annotate toolfactory/rgToolFactory2.py @ 81:6395be766c2e draft

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author fubar
date Wed, 18 Nov 2020 21:47:51 +0000
parents f423a77bc669
children 48acd0708839
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1 # rgToolFactory.py
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2 # see https://github.com/fubar2/toolfactory
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at
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9 # https://github.com/fubar2/toolfactory
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10 #
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11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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12 # Decided to
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13 # 1. Fix the toolfactory so it works - done for simplest case
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14 # 2. Fix planemo so the toolfactory function works
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15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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16 #
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17 # removed all the old complications including making the new tool use this same script
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18 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
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19 # No support for automatic HTML file creation from arbitrary outputs
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20 # essential problem is to create two command lines - one for the tool xml and a different
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21 # one to run the executable with the supplied test data and settings
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22 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
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23
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24
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25 import argparse
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26 import datetime
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27 import json
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28 import logging
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29 import os
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30 import re
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31 import shutil
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32 import subprocess
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33 import sys
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34 import tarfile
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35 import tempfile
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36 import time
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37
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38
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39 from bioblend import toolshed
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40
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41 import galaxyxml.tool as gxt
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42 import galaxyxml.tool.parameters as gxtp
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44 import lxml
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45
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46 import yaml
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48 myversion = "V2.1 July 2020"
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49 verbose = True
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50 debug = True
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51 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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52 ourdelim = "~~~"
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53 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
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54 STDIOXML = """<stdio>
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55 <exit_code range="100:" level="debug" description="shite happens" />
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56 </stdio>"""
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58 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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59 # ~~~$input_help"
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60 IPATHPOS = 0
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61 ICLPOS = 1
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62 IFMTPOS = 2
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63 ILABPOS = 3
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64 IHELPOS = 4
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65 IOCLPOS = 5
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66
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67 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
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68 ONAMEPOS = 0
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69 OFMTPOS = 1
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70 OCLPOS = 2
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71 OTESTPOS = 3
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72 OOCLPOS = 4
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75 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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76 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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77 ANAMEPOS = 0
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78 AVALPOS = 1
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79 ALABPOS = 2
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80 AHELPPOS = 3
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81 ATYPEPOS = 4
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82 ACLPOS = 5
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83 AOVERPOS = 6
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84 AOCLPOS = 7
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87 foo = len(lxml.__version__)
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88 # fug you, flake8. Say my name!
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89 FAKEEXE = "~~~REMOVE~~~ME~~~"
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90 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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91 # with override.
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94 def timenow():
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95 """return current time as a string"""
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96 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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99 def quote_non_numeric(s):
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100 """return a prequoted string for non-numerics
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101 useful for perl and Rscript parameter passing?
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102 """
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103 try:
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104 _ = float(s)
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105 return s
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106 except ValueError:
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107 return '"%s"' % s
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110 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
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111
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112
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113 def html_escape(text):
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114 """Produce entities within text."""
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115 return "".join(html_escape_table.get(c, c) for c in text)
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116
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117
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118 def html_unescape(text):
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119 """Revert entities within text. Multiple character targets so use replace"""
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120 t = text.replace("&amp;", "&")
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121 t = t.replace("&gt;", ">")
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122 t = t.replace("&lt;", "<")
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123 t = t.replace("\\$", "$")
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124 return t
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125
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126
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127 def parse_citations(citations_text):
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128 """"""
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129 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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130 citation_tuples = []
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131 for citation in citations:
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132 if citation.startswith("doi"):
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133 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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134 else:
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135 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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136 return citation_tuples
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137
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138
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139 class ScriptRunner:
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140 """Wrapper for an arbitrary script
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141 uses galaxyxml
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142
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143 """
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144
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145 def __init__(self, args=None):
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146 """
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147 prepare command line cl for running the tool here
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148 and prepare elements needed for galaxyxml tool generation
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149 """
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150 self.infiles = [x.split(ourdelim) for x in args.input_files]
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151 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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152 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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153 self.args = args
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154 self.cleanuppar()
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155 self.lastclredirect = None
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156 self.lastxclredirect = None
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157 self.cl = []
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158 self.xmlcl = []
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159 self.is_positional = self.args.parampass == "positional"
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160 if self.args.sysexe:
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161 self.executeme = self.args.sysexe
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162 else:
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163 if self.args.packages:
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164 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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165 else:
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166 self.executeme = None
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167 aCL = self.cl.append
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168 aXCL = self.xmlcl.append
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169 assert args.parampass in [
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170 "0",
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171 "argparse",
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172 "positional",
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173 ], 'args.parampass must be "0","positional" or "argparse"'
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174 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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175 self.tool_id = self.tool_name
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176 self.newtool = gxt.Tool(
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177 self.args.tool_name,
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178 self.tool_id,
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179 self.args.tool_version,
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180 self.args.tool_desc,
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181 FAKEEXE,
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182 )
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183 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
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184 self.tooloutdir = "tfout"
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185 self.repdir = "TF_run_report_tempdir"
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186 self.testdir = os.path.join(self.tooloutdir, "test-data")
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187 if not os.path.exists(self.tooloutdir):
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188 os.mkdir(self.tooloutdir)
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189 if not os.path.exists(self.testdir):
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190 os.mkdir(self.testdir) # make tests directory
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191 if not os.path.exists(self.repdir):
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192 os.mkdir(self.repdir)
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193 self.tinputs = gxtp.Inputs()
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194 self.toutputs = gxtp.Outputs()
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195 self.testparam = []
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196 if self.args.script_path:
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197 self.prepScript()
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198 if self.args.command_override:
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199 scos = open(self.args.command_override, "r").readlines()
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200 self.command_override = [x.rstrip() for x in scos]
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201 else:
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202 self.command_override = None
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203 if self.args.test_override:
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204 stos = open(self.args.test_override, "r").readlines()
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205 self.test_override = [x.rstrip() for x in stos]
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206 else:
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207 self.test_override = None
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208 if self.args.cl_prefix: # DIY CL start
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209 clp = self.args.cl_prefix.split(" ")
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210 for c in clp:
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211 aCL(c)
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212 aXCL(c)
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213 else:
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214 if self.args.script_path:
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215 aCL(self.executeme)
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216 aCL(self.sfile)
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217 aXCL(self.executeme)
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218 aXCL("$runme")
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219 else:
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220 aCL(self.executeme) # this little CL will just run
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221 aXCL(self.executeme)
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222 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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223 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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224
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225 if self.args.parampass == "0":
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226 self.clsimple()
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227 else:
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228 clsuffix = []
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229 xclsuffix = []
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230 for i, p in enumerate(self.infiles):
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231 if p[IOCLPOS] == "STDIN":
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232 appendme = [
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233 p[IOCLPOS],
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234 p[ICLPOS],
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235 p[IPATHPOS],
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236 "< %s" % p[IPATHPOS],
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237 ]
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238 xappendme = [
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239 p[IOCLPOS],
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240 p[ICLPOS],
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241 p[IPATHPOS],
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242 "< $%s" % p[ICLPOS],
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243 ]
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244 else:
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245 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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246 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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247 clsuffix.append(appendme)
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248 xclsuffix.append(xappendme)
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249 for i, p in enumerate(self.outfiles):
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250 if p[OOCLPOS] == "STDOUT":
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251 self.lastclredirect = [">", p[ONAMEPOS]]
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252 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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253 else:
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254 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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255 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
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256 for p in self.addpar:
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257 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
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258 xclsuffix.append(
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259 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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260 )
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261 clsuffix.sort()
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262 xclsuffix.sort()
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263 self.xclsuffix = xclsuffix
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264 self.clsuffix = clsuffix
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265 if self.args.parampass == "positional":
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266 self.clpositional()
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267 else:
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268 self.clargparse()
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269
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270 def prepScript(self):
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271 rx = open(self.args.script_path, "r").readlines()
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272 rx = [x.rstrip() for x in rx]
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273 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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274 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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275 self.script = "\n".join(rx)
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276 fhandle, self.sfile = tempfile.mkstemp(
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277 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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278 )
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279 tscript = open(self.sfile, "w")
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280 tscript.write(self.script)
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281 tscript.close()
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282 self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx])
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283 self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
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284 art = "%s.%s" % (self.tool_name, self.executeme)
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285 artifact = open(art, "wb")
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286 artifact.write(bytes(self.script, "utf8"))
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287 artifact.close()
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288
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289 def cleanuppar(self):
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290 """ positional parameters are complicated by their numeric ordinal"""
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291 for i, p in enumerate(self.infiles):
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292 if self.args.parampass == "positional":
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293 assert p[
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294 ICLPOS
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295 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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296 p[ICLPOS],
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297 p[ILABPOS],
48
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298 )
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299 p.append(p[ICLPOS])
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300 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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301 scl = "input%d" % (i + 1)
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302 p[ICLPOS] = scl
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303 self.infiles[i] = p
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parents:
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304 for i, p in enumerate(
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305 self.outfiles
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parents:
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306 ): # trying to automagically gather using extensions
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307 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
75
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diff changeset
308 assert p[
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309 OCLPOS
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310 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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311 p[OCLPOS],
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312 p[ONAMEPOS],
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313 )
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314 p.append(p[OCLPOS])
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315 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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316 scl = p[ONAMEPOS]
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317 p[OCLPOS] = scl
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318 self.outfiles[i] = p
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319 for i, p in enumerate(self.addpar):
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parents:
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320 if self.args.parampass == "positional":
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321 assert p[
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322 ACLPOS
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323 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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parents: 74
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324 p[ACLPOS],
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parents: 74
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325 p[ANAMEPOS],
48
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parents:
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326 )
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parents:
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327 p.append(p[ACLPOS])
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parents:
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328 if p[ACLPOS].isdigit():
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parents:
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329 scl = "input%s" % p[ACLPOS]
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parents:
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330 p[ACLPOS] = scl
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parents:
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331 self.addpar[i] = p
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parents:
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332
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333 def clsimple(self):
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334 """no parameters - uses < and > for i/o"""
48
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parents:
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335 aCL = self.cl.append
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parents:
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336 aXCL = self.xmlcl.append
62
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parents: 57
diff changeset
337
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parents: 57
diff changeset
338 if len(self.infiles) > 0:
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diff changeset
339 aCL("<")
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diff changeset
340 aCL(self.infiles[0][IPATHPOS])
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341 aXCL("<")
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342 aXCL("$%s" % self.infiles[0][ICLPOS])
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parents: 57
diff changeset
343 if len(self.outfiles) > 0:
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parents: 57
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344 aCL(">")
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345 aCL(self.outfiles[0][OCLPOS])
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parents: 57
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346 aXCL(">")
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347 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
48
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parents:
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348
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349 def clpositional(self):
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parents:
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350 # inputs in order then params
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parents:
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351 aCL = self.cl.append
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parents:
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352 for (o_v, k, v, koverride) in self.clsuffix:
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parents:
diff changeset
353 if " " in v:
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parents:
diff changeset
354 aCL("%s" % v)
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parents:
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355 else:
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parents:
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356 aCL(v)
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parents:
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357 aXCL = self.xmlcl.append
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parents:
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358 for (o_v, k, v, koverride) in self.xclsuffix:
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parents:
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359 aXCL(v)
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parents:
diff changeset
360 if self.lastxclredirect:
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parents:
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361 aXCL(self.lastxclredirect[0])
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parents:
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362 aXCL(self.lastxclredirect[1])
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parents:
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363
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parents:
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364 def clargparse(self):
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365 """argparse style"""
48
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fubar
parents:
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366 aCL = self.cl.append
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parents:
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367 aXCL = self.xmlcl.append
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368 # inputs then params in argparse named form
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parents:
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369 for (o_v, k, v, koverride) in self.xclsuffix:
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parents:
diff changeset
370 if koverride > "":
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parents:
diff changeset
371 k = koverride
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parents:
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372 elif len(k.strip()) == 1:
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parents:
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373 k = "-%s" % k
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parents:
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374 else:
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parents:
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375 k = "--%s" % k
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fubar
parents:
diff changeset
376 aXCL(k)
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parents:
diff changeset
377 aXCL(v)
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parents:
diff changeset
378 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
379 if koverride > "":
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parents:
diff changeset
380 k = koverride
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parents:
diff changeset
381 elif len(k.strip()) == 1:
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parents:
diff changeset
382 k = "-%s" % k
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parents:
diff changeset
383 else:
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parents:
diff changeset
384 k = "--%s" % k
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fubar
parents:
diff changeset
385 aCL(k)
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fubar
parents:
diff changeset
386 aCL(v)
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fubar
parents:
diff changeset
387
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parents:
diff changeset
388 def getNdash(self, newname):
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fubar
parents:
diff changeset
389 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
390 ndash = 0
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fubar
parents:
diff changeset
391 else:
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fubar
parents:
diff changeset
392 ndash = 2
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fubar
parents:
diff changeset
393 if len(newname) < 2:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
394 ndash = 1
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fubar
parents:
diff changeset
395 return ndash
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396
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fubar
parents:
diff changeset
397 def doXMLparam(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 """flake8 made me do this..."""
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 for p in self.outfiles:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
400 newname, newfmt, newcl, test, oldcl = p
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 ndash = self.getNdash(newcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 if oldcl == "STDOUT":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406 aparm.positional = 9999999
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 aparm.command_line_override = "> $%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
409 aparm.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
410 aparm.command_line_override = "$%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
411 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
412 usetest = None
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
413 ld = None
50
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fubar
parents: 49
diff changeset
414 if test > "":
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fubar
parents: 49
diff changeset
415 if test.startswith("diff"):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
416 usetest = "diff"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
417 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
418 ld = int(test.split(":")[1])
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
419 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
420 usetest = test
50
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fubar
parents: 49
diff changeset
421 tp = gxtp.TestOutput(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
422 name=newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
423 value="%s_sample" % newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
424 format=newfmt,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
425 compare=usetest,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
426 lines_diff=ld,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
427 delta=None,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
428 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
429 self.testparam.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
430 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
431 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
432 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
434 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
435 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
436 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
438 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 for p in self.addpar:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
486 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 if self.is_positional:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
488 aparm.positional = int(oldcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
489 self.tinputs.append(aparm)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
490 tparm = gxtp.TestParam(newname, value=newval)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
491 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
492
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
493 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
494 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
495 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
496 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
497 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
498 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
499 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
500 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
501 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
502 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
503 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
504 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
505 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
506 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
507 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
508 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
509 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
510 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
511 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
512 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
513 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
514 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
515 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
516 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
517 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
518 self.testparam.append(tp)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
519 if len(self.outfiles) > 0:
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
520 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
521 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
522 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
523 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
524 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
525 self.toutputs.append(anout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
526 tp = gxtp.TestOutput(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
527 name=newname, value="%s_sample" % newname, format=newfmt
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
528 )
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
529 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
530
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
531 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
532 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
533 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
534 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
535 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
536 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
537 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
538 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
539 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
540 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
541 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
542 helptext = open(self.args.help_text, "r").readlines()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
543 safertext = [html_escape(x) for x in helptext]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
544 if False and self.args.script_path:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
545 scrp = self.script.split("\n")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
546 scrpt = [" %s" % x for x in scrp] # try to stop templating
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
547 scrpt.insert(0, "```\n")
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
548 if len(scrpt) > 300:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
549 safertext = (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
550 safertext + scrpt[:100] + \
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
551 [">500 lines - stuff deleted", "......"] + scrpt[-100:]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
552 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
553 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
554 safertext = safertext + scrpt
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
555 safertext.append("\n```")
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
556 self.newtool.help = "\n".join([x for x in safertext])
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
557 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
558 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
559 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
560 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
561 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
562 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
563 self.newtool.version_command = None # do not want
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
564 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
565 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
566 for d in self.args.packages.split(","):
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
567 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
568 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
569 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
570 packg = d
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
571 ver = ""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
572 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
573 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
574 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
575 self.newtool.requirements = requirements
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
576 if self.args.parampass == "0":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
577 self.doNoXMLparam()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
578 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
579 self.doXMLparam()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
580 self.newtool.outputs = self.toutputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
581 self.newtool.inputs = self.tinputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
582 if self.args.script_path:
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
583 configfiles = gxtp.Configfiles()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
584 configfiles.append(gxtp.Configfile(name="runme", text=self.script))
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
585 self.newtool.configfiles = configfiles
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
586 tests = gxtp.Tests()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
587 test_a = gxtp.Test()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
588 for tp in self.testparam:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
589 test_a.append(tp)
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fubar
parents:
diff changeset
590 tests.append(test_a)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
591 self.newtool.tests = tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
592 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
593 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
594 % (self.args.user_email, timenow())
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
595 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
596 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
597 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
598 "Cite: Creating re-usable tools from scripts doi: \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
599 10.1093/bioinformatics/bts573"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
600 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
601 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
602 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
603 if (
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
604 self.test_override
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
605 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
606 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
607 part2 = exml.split("</tests>")[1]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
608 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
609 exml = fixed
63
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fubar
parents: 62
diff changeset
610 exml = exml.replace('range="1:"', 'range="1000:"')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
611 xf = open("%s.xml" % self.tool_name, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
612 xf.write(exml)
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fubar
parents:
diff changeset
613 xf.write("\n")
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fubar
parents:
diff changeset
614 xf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
615 # ready for the tarball
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
616
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fubar
parents:
diff changeset
617 def run(self):
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fubar
parents:
diff changeset
618 """
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
619 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
620 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
621 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
622 automagically selected
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
623 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
624 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
625 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
626 if self.args.parampass != "0":
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
627 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
628 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
629 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
630 ste = open(self.elog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
631 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
632 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
633 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
634 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
635 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
636 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
637 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
638 sto.write(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
639 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
640 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
641 sto.flush()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
642 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
643 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
644 ste.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
645 retval = p.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
646 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
647 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
648 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
649 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
650 sti = sys.stdin
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
651 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
652 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
653 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
654 sto = sys.stdout
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
655 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
656 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
657 retval = p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
658 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
659 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
660 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
661 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
662 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
663 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
664 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
665 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
666 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
667 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
668
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
669 def shedLoad(self):
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
670 """
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
671 {'deleted': False,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
672 'description': 'Tools for manipulating data',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
673 'id': '175812cd7caaf439',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
674 'model_class': 'Category',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
675 'name': 'Text Manipulation',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
676 'url': '/api/categories/175812cd7caaf439'}]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
677
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
678
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
679 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
680 if os.path.exists(self.tlog):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
681 sto = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
682 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
683 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
684
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
685 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
686 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
687 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
688 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
689 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
690 rids = [x.get("id", "?") for x in repos]
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
691 sto.write(f"############names={rnames} rids={rids}\n")
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
692 cat = "ToolFactory generated tools"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
693 if self.args.tool_name not in rnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
694 tscat = ts.categories.get_categories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
695 cnames = [x.get("name", "?") for x in tscat]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
696 cids = [x.get("id", "?") for x in tscat]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
697 catID = None
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
698 if cat in cnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
699 ci = cnames.index(cat)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
700 catID = cids[ci]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
701 res = ts.repositories.create_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
702 name=self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
703 synopsis="Synopsis:%s" % self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
704 description=self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
705 type="unrestricted",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
706 remote_repository_url=self.args.toolshed_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
707 homepage_url=None,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
708 category_ids=catID,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
709 )
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
710 tid = res.get("id", None)
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
711 sto.write(f"##########create res={res}\n")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
712 else:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
713 i = rnames.index(self.args.tool_name)
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
714 tid = rids[i]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
715 res = ts.repositories.update_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
716 id=tid, tar_ball_path=self.newtarpath, commit_message=None
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
717 )
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
718 sto.write(f"#####update res={res}\n")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
719 sto.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
720
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
721 def eph_galaxy_load(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
722 """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
723 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
724 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
725 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
726 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
727 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
728 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
729 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
730 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
731 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
732 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
733 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
734 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
735 "--name",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
736 self.args.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
737 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
738 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
739 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
740 self.args.toolshed_url,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
741 "--section_label",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
742 "ToolFactory",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
743 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
744 tout.write("running\n%s\n" % " ".join(cll))
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
745 p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
746 tout.write(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
747 "installed %s - got retcode %d\n" % (self.args.tool_name, p.returncode)
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
748 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
749 tout.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
750 return p.returncode
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
751
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
752 def planemo_shedload(self):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
753 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
754 planemo shed_create --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
755 planemo shed_init --name=<name>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
756 --owner=<shed_username>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
757 --description=<short description>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
758 [--remote_repository_url=<URL to .shed.yml on github>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
759 [--homepage_url=<Homepage for tool.>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
760 [--long_description=<long description>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
761 [--category=<category name>]*
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
762
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
763
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
764 planemo shed_update --check_diff --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
765 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
766 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
767 tout = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
768 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
769 tout = open(self.tlog, "w")
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
770 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
771 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
772 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
773 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
774 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
775 rids = [x.get("id", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
776 #cat = "ToolFactory generated tools"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
777 if self.args.tool_name not in rnames:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
778 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
779 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
780 "shed_create",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
781 "--shed_target",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
782 "local",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
783 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
784 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
785 "--name",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
786 self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
787 "--shed_key",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
788 self.args.toolshed_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
789 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
790 try:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
791 p = subprocess.run(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
792 cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
793 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
794 except:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
795 pass
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
796 if p.returncode != 0:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
797 tout.write("Repository %s exists\n" % self.args.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
798 else:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
799 tout.write("initiated %s\n" % self.args.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
800 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
801 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
802 "shed_upload",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
803 "--shed_target",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
804 "local",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
805 "--owner",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
806 "fubar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
807 "--name",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
808 self.args.tool_name,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
809 "--shed_key",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
810 self.args.toolshed_api_key,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
811 "--tar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
812 self.newtarpath,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
813 ]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
814 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
815 tout.write("Ran %s got %d\n" % (" ".join(cll), p.returncode))
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
816 tout.close()
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
817 return p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
818
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
819 def eph_test(self, genoutputs=True):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
820 """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
821 """
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
822 if os.path.exists(self.tlog):
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
823 tout = open(self.tlog, "a")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
824 else:
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
825 tout = open(self.tlog, "w")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
826 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
827 "shed-tools",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
828 "test",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
829 "-g",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
830 self.args.galaxy_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
831 "-a",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
832 self.args.galaxy_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
833 "--name",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
834 self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
835 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
836 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
837 ]
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
838 if genoutputs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
839 dummy, tfile = tempfile.mkstemp()
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
840 p = subprocess.run(
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
841 cll, shell=False, stderr=dummy, stdout=dummy
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
842 )
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
843
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
844 with open('tool_test_output.json','rb') as f:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
845 s = json.loads(f.read())
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
846 print('read %s' % s)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
847 cl = s['tests'][0]['data']['job']['command_line'].split()
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
848 n = cl.index('--script_path')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
849 jobdir = cl[n+1]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
850 jobdir = jobdir.replace('"','')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
851 jobdir = jobdir.split('/configs')[0]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
852 print('jobdir=%s' % jobdir)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
853
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
854 #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\"
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
855 src = os.path.join(jobdir,'working',self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
856 if os.path.exists(src):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
857 dest = os.path.join(self.testdir, self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
858 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
859 else:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
860 tout.write('No toolshed archive found after first ephemeris test - not a good sign')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
861 ephouts = os.path.join(jobdir,'working','tfout','test-data')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
862 with os.scandir(ephouts) as outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
863 for entry in outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
864 if not entry.is_file():
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
865 continue
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
866 dest = os.path.join(self.tooloutdir, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
867 src = os.path.join(ephouts, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
868 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
869 else:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
870 p = subprocess.run(
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
871 cll, shell=False, stderr=tout, stdout=tout)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
872 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode))
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
873 tout.close()
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
874 return p.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
875
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
876 def planemo_test(self, genoutputs=True):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
877 """planemo is a requirement so is available for testing
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
878 and for generating test outputs if command or test overrides are supplied
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
879 test outputs are sent to repdir for display
81
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
880 planemo test --engine docker_galaxy --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
881
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
882 Planemo runs:
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
883 python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
884 /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
885 --with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
886 --structured-data-file
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
887 /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
888
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
889
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
890 for the planemo-biocontainer,
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
891 planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
892
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
893 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
894 xreal = "%s.xml" % self.tool_name
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
895 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
896 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
897 tout = open(self.tlog, "a")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
898 else:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
899 tout = open(self.tlog, "w")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
900 if genoutputs:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
901 dummy, tfile = tempfile.mkstemp()
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
902 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
903 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
904 "test",
81
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
905 "--conda_dependency_resolution",
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
906 "--test_data", os.path.abspath(self.testdir),
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
907 "--test_output", os.path.abspath(tool_test_path),
81
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
908 "--skip_venv",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
909 "--galaxy_root",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
910 self.args.galaxy_root,
74
3d4324df911b Uploaded
fubar
parents: 72
diff changeset
911 "--update_test_data",
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
912 os.path.abspath(xreal),
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
913 ]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
914 p = subprocess.run(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
915 cll,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
916 shell=False,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
917 cwd=self.tooloutdir,
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
918 stderr=dummy,
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
919 stdout=dummy,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
920 )
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
921
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
922 else:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
923 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
924 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
925 "test",
81
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
926 "--conda_dependency_resolution",
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
927 "--test_data", os.path.abspath(self.testdir),
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
928 "--test_output", os.path.abspath(tool_test_path),
81
6395be766c2e Uploaded
fubar
parents: 80
diff changeset
929 "--skip_venv",
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
930 "--galaxy_root",
74
3d4324df911b Uploaded
fubar
parents: 72
diff changeset
931 self.args.galaxy_root,
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
932 os.path.abspath(xreal),
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
933 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
934 p = subprocess.run(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
935 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
936 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
937 tout.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
938 return p.returncode
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
939
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
940 def writeShedyml(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
941 """for planemo"""
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
942 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
943 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
944 yamlf = open(yfname, "w")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
945 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
946 "name": self.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
947 "owner": yuser,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
948 "type": "unrestricted",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
949 "description": self.args.tool_desc,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
950 "synopsis": self.args.tool_desc,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
951 "category": "TF Generated Tools",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
952 }
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
953 yaml.dump(odict, yamlf, allow_unicode=True)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
954 yamlf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
955
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
956 def makeTool(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
957 """write xmls and input samples into place"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
958 self.makeXML()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
959 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
960 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
961 if not os.path.exists(stname):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
962 shutil.copyfile(self.sfile, stname)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
963 xreal = "%s.xml" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
964 xout = os.path.join(self.tooloutdir, xreal)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
965 shutil.copyfile(xreal, xout)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
966 for p in self.infiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
967 pth = p[IPATHPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
968 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
969 shutil.copyfile(pth, dest)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
970
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
971 def makeToolTar(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
972 """move outputs into test-data and prepare the tarball"""
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
973 excludeme = "tool_test_output"
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
974
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
975 def exclude_function(tarinfo):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
976 filename = tarinfo.name
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
977 return (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
978 None
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
979 if filename.startswith(excludeme)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
980 else tarinfo
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diff changeset
981 )
66
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982
50
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diff changeset
983 for p in self.outfiles:
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diff changeset
984 src = p[ONAMEPOS]
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diff changeset
985 if os.path.isfile(src):
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diff changeset
986 dest = os.path.join(self.testdir, "%s_sample" % src)
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diff changeset
987 shutil.copyfile(src, dest)
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diff changeset
988 dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS]))
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diff changeset
989 shutil.copyfile(src, dest)
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990 else:
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diff changeset
991 print(
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diff changeset
992 "### problem - output file %s not found in tooloutdir %s"
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diff changeset
993 % (src, self.tooloutdir)
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diff changeset
994 )
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diff changeset
995 tf = tarfile.open(self.newtarpath, "w:gz")
66
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996 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
50
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diff changeset
997 tf.close()
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diff changeset
998 shutil.copyfile(self.newtarpath, self.args.new_tool)
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diff changeset
999
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diff changeset
1000 def moveRunOutputs(self):
75
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1001 """need to move planemo or run outputs into toolfactory collection"""
50
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diff changeset
1002 with os.scandir(self.tooloutdir) as outs:
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diff changeset
1003 for entry in outs:
80
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parents: 78
diff changeset
1004 if not entry.is_file():
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diff changeset
1005 continue
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diff changeset
1006 if "." in entry.name:
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diff changeset
1007 nayme, ext = os.path.splitext(entry.name)
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1008 if ext in ['.yml','.xml','.json','.yaml']:
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diff changeset
1009 ext = f'{ext}.txt'
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1010 else:
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diff changeset
1011 ext = ".txt"
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1012 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
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1013 dest = os.path.join(self.repdir, ofn)
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1014 src = os.path.join(self.tooloutdir, entry.name)
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diff changeset
1015 shutil.copyfile(src, dest)
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diff changeset
1016 with os.scandir(self.testdir) as outs:
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parents: 78
diff changeset
1017 for entry in outs:
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parents: 78
diff changeset
1018 if not entry.is_file():
50
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parents: 49
diff changeset
1019 continue
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parents: 49
diff changeset
1020 if "." in entry.name:
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diff changeset
1021 nayme, ext = os.path.splitext(entry.name)
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diff changeset
1022 else:
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diff changeset
1023 ext = ".txt"
80
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diff changeset
1024 newname = f"{entry.name}{ext}"
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diff changeset
1025 dest = os.path.join(self.repdir, newname)
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diff changeset
1026 src = os.path.join(self.testdir, entry.name)
50
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parents: 49
diff changeset
1027 shutil.copyfile(src, dest)
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parents: 49
diff changeset
1028
49
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diff changeset
1029
76
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diff changeset
1030
48
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parents:
diff changeset
1031 def main():
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parents:
diff changeset
1032 """
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parents:
diff changeset
1033 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
49
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parents: 48
diff changeset
1034 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1035 --tool_name "foo" --interpreter "Rscript"
48
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parents:
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1036 </command>
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parents:
diff changeset
1037 """
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parents:
diff changeset
1038 parser = argparse.ArgumentParser()
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parents:
diff changeset
1039 a = parser.add_argument
49
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1040 a("--script_path", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1041 a("--history_test", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1042 a("--cl_prefix", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1043 a("--sysexe", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1044 a("--packages", default=None)
76
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diff changeset
1045 a("--tool_name", default="newtool")
72
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parents: 69
diff changeset
1046 a("--tool_dir", default=None)
48
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parents:
diff changeset
1047 a("--input_files", default=[], action="append")
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parents:
diff changeset
1048 a("--output_files", default=[], action="append")
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parents:
diff changeset
1049 a("--user_email", default="Unknown")
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parents:
diff changeset
1050 a("--bad_user", default=None)
49
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1051 a("--make_Tool", default="runonly")
48
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parents:
diff changeset
1052 a("--help_text", default=None)
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parents:
diff changeset
1053 a("--tool_desc", default=None)
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parents:
diff changeset
1054 a("--tool_version", default=None)
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parents:
diff changeset
1055 a("--citations", default=None)
49
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1056 a("--command_override", default=None)
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1057 a("--test_override", default=None)
48
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parents:
diff changeset
1058 a("--additional_parameters", action="append", default=[])
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parents:
diff changeset
1059 a("--edit_additional_parameters", action="store_true", default=False)
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parents:
diff changeset
1060 a("--parampass", default="positional")
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parents:
diff changeset
1061 a("--tfout", default="./tfout")
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parents:
diff changeset
1062 a("--new_tool", default="new_tool")
49
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1063 a("--galaxy_url", default="http://localhost:8080")
75
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diff changeset
1064 a(
76
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diff changeset
1065 "--toolshed_url", default="http://localhost:9009")
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parents: 75
diff changeset
1066 # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails
63
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parents: 62
diff changeset
1067 a("--toolshed_api_key", default="fakekey")
50
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parents: 49
diff changeset
1068 a("--galaxy_api_key", default="fakekey")
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parents: 49
diff changeset
1069 a("--galaxy_root", default="/galaxy-central")
48
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parents:
diff changeset
1070 args = parser.parse_args()
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parents:
diff changeset
1071 assert not args.bad_user, (
5a7a5b06bce0 Uploaded
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parents:
diff changeset
1072 '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
1073 % (args.bad_user, args.bad_user)
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parents:
diff changeset
1074 )
49
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1075 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
48
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parents:
diff changeset
1076 assert (
49
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diff changeset
1077 args.sysexe or args.packages
48
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parents:
diff changeset
1078 ), "## Tool Factory wrapper expects an interpreter or an executable package"
49
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1079 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
48
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parents:
diff changeset
1080 # remove quotes we need to deal with spaces in CL params
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parents:
diff changeset
1081 for i, x in enumerate(args.additional_parameters):
49
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1082 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
48
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parents:
diff changeset
1083 r = ScriptRunner(args)
49
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1084 r.writeShedyml()
35a912ce0c83 Can now make the bwa example from planemo :)
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diff changeset
1085 r.makeTool()
66
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parents: 65
diff changeset
1086 if args.make_Tool == "generate":
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diff changeset
1087 retcode = r.run()
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parents: 65
diff changeset
1088 r.moveRunOutputs()
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diff changeset
1089 r.makeToolTar()
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parents: 65
diff changeset
1090 else:
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parents: 65
diff changeset
1091 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR
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parents: 65
diff changeset
1092 r.moveRunOutputs()
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diff changeset
1093 r.makeToolTar()
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parents: 65
diff changeset
1094 retcode = r.planemo_test(genoutputs=False)
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parents: 65
diff changeset
1095 r.moveRunOutputs()
80
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diff changeset
1096 r.makeToolTar()
76
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diff changeset
1097 print(f"second planemo_test returned {retcode}")
66
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parents: 65
diff changeset
1098 if args.make_Tool == "gentestinstall":
80
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diff changeset
1099 r.shedLoad()
66
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parents: 65
diff changeset
1100 r.eph_galaxy_load()
63
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parents: 62
diff changeset
1101
48
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parents:
diff changeset
1102
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parents:
diff changeset
1103 if __name__ == "__main__":
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parents:
diff changeset
1104 main()