import toolshed
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42
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43 # import docker
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44
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45 import galaxyxml.tool as gxt
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46 import galaxyxml.tool.parameters as gxtp
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47
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48 import lxml
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50 import yaml
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51
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52 myversion = "V2.1 July 2020"
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53 verbose = True
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54 debug = True
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55 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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56 ourdelim = "~~~"
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57 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
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58 STDIOXML = """<stdio>
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59 <exit_code range="100:" level="debug" description="shite happens" />
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60 </stdio>"""
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61
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62 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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63 # ~~~$input_help"
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64 IPATHPOS = 0
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65 ICLPOS = 1
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66 IFMTPOS = 2
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67 ILABPOS = 3
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68 IHELPOS = 4
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69 IOCLPOS = 5
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70
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71 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
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72 ONAMEPOS = 0
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73 OFMTPOS = 1
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74 OCLPOS = 2
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75 OTESTPOS = 3
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76 OOCLPOS = 4
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79 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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80 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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81 ANAMEPOS = 0
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82 AVALPOS = 1
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83 ALABPOS = 2
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84 AHELPPOS = 3
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85 ATYPEPOS = 4
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86 ACLPOS = 5
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87 AOVERPOS = 6
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88 AOCLPOS = 7
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91 foo = len(lxml.__version__)
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92 # fug you, flake8. Say my name!
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93 FAKEEXE = "~~~REMOVE~~~ME~~~"
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94 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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95 # with override.
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98 def timenow():
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99 """return current time as a string"""
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100 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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101
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102
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103 def quote_non_numeric(s):
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104 """return a prequoted string for non-numerics
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105 useful for perl and Rscript parameter passing?
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106 """
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107 try:
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108 _ = float(s)
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109 return s
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110 except ValueError:
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111 return '"%s"' % s
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112
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114 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
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115
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116
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117 def html_escape(text):
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118 """Produce entities within text."""
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119 return "".join(html_escape_table.get(c, c) for c in text)
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120
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121
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122 def html_unescape(text):
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123 """Revert entities within text. Multiple character targets so use replace"""
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124 t = text.replace("&amp;", "&")
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125 t = t.replace("&gt;", ">")
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126 t = t.replace("&lt;", "<")
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127 t = t.replace("\\$", "$")
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128 return t
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129
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130
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131 def parse_citations(citations_text):
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132 """"""
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133 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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134 citation_tuples = []
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135 for citation in citations:
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136 if citation.startswith("doi"):
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137 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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138 else:
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139 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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140 return citation_tuples
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141
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142
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143 class ScriptRunner:
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144 """Wrapper for an arbitrary script
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145 uses galaxyxml
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146
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147 """
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148
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149 def __init__(self, args=None):
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150 """
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151 prepare command line cl for running the tool here
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152 and prepare elements needed for galaxyxml tool generation
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153 """
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154 self.infiles = [x.split(ourdelim) for x in args.input_files]
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155 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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156 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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157 self.args = args
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158 self.cleanuppar()
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159 self.lastclredirect = None
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160 self.lastxclredirect = None
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161 self.cl = []
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162 self.xmlcl = []
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163 self.is_positional = self.args.parampass == "positional"
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164 if self.args.sysexe:
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165 self.executeme = self.args.sysexe
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166 else:
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167 if self.args.packages:
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168 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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169 else:
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170 self.executeme = None
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171 aCL = self.cl.append
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172 aXCL = self.xmlcl.append
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173 assert args.parampass in [
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174 "0",
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175 "argparse",
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176 "positional",
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177 ], 'args.parampass must be "0","positional" or "argparse"'
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178 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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179 self.tool_id = self.tool_name
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180 self.newtool = gxt.Tool(
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181 self.args.tool_name,
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182 self.tool_id,
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183 self.args.tool_version,
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184 self.args.tool_desc,
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185 FAKEEXE,
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186 )
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187 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
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188 self.tooloutdir = "./tfout"
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189 self.repdir = "./TF_run_report_tempdir"
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190 self.testdir = os.path.join(self.tooloutdir, "test-data")
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191 if not os.path.exists(self.tooloutdir):
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192 os.mkdir(self.tooloutdir)
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193 if not os.path.exists(self.testdir):
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194 os.mkdir(self.testdir) # make tests directory
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195 if not os.path.exists(self.repdir):
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196 os.mkdir(self.repdir)
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197 self.tinputs = gxtp.Inputs()
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198 self.toutputs = gxtp.Outputs()
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199 self.testparam = []
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200 if self.args.script_path:
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201 self.prepScript()
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202 if self.args.command_override:
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203 scos = open(self.args.command_override, "r").readlines()
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204 self.command_override = [x.rstrip() for x in scos]
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205 else:
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206 self.command_override = None
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207 if self.args.test_override:
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208 stos = open(self.args.test_override, "r").readlines()
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209 self.test_override = [x.rstrip() for x in stos]
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210 else:
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211 self.test_override = None
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212 if self.args.cl_prefix: # DIY CL start
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213 clp = self.args.cl_prefix.split(" ")
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214 for c in clp:
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215 aCL(c)
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216 aXCL(c)
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217 else:
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218 if self.args.script_path:
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219 aCL(self.executeme)
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220 aCL(self.sfile)
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221 aXCL(self.executeme)
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222 aXCL("$runme")
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223 else:
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224 aCL(self.executeme) # this little CL will just run
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225 aXCL(self.executeme)
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226 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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227 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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228
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229 if self.args.parampass == "0":
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230 self.clsimple()
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231 else:
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232 clsuffix = []
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233 xclsuffix = []
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234 for i, p in enumerate(self.infiles):
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235 if p[IOCLPOS] == "STDIN":
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236 appendme = [
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237 p[IOCLPOS],
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238 p[ICLPOS],
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239 p[IPATHPOS],
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240 "< %s" % p[IPATHPOS],
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241 ]
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242 xappendme = [
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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 "< $%s" % p[ICLPOS],
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247 ]
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248 else:
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249 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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250 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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251 clsuffix.append(appendme)
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252 xclsuffix.append(xappendme)
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253 for i, p in enumerate(self.outfiles):
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254 if p[OOCLPOS] == "STDOUT":
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255 self.lastclredirect = [">", p[ONAMEPOS]]
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256 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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257 else:
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258 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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259 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
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260 for p in self.addpar:
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261 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
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262 xclsuffix.append(
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263 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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264 )
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265 clsuffix.sort()
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266 xclsuffix.sort()
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267 self.xclsuffix = xclsuffix
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268 self.clsuffix = clsuffix
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269 if self.args.parampass == "positional":
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270 self.clpositional()
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271 else:
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272 self.clargparse()
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273
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274 def prepScript(self):
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275 rx = open(self.args.script_path, "r").readlines()
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276 rx = [x.rstrip() for x in rx]
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277 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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278 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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279 self.script = "\n".join(rx)
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280 fhandle, self.sfile = tempfile.mkstemp(
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281 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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282 )
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283 tscript = open(self.sfile, "w")
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284 tscript.write(self.script)
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285 tscript.close()
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286 self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx])
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287 self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
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288 art = "%s.%s" % (self.tool_name, self.executeme)
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289 artifact = open(art, "wb")
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290 artifact.write(bytes(self.script, "utf8"))
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291 artifact.close()
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292
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293 def cleanuppar(self):
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294 """ positional parameters are complicated by their numeric ordinal"""
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295 for i, p in enumerate(self.infiles):
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296 if self.args.parampass == "positional":
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297 assert p[
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298 ICLPOS
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299 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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300 p[ICLPOS],
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301 p[ILABPOS],
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302 )
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303 p.append(p[ICLPOS])
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304 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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305 scl = "input%d" % (i + 1)
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306 p[ICLPOS] = scl
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307 self.infiles[i] = p
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308 for i, p in enumerate(
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309 self.outfiles
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310 ): # trying to automagically gather using extensions
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311 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
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312 assert p[
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313 OCLPOS
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314 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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315 p[OCLPOS],
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316 p[ONAMEPOS],
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317 )
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318 p.append(p[OCLPOS])
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319 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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320 scl = p[ONAMEPOS]
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321 p[OCLPOS] = scl
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322 self.outfiles[i] = p
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323 for i, p in enumerate(self.addpar):
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324 if self.args.parampass == "positional":
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325 assert p[
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326 ACLPOS
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327 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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328 p[ACLPOS],
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329 p[ANAMEPOS],
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330 )
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331 p.append(p[ACLPOS])
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332 if p[ACLPOS].isdigit():
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333 scl = "input%s" % p[ACLPOS]
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334 p[ACLPOS] = scl
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335 self.addpar[i] = p
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336
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337 def clsimple(self):
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338 """no parameters - uses < and > for i/o"""
48
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339 aCL = self.cl.append
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340 aXCL = self.xmlcl.append
62
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341
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342 if len(self.infiles) > 0:
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343 aCL("<")
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344 aCL(self.infiles[0][IPATHPOS])
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345 aXCL("<")
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346 aXCL("$%s" % self.infiles[0][ICLPOS])
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347 if len(self.outfiles) > 0:
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348 aCL(">")
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349 aCL(self.outfiles[0][OCLPOS])
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350 aXCL(">")
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351 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
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352
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353 def clpositional(self):
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354 # inputs in order then params
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355 aCL = self.cl.append
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356 for (o_v, k, v, koverride) in self.clsuffix:
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357 if " " in v:
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358 aCL("%s" % v)
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parents:
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359 else:
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360 aCL(v)
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361 aXCL = self.xmlcl.append
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362 for (o_v, k, v, koverride) in self.xclsuffix:
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363 aXCL(v)
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364 if self.lastxclredirect:
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365 aXCL(self.lastxclredirect[0])
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366 aXCL(self.lastxclredirect[1])
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367
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368 def clargparse(self):
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369 """argparse style"""
48
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370 aCL = self.cl.append
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371 aXCL = self.xmlcl.append
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372 # inputs then params in argparse named form
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373 for (o_v, k, v, koverride) in self.xclsuffix:
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374 if koverride > "":
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parents:
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375 k = koverride
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parents:
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376 elif len(k.strip()) == 1:
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377 k = "-%s" % k
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378 else:
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379 k = "--%s" % k
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380 aXCL(k)
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381 aXCL(v)
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parents:
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382 for (o_v, k, v, koverride) in self.clsuffix:
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parents:
diff changeset
383 if koverride > "":
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parents:
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384 k = koverride
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parents:
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385 elif len(k.strip()) == 1:
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386 k = "-%s" % k
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diff changeset
387 else:
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fubar
parents:
diff changeset
388 k = "--%s" % k
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fubar
parents:
diff changeset
389 aCL(k)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
390 aCL(v)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392 def getNdash(self, newname):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
393 if self.is_positional:
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fubar
parents:
diff changeset
394 ndash = 0
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396 ndash = 2
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397 if len(newname) < 2:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 ndash = 1
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 return ndash
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 def doXMLparam(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 """flake8 made me do this..."""
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 for p in self.outfiles:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
404 newname, newfmt, newcl, test, oldcl = p
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 ndash = self.getNdash(newcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
409 if oldcl == "STDOUT":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
410 aparm.positional = 9999999
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
411 aparm.command_line_override = "> $%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
412 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
413 aparm.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
414 aparm.command_line_override = "$%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
415 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
416 usetest = None
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
417 ld = None
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
418 if test > "":
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
419 if test.startswith("diff"):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
420 usetest = "diff"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
421 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
422 ld = int(test.split(":")[1])
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
423 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
424 usetest = test
50
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fubar
parents: 49
diff changeset
425 tp = gxtp.TestOutput(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
426 name=newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
427 value="%s_sample" % newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
428 format=newfmt,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
429 compare=usetest,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
430 lines_diff=ld,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
431 delta=None,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
432 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 self.testparam.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
434 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
435 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
436 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
438 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 for p in self.addpar:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
486 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
488 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
489 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
490 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
491 if self.is_positional:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
492 aparm.positional = int(oldcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
493 self.tinputs.append(aparm)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
494 tparm = gxtp.TestParam(newname, value=newval)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
495 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
496
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
497 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
498 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
499 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
500 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
501 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
502 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
503 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
504 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
505 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
506 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
507 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
508 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
509 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
510 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
511 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
512 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
513 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
514 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
515 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
516 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
517 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
518 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
519 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
520 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
521 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
522 self.testparam.append(tp)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
523 if len(self.outfiles) > 0:
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
524 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
525 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
526 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
527 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
528 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
529 self.toutputs.append(anout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
530 tp = gxtp.TestOutput(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
531 name=newname, value="%s_sample" % newname, format=newfmt
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
532 )
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
533 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
534
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
535 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
536 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
537 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
538 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
539 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
540 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
541 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
542 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
543 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
544 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
545 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
546 helptext = open(self.args.help_text, "r").readlines()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
547 safertext = [html_escape(x) for x in helptext]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
548 if False and self.args.script_path:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
549 scrp = self.script.split("\n")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
550 scrpt = [" %s" % x for x in scrp] # try to stop templating
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
551 scrpt.insert(0, "```\n")
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
552 if len(scrpt) > 300:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
553 safertext = (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
554 safertext + scrpt[:100] + \
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
555 [">500 lines - stuff deleted", "......"] + scrpt[-100:]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
556 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
557 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
558 safertext = safertext + scrpt
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
559 safertext.append("\n```")
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
560 self.newtool.help = "\n".join([x for x in safertext])
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
561 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
562 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
563 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
564 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
565 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
566 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
567 self.newtool.version_command = None # do not want
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
568 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
569 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
570 for d in self.args.packages.split(","):
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
571 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
572 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
573 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
574 packg = d
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
575 ver = ""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
576 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
577 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
578 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
579 self.newtool.requirements = requirements
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
580 if self.args.parampass == "0":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
581 self.doNoXMLparam()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
582 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
583 self.doXMLparam()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
584 self.newtool.outputs = self.toutputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
585 self.newtool.inputs = self.tinputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
586 if self.args.script_path:
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
587 configfiles = gxtp.Configfiles()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
588 configfiles.append(gxtp.Configfile(name="runme", text=self.script))
50
bf432f4486c7 Uploaded
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parents: 49
diff changeset
589 self.newtool.configfiles = configfiles
48
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fubar
parents:
diff changeset
590 tests = gxtp.Tests()
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fubar
parents:
diff changeset
591 test_a = gxtp.Test()
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fubar
parents:
diff changeset
592 for tp in self.testparam:
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fubar
parents:
diff changeset
593 test_a.append(tp)
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fubar
parents:
diff changeset
594 tests.append(test_a)
50
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fubar
parents: 49
diff changeset
595 self.newtool.tests = tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
596 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
597 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
598 % (self.args.user_email, timenow())
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
599 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
600 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
601 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
602 "Cite: Creating re-usable tools from scripts doi: \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
603 10.1093/bioinformatics/bts573"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
604 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
605 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
606 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
607 if (
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
608 self.test_override
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
609 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
610 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
611 part2 = exml.split("</tests>")[1]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
612 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
613 exml = fixed
63
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parents: 62
diff changeset
614 exml = exml.replace('range="1:"', 'range="1000:"')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
615 xf = open("%s.xml" % self.tool_name, "w")
48
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fubar
parents:
diff changeset
616 xf.write(exml)
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fubar
parents:
diff changeset
617 xf.write("\n")
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fubar
parents:
diff changeset
618 xf.close()
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fubar
parents:
diff changeset
619 # ready for the tarball
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
620
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fubar
parents:
diff changeset
621 def run(self):
5a7a5b06bce0 Uploaded
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parents:
diff changeset
622 """
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
623 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
624 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
625 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
626 automagically selected
48
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fubar
parents:
diff changeset
627 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
628 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
629 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
630 if self.args.parampass != "0":
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
631 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
632 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
633 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
634 ste = open(self.elog, "w")
48
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fubar
parents:
diff changeset
635 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
636 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
637 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
638 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
639 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
640 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
641 sto = open(self.tlog, "w")
48
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fubar
parents:
diff changeset
642 sto.write(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
643 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
644 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
645 sto.flush()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
646 subp = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
647 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
648 ste.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
649 retval = subp.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
650 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
651 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
652 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
653 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
654 sti = sys.stdin
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
655 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
656 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
657 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
658 sto = sys.stdout
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
659 subp = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
660 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
661 retval = subp.returncode
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
662 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
663 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
664 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
665 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
666 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
667 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
668 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
669 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
670 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
671 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
672
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
673 def shedLoad(self):
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
674 """
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
675 {'deleted': False,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
676 'description': 'Tools for manipulating data',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
677 'id': '175812cd7caaf439',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
678 'model_class': 'Category',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
679 'name': 'Text Manipulation',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
680 'url': '/api/categories/175812cd7caaf439'}]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
681
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
682
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
683 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
684 if os.path.exists(self.tlog):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
685 sto = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
686 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
687 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
688
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
689 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
690 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
691 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
692 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
693 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
694 rids = [x.get("id", "?") for x in repos]
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
695 sto.write(f"############names={rnames} rids={rids}\n")
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
696 tfcat = "ToolFactory generated tools"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
697 if self.args.tool_name not in rnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
698 tscat = ts.categories.get_categories()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
699 cnames = [x.get("name", "?").strip() for x in tscat]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
700 cids = [x.get("id", "?") for x in tscat]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
701 catID = None
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
702 if tfcat.strip() in cnames:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
703 ci = cnames.index(tfcat)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
704 catID = cids[ci]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
705 res = ts.repositories.create_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
706 name=self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
707 synopsis="Synopsis:%s" % self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
708 description=self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
709 type="unrestricted",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
710 remote_repository_url=self.args.toolshed_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
711 homepage_url=None,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
712 category_ids=catID,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
713 )
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
714 tid = res.get("id", None)
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
715 sto.write(f"##########create res={res}\n")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
716 else:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
717 i = rnames.index(self.args.tool_name)
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
718 tid = rids[i]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
719 res = ts.repositories.update_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
720 id=tid, tar_ball_path=self.newtarpath, commit_message=None
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
721 )
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
722 sto.write(f"#####update res={res}\n")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
723 sto.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
724
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
725 def eph_galaxy_load(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
726 """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
727 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
728 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
729 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
730 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
731 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
732 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
733 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
734 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
735 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
736 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
737 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
738 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
739 "--name",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
740 self.args.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
741 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
742 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
743 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
744 self.args.toolshed_url,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
745 "--section_label",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
746 "ToolFactory",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
747 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
748 tout.write("running\n%s\n" % " ".join(cll))
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
749 subp = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
750 tout.write(
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
751 "installed %s - got retcode %d\n" % (self.args.tool_name, subp.returncode)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
752 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
753 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
754 return subp.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
755
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
756 def planemo_shedload(self):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
757 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
758 planemo shed_create --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
759 planemo shed_init --name=<name>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
760 --owner=<shed_username>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
761 --description=<short description>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
762 [--remote_repository_url=<URL to .shed.yml on github>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
763 [--homepage_url=<Homepage for tool.>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
764 [--long_description=<long description>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
765 [--category=<category name>]*
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
766
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
767
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
768 planemo shed_update --check_diff --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
769 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
770 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
771 tout = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
772 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
773 tout = open(self.tlog, "w")
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
774 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
775 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
776 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
777 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
778 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
779 rids = [x.get("id", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
780 #cat = "ToolFactory generated tools"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
781 if self.args.tool_name not in rnames:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
782 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
783 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
784 "shed_create",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
785 "--shed_target",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
786 "local",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
787 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
788 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
789 "--name",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
790 self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
791 "--shed_key",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
792 self.args.toolshed_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
793 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
794 try:
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
795 subp = subprocess.run(
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
796 cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
797 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
798 except:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
799 pass
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
800 if subp.returncode != 0:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
801 tout.write("Repository %s exists\n" % self.args.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
802 else:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
803 tout.write("initiated %s\n" % self.args.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
804 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
805 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
806 "shed_upload",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
807 "--shed_target",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
808 "local",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
809 "--owner",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
810 "fubar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
811 "--name",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
812 self.args.tool_name,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
813 "--shed_key",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
814 self.args.toolshed_api_key,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
815 "--tar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
816 self.newtarpath,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
817 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
818 subp = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
819 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
820 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
821 return subp.returncode
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
822
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
823 def eph_test(self, genoutputs=True):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
824 """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
825 """
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
826 if os.path.exists(self.tlog):
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
827 tout = open(self.tlog, "a")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
828 else:
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
829 tout = open(self.tlog, "w")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
830 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
831 "shed-tools",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
832 "test",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
833 "-g",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
834 self.args.galaxy_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
835 "-a",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
836 self.args.galaxy_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
837 "--name",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
838 self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
839 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
840 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
841 ]
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
842 if genoutputs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
843 dummy, tfile = tempfile.mkstemp()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
844 subp = subprocess.run(
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
845 cll, shell=False, stderr=dummy, stdout=dummy
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
846 )
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
847
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
848 with open('tool_test_output.json','rb') as f:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
849 s = json.loads(f.read())
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
850 print('read %s' % s)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
851 cl = s['tests'][0]['data']['job']['command_line'].split()
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
852 n = cl.index('--script_path')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
853 jobdir = cl[n+1]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
854 jobdir = jobdir.replace('"','')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
855 jobdir = jobdir.split('/configs')[0]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
856 print('jobdir=%s' % jobdir)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
857
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
858 #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\"
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
859 src = os.path.join(jobdir,'working',self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
860 if os.path.exists(src):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
861 dest = os.path.join(self.testdir, self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
862 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
863 else:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
864 tout.write('No toolshed archive found after first ephemeris test - not a good sign')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
865 ephouts = os.path.join(jobdir,'working','tfout','test-data')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
866 with os.scandir(ephouts) as outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
867 for entry in outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
868 if not entry.is_file():
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
869 continue
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
870 dest = os.path.join(self.tooloutdir, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
871 src = os.path.join(ephouts, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
872 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
873 else:
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
874 subp = subprocess.run(
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
875 cll, shell=False, stderr=tout, stdout=tout)
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
876 tout.write("eph_test Ran %s got %d" % (" ".join(cll), subp.returncode))
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
877 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
878 return subp.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
879
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
880 def planemo_test_biocontainer(self, genoutputs=True):
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
881 """planemo is a requirement so is available for testing but testing in a biocontainer
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
882 requires some fiddling to use the hacked galaxy-central .venv
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
883
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
884 Planemo runs:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
885 python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
886 /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
887 --with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
888 --structured-data-file
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
889 /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
890
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
891
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
892 for the planemo-biocontainer,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
893 planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
894
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
895 """
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
896 xreal = "%s.xml" % self.tool_name
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
897 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
898 if os.path.exists(self.tlog):
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
899 tout = open(self.tlog, "a")
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
900 else:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
901 tout = open(self.tlog, "w")
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
902 if genoutputs:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
903 dummy, tfile = tempfile.mkstemp()
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
904 cll = [
95
6d122fd54cd0 Uploaded
fubar
parents: 91
diff changeset
905 ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
906 "planemo",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
907 "test",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
908 "--test_data", self.testdir,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
909 "--test_output", tool_test_path,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
910 "--skip_venv",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
911 "--galaxy_root",
91
7176af503cdd Uploaded
fubar
parents: 87
diff changeset
912 self.args.galaxy_root,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
913 "--update_test_data",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
914 xreal,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
915 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
916 subp = subprocess.run(
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
917 cll,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
918 shell=False,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
919 cwd=self.tooloutdir,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
920 stderr=dummy,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
921 stdout=dummy,
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
922 )
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
923
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
924 else:
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
925 cll = [
95
6d122fd54cd0 Uploaded
fubar
parents: 91
diff changeset
926 ".", os.path.join(self.args.galaxy_root,'.venv','bin','activate'),"&&",
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
927 "planemo",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
928 "test",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
929 "--test_data", os.path.self.testdir,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
930 "--test_output", os.path.tool_test_path,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
931 "--skip_venv",
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
932 "--galaxy_root",
91
7176af503cdd Uploaded
fubar
parents: 87
diff changeset
933 self.args.galaxy_root,
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
934 xreal,
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
935 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
936 subp = subprocess.run(
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
937 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
938 )
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
939 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
940 return subp.returncode
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
941
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
942 def planemo_test(self, genoutputs=True):
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
943 """planemo is a requirement so is available for testing but needs a different call if
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
944 in the biocontainer - see above
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
945 and for generating test outputs if command or test overrides are supplied
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
946 test outputs are sent to repdir for display
81
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
947 planemo test --engine docker_galaxy --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
948
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
949 Planemo runs:
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
950 python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
951 /export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
952 --with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
953 --structured-data-file
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
954 /export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
955
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
956
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
957 for the planemo-biocontainer,
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
958 planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
959
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
960 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
961 xreal = "%s.xml" % self.tool_name
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
962 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
963 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
964 tout = open(self.tlog, "a")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
965 else:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
966 tout = open(self.tlog, "w")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
967 if genoutputs:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
968 dummy, tfile = tempfile.mkstemp()
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
969 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
970 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
971 "test",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
972 "--galaxy_root",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
973 self.args.galaxy_root,
74
3d4324df911b Uploaded
fubar
parents: 72
diff changeset
974 "--update_test_data",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
975 xreal,
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
976 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
977 subp = subprocess.run(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
978 cll,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
979 shell=False,
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
980 cwd=self.testdir,
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
981 stderr=dummy,
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
982 stdout=dummy,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
983 )
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
984
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
985 else:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
986 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
987 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
988 "test",
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
989 "--test_data", self.testdir,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
990 "--test_output",tool_test_path,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
991 "--galaxy_root",
74
3d4324df911b Uploaded
fubar
parents: 72
diff changeset
992 self.args.galaxy_root,
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
993 xreal,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
994 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
995 subp = subprocess.run(
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
996 cll, shell=False, cwd=self.testdir, stderr=tout, stdout=tout
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
997 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
998 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
999 return subp.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
1000
83
48acd0708839 Uploaded
fubar
parents: 81
diff changeset
1001
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1002 def gal_test(self, genoutputs=True):
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1003 """
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1004 export GALAXY_TEST_SAVE="./foo" && export GALAXY_TEST_NO_CLEANUP="1" \
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1005 && export GALAXY_TEST_TMP_DIR=./foo && sh run_tests.sh --id rgtf2 --report_file tool_tests_tool_conf.html functional.test_toolbox
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1006
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1007 """
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1008 tool_test_rep_path = os.path.join(self.repdir,f"{self.tool_name}_galaxy_test_report_html.html")
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1009 if os.path.exists(self.tlog):
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1010 tout = open(self.tlog, "a")
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1011 else:
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1012 tout = open(self.tlog, "w")
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1013 testdir = '/tmp/testdir'
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1014 ourenv = os.environ
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1015 ourenv["GALAXY_TEST_SAVE"] = os.abspath(testdir)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1016 ourenv["GALAXY_TEST_NO_CLEANUP"] = "1"
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1017 ourenv["GALAXY_TEST_TMP_DIR"] = os.abspath(testdir)
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1018 if genoutputs:
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1019
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1020 if not os.path.exists(testdir):
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1021 os.mkdir(testdir)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1022 dummy = open('failedtest.log','w')
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1023 cll = [
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1024 "sh", f"{self.args.galaxy_root}/run_tests.sh", "--id", self.args.tool_name,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1025 "--report_file", tool_test_rep_path, "functional.test_toolbox",
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1026 ]
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1027 subp = subprocess.run(
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1028 cll,
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1029 shell=False,
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1030 env = ourenv,
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1031 cwd=self.testdir,
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1032 stderr=dummy,
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1033 stdout=dummy,
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1034 )
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1035 dummy.close()
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1036 # if all went well, tgz is in ./test and down a nest of tmp directories lurk the output files
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1037 outfiles = []
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1038 for p in self.outfiles:
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1039 oname = p[ONAMEPOS]
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1040 outfiles.append(oname)
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1041 paths = []
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1042 for root, dirs, files in os.walk(testdir):
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1043 for f in files:
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1044 tout.write(f"{root} {f}\n")
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1045 if f in outfiles:
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1046 paths.append([root,f])
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1047 tout.write(f"## found output {f}")
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1048
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1049 if len(paths) != len(self.outfiles):
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1050 tout.write(f"## problem - outfiles not all found")
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1051 for path in paths:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1052 fname = path[1]
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1053 src = os.path.join(path[0],fname)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1054 dest = os.path.join(self.testdir,f"{fname}_sample")
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1055 shutil.copyfile(src,dest)
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1056 else:
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1057 cll = [
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1058 "sh", f"{self.args.galaxy_root}/run_tests.sh", "--id", self.args.tool_name,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1059 "--report_file", tool_test_rep_path, "functional.test_toolbox",
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1060 ]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1061 subp = subprocess.run(
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1062 cll, env = ourenv,
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1063 shell=False, cwd=self.testdir, stderr=tout, stdout=tout
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1064 )
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1065 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1066 return subp.returncode
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1067
97
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1068
515be7318f2b Uploaded
fubar
parents: 96
diff changeset
1069
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1070 def writeShedyml(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1071 """for planemo"""
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1072 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1073 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1074 yamlf = open(yfname, "w")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1075 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1076 "name": self.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1077 "owner": yuser,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1078 "type": "unrestricted",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1079 "description": self.args.tool_desc,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1080 "synopsis": self.args.tool_desc,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1081 "category": "TF Generated Tools",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1082 }
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1083 yaml.dump(odict, yamlf, allow_unicode=True)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1084 yamlf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
1085
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1086 def makeTool(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1087 """write xmls and input samples into place"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1088 self.makeXML()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1089 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1090 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1091 if not os.path.exists(stname):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1092 shutil.copyfile(self.sfile, stname)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1093 xreal = "%s.xml" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1094 xout = os.path.join(self.tooloutdir, xreal)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1095 shutil.copyfile(xreal, xout)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1096 for p in self.infiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1097 pth = p[IPATHPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1098 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1099 shutil.copyfile(pth, dest)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
1100
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1101 def makeToolTar(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1102 """move outputs into test-data and prepare the tarball"""
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1103 excludeme = "tool_test_output"
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1104
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1105 def exclude_function(tarinfo):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1106 filename = tarinfo.name
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1107 return (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1108 None
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1109 if filename.startswith(excludeme)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1110 else tarinfo
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1111 )
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1112
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1113 for p in self.outfiles:
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
1114 oname = p[ONAMEPOS]
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
1115 src = os.path.join(self.testdir,oname)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1116 if os.path.isfile(src):
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
1117 dest = os.path.join(self.testdir, "%s_sample" % oname)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1118 shutil.copyfile(src, dest)
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
1119 dest = os.path.join(self.repdir, "%s.sample" % (oname))
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1120 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1121 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1122 print(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1123 "### problem - output file %s not found in tooloutdir %s"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1124 % (src, self.tooloutdir)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1125 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1126 tf = tarfile.open(self.newtarpath, "w:gz")
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
1127 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1128 tf.close()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1129 shutil.copyfile(self.newtarpath, self.args.new_tool)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1130
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1131 def fakeToolTar(self):
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1132 """move fake outputs into test-data and prepare the tarball"""
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1133 excludeme = "tool_test_output"
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1134
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1135 def exclude_function(tarinfo):
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1136 filename = tarinfo.name
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1137 return (
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1138 None
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1139 if filename.startswith(excludeme)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1140 else tarinfo
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1141 )
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1142
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1143 for p in self.outfiles:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1144 oname = p[ONAMEPOS]
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1145 src = os.path.join(self.testdir,oname)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1146 if os.path.isfile(src):
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1147 dest = os.path.join(self.testdir, "%s_sample" % oname)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1148 shutil.copyfile(src, dest)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1149 dest = os.path.join(self.repdir, "%s.sample" % (oname))
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1150 shutil.copyfile(src, dest)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1151 else:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1152 with open(src,'w') as fayk:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1153 fayk.write('fake!\n')
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1154 dest = os.path.join(self.testdir, "%s_sample" % oname)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1155 shutil.copyfile(src, dest)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1156 print(
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1157 "### problem - output file %s not found in tooloutdir %s so faked"
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1158 % (src, self.tooloutdir)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1159 )
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1160 tf = tarfile.open(self.newtarpath, "w:gz")
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1161 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1162 tf.close()
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1163 shutil.copyfile(self.newtarpath, self.args.new_tool)
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1164
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
1165
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1166 def moveRunOutputs(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
1167 """need to move planemo or run outputs into toolfactory collection"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1168 with os.scandir(self.tooloutdir) as outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
1169 for entry in outs:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1170 if not entry.is_file():
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
1171 continue
f423a77bc669 Uploaded
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parents: 78
diff changeset
1172 if "." in entry.name:
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1173 nayme, ext = os.path.splitext(entry.name)
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1174 if ext in ['.yml','.xml','.json','.yaml']:
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1175 ext = f'{ext}.txt'
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1176 else:
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1177 ext = ".txt"
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1178 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
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1179 dest = os.path.join(self.repdir, ofn)
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1180 src = os.path.join(self.tooloutdir, entry.name)
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1181 shutil.copyfile(src, dest)
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1182 with os.scandir(self.testdir) as outs:
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1183 for entry in outs:
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diff changeset
1184 if not entry.is_file():
50
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1185 continue
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diff changeset
1186 if "." in entry.name:
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diff changeset
1187 nayme, ext = os.path.splitext(entry.name)
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diff changeset
1188 else:
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1189 ext = ".txt"
80
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1190 newname = f"{entry.name}{ext}"
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1191 dest = os.path.join(self.repdir, newname)
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1192 src = os.path.join(self.testdir, entry.name)
50
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1193 shutil.copyfile(src, dest)
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1194
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1195
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1196
48
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1197 def main():
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1198 """
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1199 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
49
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diff changeset
1200 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
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diff changeset
1201 --tool_name "foo" --interpreter "Rscript"
48
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1202 </command>
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1203 """
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1204 parser = argparse.ArgumentParser()
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1205 a = parser.add_argument
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diff changeset
1206 a("--script_path", default=None)
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diff changeset
1207 a("--history_test", default=None)
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diff changeset
1208 a("--cl_prefix", default=None)
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diff changeset
1209 a("--sysexe", default=None)
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diff changeset
1210 a("--packages", default=None)
76
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diff changeset
1211 a("--tool_name", default="newtool")
72
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diff changeset
1212 a("--tool_dir", default=None)
48
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1213 a("--input_files", default=[], action="append")
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1214 a("--output_files", default=[], action="append")
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1215 a("--user_email", default="Unknown")
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1216 a("--bad_user", default=None)
49
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1217 a("--make_Tool", default="runonly")
48
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1218 a("--help_text", default=None)
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1219 a("--tool_desc", default=None)
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1220 a("--tool_version", default=None)
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diff changeset
1221 a("--citations", default=None)
49
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diff changeset
1222 a("--command_override", default=None)
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1223 a("--test_override", default=None)
48
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diff changeset
1224 a("--additional_parameters", action="append", default=[])
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diff changeset
1225 a("--edit_additional_parameters", action="store_true", default=False)
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diff changeset
1226 a("--parampass", default="positional")
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parents:
diff changeset
1227 a("--tfout", default="./tfout")
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parents:
diff changeset
1228 a("--new_tool", default="new_tool")
49
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1229 a("--galaxy_url", default="http://localhost:8080")
75
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diff changeset
1230 a(
76
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diff changeset
1231 "--toolshed_url", default="http://localhost:9009")
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diff changeset
1232 # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails
63
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diff changeset
1233 a("--toolshed_api_key", default="fakekey")
50
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parents: 49
diff changeset
1234 a("--galaxy_api_key", default="fakekey")
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diff changeset
1235 a("--galaxy_root", default="/galaxy-central")
48
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parents:
diff changeset
1236 args = parser.parse_args()
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diff changeset
1237 assert not args.bad_user, (
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diff changeset
1238 '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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parents:
diff changeset
1239 % (args.bad_user, args.bad_user)
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parents:
diff changeset
1240 )
49
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diff changeset
1241 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
48
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parents:
diff changeset
1242 assert (
49
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diff changeset
1243 args.sysexe or args.packages
48
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parents:
diff changeset
1244 ), "## Tool Factory wrapper expects an interpreter or an executable package"
49
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diff changeset
1245 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
48
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parents:
diff changeset
1246 # remove quotes we need to deal with spaces in CL params
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diff changeset
1247 for i, x in enumerate(args.additional_parameters):
49
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diff changeset
1248 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
48
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parents:
diff changeset
1249 r = ScriptRunner(args)
49
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1250 r.writeShedyml()
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1251 r.makeTool()
66
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parents: 65
diff changeset
1252 if args.make_Tool == "generate":
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diff changeset
1253 retcode = r.run()
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parents: 65
diff changeset
1254 r.moveRunOutputs()
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diff changeset
1255 r.makeToolTar()
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diff changeset
1256 else:
98
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parents: 97
diff changeset
1257 r.fakeToolTar()
97
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diff changeset
1258 r.shedLoad()
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parents: 96
diff changeset
1259 r.eph_galaxy_load()
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parents: 96
diff changeset
1260 retcode = r.gal_test(genoutputs=True) # this fails
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parents: 96
diff changeset
1261 r.makeToolTar()
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parents: 96
diff changeset
1262 retcode = r.gal_test(genoutputs=False)
66
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parents: 65
diff changeset
1263 r.moveRunOutputs()
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parents: 65
diff changeset
1264 r.makeToolTar()
97
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parents: 96
diff changeset
1265 print(f"second galaxy_test returned {retcode}")
63
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parents: 62
diff changeset
1266
48
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parents:
diff changeset
1267
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diff changeset
1268 if __name__ == "__main__":
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parents:
diff changeset
1269 main()