annotate toolfactory/rgToolFactory2.py @ 80:f423a77bc669 draft

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author fubar
date Tue, 17 Nov 2020 09:04:25 +0000
parents 89aca6c67405
children 6395be766c2e
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2 # rgToolFactory.py
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3 # see https://github.com/fubar2/toolfactory
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4 #
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5 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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6 #
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7 # all rights reserved
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8 # Licensed under the LGPL
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9 # suggestions for improvement and bug fixes welcome at
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10 # https://github.com/fubar2/toolfactory
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11 #
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12 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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13 # Decided to
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14 # 1. Fix the toolfactory so it works - done for simplest case
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15 # 2. Fix planemo so the toolfactory function works
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16 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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17 #
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18 # removed all the old complications including making the new tool use this same script
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19 # galaxyxml now generates the tool xml https://github.com/hexylena/galaxyxml
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20 # No support for automatic HTML file creation from arbitrary outputs
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21 # essential problem is to create two command lines - one for the tool xml and a different
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22 # one to run the executable with the supplied test data and settings
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23 # Be simpler to write the tool, then run it with planemo and soak up the test outputs.
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24
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25
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26 import argparse
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27 import datetime
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28 import json
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29 import logging
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30 import os
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31 import re
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32 import shutil
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33 import subprocess
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34 import sys
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35 import tarfile
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36 import tempfile
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37 import time
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38
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40 from bioblend import toolshed
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41
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42 import galaxyxml.tool as gxt
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43 import galaxyxml.tool.parameters as gxtp
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44
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45 import lxml
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46
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47 import yaml
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49 myversion = "V2.1 July 2020"
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50 verbose = True
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51 debug = True
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52 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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53 ourdelim = "~~~"
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54 ALOT = 10000000 # srsly. command or test overrides use read() so just in case
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55 STDIOXML = """<stdio>
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56 <exit_code range="100:" level="debug" description="shite happens" />
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57 </stdio>"""
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58
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59 # --input_files="$input_files~~~$CL~~~$input_formats~~~$input_label
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60 # ~~~$input_help"
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61 IPATHPOS = 0
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62 ICLPOS = 1
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63 IFMTPOS = 2
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64 ILABPOS = 3
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65 IHELPOS = 4
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66 IOCLPOS = 5
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67
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68 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.CL~~~otab.history_test
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69 ONAMEPOS = 0
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70 OFMTPOS = 1
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71 OCLPOS = 2
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72 OTESTPOS = 3
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73 OOCLPOS = 4
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76 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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77 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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78 ANAMEPOS = 0
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79 AVALPOS = 1
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80 ALABPOS = 2
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81 AHELPPOS = 3
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82 ATYPEPOS = 4
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83 ACLPOS = 5
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84 AOVERPOS = 6
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85 AOCLPOS = 7
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88 foo = len(lxml.__version__)
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89 # fug you, flake8. Say my name!
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90 FAKEEXE = "~~~REMOVE~~~ME~~~"
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91 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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92 # with override.
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95 def timenow():
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96 """return current time as a string"""
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97 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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100 def quote_non_numeric(s):
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101 """return a prequoted string for non-numerics
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102 useful for perl and Rscript parameter passing?
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103 """
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104 try:
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105 _ = float(s)
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106 return s
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107 except ValueError:
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108 return '"%s"' % s
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111 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$"}
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112
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113
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114 def html_escape(text):
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115 """Produce entities within text."""
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116 return "".join(html_escape_table.get(c, c) for c in text)
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117
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118
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119 def html_unescape(text):
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120 """Revert entities within text. Multiple character targets so use replace"""
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121 t = text.replace("&amp;", "&")
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122 t = t.replace("&gt;", ">")
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123 t = t.replace("&lt;", "<")
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124 t = t.replace("\\$", "$")
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125 return t
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126
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127
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128 def parse_citations(citations_text):
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129 """"""
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130 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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131 citation_tuples = []
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132 for citation in citations:
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133 if citation.startswith("doi"):
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134 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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135 else:
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136 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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137 return citation_tuples
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138
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139
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140 class ScriptRunner:
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141 """Wrapper for an arbitrary script
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142 uses galaxyxml
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143
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144 """
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145
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146 def __init__(self, args=None):
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147 """
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148 prepare command line cl for running the tool here
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149 and prepare elements needed for galaxyxml tool generation
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150 """
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151 self.infiles = [x.split(ourdelim) for x in args.input_files]
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152 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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153 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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154 self.args = args
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155 self.cleanuppar()
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156 self.lastclredirect = None
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157 self.lastxclredirect = None
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158 self.cl = []
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159 self.xmlcl = []
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160 self.is_positional = self.args.parampass == "positional"
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161 if self.args.sysexe:
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162 self.executeme = self.args.sysexe
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163 else:
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164 if self.args.packages:
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165 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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166 else:
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167 self.executeme = None
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168 aCL = self.cl.append
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169 aXCL = self.xmlcl.append
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170 assert args.parampass in [
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171 "0",
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172 "argparse",
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173 "positional",
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174 ], 'args.parampass must be "0","positional" or "argparse"'
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175 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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176 self.tool_id = self.tool_name
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177 self.newtool = gxt.Tool(
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178 self.args.tool_name,
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179 self.tool_id,
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180 self.args.tool_version,
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181 self.args.tool_desc,
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182 FAKEEXE,
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183 )
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184 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
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185 self.tooloutdir = "tfout"
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186 self.repdir = "TF_run_report_tempdir"
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187 self.testdir = os.path.join(self.tooloutdir, "test-data")
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188 if not os.path.exists(self.tooloutdir):
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189 os.mkdir(self.tooloutdir)
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190 if not os.path.exists(self.testdir):
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191 os.mkdir(self.testdir) # make tests directory
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192 if not os.path.exists(self.repdir):
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193 os.mkdir(self.repdir)
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194 self.tinputs = gxtp.Inputs()
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195 self.toutputs = gxtp.Outputs()
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196 self.testparam = []
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197 if self.args.script_path:
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diff changeset
198 self.prepScript()
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199 if self.args.command_override:
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200 scos = open(self.args.command_override, "r").readlines()
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201 self.command_override = [x.rstrip() for x in scos]
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202 else:
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203 self.command_override = None
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204 if self.args.test_override:
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205 stos = open(self.args.test_override, "r").readlines()
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206 self.test_override = [x.rstrip() for x in stos]
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207 else:
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diff changeset
208 self.test_override = None
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209 if self.args.cl_prefix: # DIY CL start
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diff changeset
210 clp = self.args.cl_prefix.split(" ")
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211 for c in clp:
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212 aCL(c)
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213 aXCL(c)
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214 else:
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215 if self.args.script_path:
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216 aCL(self.executeme)
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217 aCL(self.sfile)
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218 aXCL(self.executeme)
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219 aXCL("$runme")
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220 else:
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221 aCL(self.executeme) # this little CL will just run
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222 aXCL(self.executeme)
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223 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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224 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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225
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226 if self.args.parampass == "0":
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227 self.clsimple()
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228 else:
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229 clsuffix = []
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230 xclsuffix = []
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231 for i, p in enumerate(self.infiles):
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232 if p[IOCLPOS] == "STDIN":
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233 appendme = [
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234 p[IOCLPOS],
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235 p[ICLPOS],
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236 p[IPATHPOS],
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237 "< %s" % p[IPATHPOS],
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238 ]
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239 xappendme = [
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240 p[IOCLPOS],
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241 p[ICLPOS],
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242 p[IPATHPOS],
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243 "< $%s" % p[ICLPOS],
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244 ]
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245 else:
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246 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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247 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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248 clsuffix.append(appendme)
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249 xclsuffix.append(xappendme)
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250 for i, p in enumerate(self.outfiles):
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251 if p[OOCLPOS] == "STDOUT":
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252 self.lastclredirect = [">", p[ONAMEPOS]]
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253 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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254 else:
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255 clsuffix.append([p[OOCLPOS], p[OCLPOS], p[ONAMEPOS], ""])
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256 xclsuffix.append([p[OOCLPOS], p[OCLPOS], "$%s" % p[ONAMEPOS], ""])
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257 for p in self.addpar:
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258 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
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259 xclsuffix.append(
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260 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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261 )
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262 clsuffix.sort()
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263 xclsuffix.sort()
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264 self.xclsuffix = xclsuffix
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265 self.clsuffix = clsuffix
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266 if self.args.parampass == "positional":
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267 self.clpositional()
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268 else:
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269 self.clargparse()
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270
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271 def prepScript(self):
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272 rx = open(self.args.script_path, "r").readlines()
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273 rx = [x.rstrip() for x in rx]
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274 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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275 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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276 self.script = "\n".join(rx)
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277 fhandle, self.sfile = tempfile.mkstemp(
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278 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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279 )
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280 tscript = open(self.sfile, "w")
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281 tscript.write(self.script)
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282 tscript.close()
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283 self.indentedScript = " %s" % "\n".join([" %s" % html_escape(x) for x in rx])
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284 self.escapedScript = "%s" % "\n".join([" %s" % html_escape(x) for x in rx])
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285 art = "%s.%s" % (self.tool_name, self.executeme)
48
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286 artifact = open(art, "wb")
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287 artifact.write(bytes(self.script, "utf8"))
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288 artifact.close()
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289
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290 def cleanuppar(self):
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291 """ positional parameters are complicated by their numeric ordinal"""
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292 for i, p in enumerate(self.infiles):
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parents:
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293 if self.args.parampass == "positional":
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294 assert p[
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parents: 74
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295 ICLPOS
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296 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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diff changeset
297 p[ICLPOS],
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diff changeset
298 p[ILABPOS],
48
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299 )
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parents:
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300 p.append(p[ICLPOS])
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parents:
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301 if p[ICLPOS].isdigit() or self.args.parampass == "0":
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parents:
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302 scl = "input%d" % (i + 1)
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303 p[ICLPOS] = scl
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parents:
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304 self.infiles[i] = p
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parents:
diff changeset
305 for i, p in enumerate(
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306 self.outfiles
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parents:
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307 ): # trying to automagically gather using extensions
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parents:
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308 if self.args.parampass == "positional" and p[OCLPOS] != "STDOUT":
75
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parents: 74
diff changeset
309 assert p[
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parents: 74
diff changeset
310 OCLPOS
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parents: 74
diff changeset
311 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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parents: 74
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312 p[OCLPOS],
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parents: 74
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313 p[ONAMEPOS],
48
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parents:
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314 )
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parents:
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315 p.append(p[OCLPOS])
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parents:
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316 if p[OCLPOS].isdigit() or p[OCLPOS] == "STDOUT":
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parents:
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317 scl = p[ONAMEPOS]
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parents:
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318 p[OCLPOS] = scl
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319 self.outfiles[i] = p
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parents:
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320 for i, p in enumerate(self.addpar):
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parents:
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321 if self.args.parampass == "positional":
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parents: 74
diff changeset
322 assert p[
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parents: 74
diff changeset
323 ACLPOS
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parents: 74
diff changeset
324 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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parents: 74
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325 p[ACLPOS],
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parents: 74
diff changeset
326 p[ANAMEPOS],
48
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parents:
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327 )
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parents:
diff changeset
328 p.append(p[ACLPOS])
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parents:
diff changeset
329 if p[ACLPOS].isdigit():
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fubar
parents:
diff changeset
330 scl = "input%s" % p[ACLPOS]
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fubar
parents:
diff changeset
331 p[ACLPOS] = scl
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parents:
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332 self.addpar[i] = p
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parents:
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333
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parents:
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334 def clsimple(self):
75
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diff changeset
335 """no parameters - uses < and > for i/o"""
48
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parents:
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336 aCL = self.cl.append
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parents:
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337 aXCL = self.xmlcl.append
62
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parents: 57
diff changeset
338
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parents: 57
diff changeset
339 if len(self.infiles) > 0:
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parents: 57
diff changeset
340 aCL("<")
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parents: 57
diff changeset
341 aCL(self.infiles[0][IPATHPOS])
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parents: 57
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342 aXCL("<")
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parents: 57
diff changeset
343 aXCL("$%s" % self.infiles[0][ICLPOS])
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parents: 57
diff changeset
344 if len(self.outfiles) > 0:
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parents: 57
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345 aCL(">")
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parents: 57
diff changeset
346 aCL(self.outfiles[0][OCLPOS])
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parents: 57
diff changeset
347 aXCL(">")
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diff changeset
348 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
48
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parents:
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349
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350 def clpositional(self):
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parents:
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351 # inputs in order then params
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parents:
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352 aCL = self.cl.append
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parents:
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353 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
354 if " " in v:
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fubar
parents:
diff changeset
355 aCL("%s" % v)
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fubar
parents:
diff changeset
356 else:
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fubar
parents:
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357 aCL(v)
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parents:
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358 aXCL = self.xmlcl.append
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fubar
parents:
diff changeset
359 for (o_v, k, v, koverride) in self.xclsuffix:
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parents:
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360 aXCL(v)
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parents:
diff changeset
361 if self.lastxclredirect:
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parents:
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362 aXCL(self.lastxclredirect[0])
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fubar
parents:
diff changeset
363 aXCL(self.lastxclredirect[1])
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parents:
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364
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fubar
parents:
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365 def clargparse(self):
75
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parents: 74
diff changeset
366 """argparse style"""
48
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fubar
parents:
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367 aCL = self.cl.append
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fubar
parents:
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368 aXCL = self.xmlcl.append
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parents:
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369 # inputs then params in argparse named form
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parents:
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370 for (o_v, k, v, koverride) in self.xclsuffix:
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fubar
parents:
diff changeset
371 if koverride > "":
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fubar
parents:
diff changeset
372 k = koverride
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parents:
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373 elif len(k.strip()) == 1:
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parents:
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374 k = "-%s" % k
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fubar
parents:
diff changeset
375 else:
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parents:
diff changeset
376 k = "--%s" % k
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fubar
parents:
diff changeset
377 aXCL(k)
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fubar
parents:
diff changeset
378 aXCL(v)
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fubar
parents:
diff changeset
379 for (o_v, k, v, koverride) in self.clsuffix:
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fubar
parents:
diff changeset
380 if koverride > "":
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fubar
parents:
diff changeset
381 k = koverride
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fubar
parents:
diff changeset
382 elif len(k.strip()) == 1:
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parents:
diff changeset
383 k = "-%s" % k
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fubar
parents:
diff changeset
384 else:
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parents:
diff changeset
385 k = "--%s" % k
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fubar
parents:
diff changeset
386 aCL(k)
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fubar
parents:
diff changeset
387 aCL(v)
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fubar
parents:
diff changeset
388
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fubar
parents:
diff changeset
389 def getNdash(self, newname):
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fubar
parents:
diff changeset
390 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391 ndash = 0
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392 else:
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fubar
parents:
diff changeset
393 ndash = 2
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
394 if len(newname) < 2:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 ndash = 1
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
396 return ndash
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
398 def doXMLparam(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399 """flake8 made me do this..."""
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 for p in self.outfiles:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
401 newname, newfmt, newcl, test, oldcl = p
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 ndash = self.getNdash(newcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 aparm = gxtp.OutputData(newcl, format=newfmt, num_dashes=ndash)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406 if oldcl == "STDOUT":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 aparm.positional = 9999999
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408 aparm.command_line_override = "> $%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
409 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
410 aparm.positional = int(oldcl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
411 aparm.command_line_override = "$%s" % newcl
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
412 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
413 usetest = None
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
414 ld = None
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
415 if test > "":
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
416 if test.startswith("diff"):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
417 usetest = "diff"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
418 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
419 ld = int(test.split(":")[1])
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
420 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
421 usetest = test
50
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fubar
parents: 49
diff changeset
422 tp = gxtp.TestOutput(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
423 name=newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
424 value="%s_sample" % newcl,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
425 format=newfmt,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
426 compare=usetest,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
427 lines_diff=ld,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
428 delta=None,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
429 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
430 self.testparam.append(tp)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
431 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
432 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
433 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
434 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
435 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
436 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
437 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
438 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
439 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
440 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
441 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
442 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
443 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
444 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
445 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
446 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
447 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
448 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
449 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
450 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
451 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
452 for p in self.addpar:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
453 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
454 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
455 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
456 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
457 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
486 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
488 if self.is_positional:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
489 aparm.positional = int(oldcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
490 self.tinputs.append(aparm)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
491 tparm = gxtp.TestParam(newname, value=newval)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
492 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
493
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
494 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
495 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
496 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
497 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
498 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
499 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
500 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
501 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
502 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
503 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
504 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
505 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
506 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
507 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
508 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
509 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
510 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
511 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
512 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
513 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
514 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
515 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
516 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
517 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
518 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
519 self.testparam.append(tp)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
520 if len(self.outfiles) > 0:
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
521 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
522 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
523 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
524 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
525 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
526 self.toutputs.append(anout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
527 tp = gxtp.TestOutput(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
528 name=newname, value="%s_sample" % newname, format=newfmt
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
529 )
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
530 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
531
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
532 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
533 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
534 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
535 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
536 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
537 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
538 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
539 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
540 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
541 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
542 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
543 helptext = open(self.args.help_text, "r").readlines()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
544 safertext = [html_escape(x) for x in helptext]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
545 if False and self.args.script_path:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
546 scrp = self.script.split("\n")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
547 scrpt = [" %s" % x for x in scrp] # try to stop templating
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
548 scrpt.insert(0, "```\n")
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
549 if len(scrpt) > 300:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
550 safertext = (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
551 safertext + scrpt[:100] + \
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
552 [">500 lines - stuff deleted", "......"] + scrpt[-100:]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
553 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
554 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
555 safertext = safertext + scrpt
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
556 safertext.append("\n```")
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
557 self.newtool.help = "\n".join([x for x in safertext])
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
558 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
559 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
560 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
561 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
562 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
563 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
564 self.newtool.version_command = None # do not want
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
565 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
566 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
567 for d in self.args.packages.split(","):
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
568 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
569 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
570 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
571 packg = d
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
572 ver = ""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
573 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
574 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
575 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
576 self.newtool.requirements = requirements
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
577 if self.args.parampass == "0":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
578 self.doNoXMLparam()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
579 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
580 self.doXMLparam()
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
581 self.newtool.outputs = self.toutputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
582 self.newtool.inputs = self.tinputs
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
583 if self.args.script_path:
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
584 configfiles = gxtp.Configfiles()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
585 configfiles.append(gxtp.Configfile(name="runme", text=self.script))
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
586 self.newtool.configfiles = configfiles
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
587 tests = gxtp.Tests()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
588 test_a = gxtp.Test()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
589 for tp in self.testparam:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
590 test_a.append(tp)
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fubar
parents:
diff changeset
591 tests.append(test_a)
50
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fubar
parents: 49
diff changeset
592 self.newtool.tests = tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
593 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
594 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
595 % (self.args.user_email, timenow())
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
596 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
597 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
598 self.newtool.add_comment(
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
599 "Cite: Creating re-usable tools from scripts doi: \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
600 10.1093/bioinformatics/bts573"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
601 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
602 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
603 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
604 if (
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
605 self.test_override
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
606 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
607 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
608 part2 = exml.split("</tests>")[1]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
609 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
610 exml = fixed
63
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fubar
parents: 62
diff changeset
611 exml = exml.replace('range="1:"', 'range="1000:"')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
612 xf = open("%s.xml" % self.tool_name, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
613 xf.write(exml)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
614 xf.write("\n")
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fubar
parents:
diff changeset
615 xf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
616 # ready for the tarball
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
617
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fubar
parents:
diff changeset
618 def run(self):
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fubar
parents:
diff changeset
619 """
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
620 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
621 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
622 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
623 automagically selected
48
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fubar
parents:
diff changeset
624 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
625 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
626 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
627 if self.args.parampass != "0":
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
628 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
629 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
630 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
631 ste = open(self.elog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
632 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
633 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
634 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
635 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
636 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
637 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
638 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
639 sto.write(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
640 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
641 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
642 sto.flush()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
643 p = subprocess.run(self.cl, shell=False, stdout=sto, stderr=ste)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
644 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
645 ste.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
646 retval = p.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
647 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
648 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
649 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
650 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
651 sti = sys.stdin
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
652 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
653 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
654 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
655 sto = sys.stdout
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
656 p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
657 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
658 retval = p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
659 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
660 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
661 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
662 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
663 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
664 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
665 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
666 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
667 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
668 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
669
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
670 def shedLoad(self):
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
671 """
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
672 {'deleted': False,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
673 'description': 'Tools for manipulating data',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
674 'id': '175812cd7caaf439',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
675 'model_class': 'Category',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
676 'name': 'Text Manipulation',
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
677 'url': '/api/categories/175812cd7caaf439'}]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
678
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
679
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
680 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
681 if os.path.exists(self.tlog):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
682 sto = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
683 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
684 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
685
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
686 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
687 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
688 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
689 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
690 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
691 rids = [x.get("id", "?") for x in repos]
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
692 sto.write(f"############names={rnames} rids={rids}\n")
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
693 cat = "ToolFactory generated tools"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
694 if self.args.tool_name not in rnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
695 tscat = ts.categories.get_categories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
696 cnames = [x.get("name", "?") for x in tscat]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
697 cids = [x.get("id", "?") for x in tscat]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
698 catID = None
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
699 if cat in cnames:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
700 ci = cnames.index(cat)
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
701 catID = cids[ci]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
702 res = ts.repositories.create_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
703 name=self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
704 synopsis="Synopsis:%s" % self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
705 description=self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
706 type="unrestricted",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
707 remote_repository_url=self.args.toolshed_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
708 homepage_url=None,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
709 category_ids=catID,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
710 )
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
711 tid = res.get("id", None)
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
712 sto.write(f"##########create res={res}\n")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
713 else:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
714 i = rnames.index(self.args.tool_name)
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
715 tid = rids[i]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
716 res = ts.repositories.update_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
717 id=tid, tar_ball_path=self.newtarpath, commit_message=None
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
718 )
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
719 sto.write(f"#####update res={res}\n")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
720 sto.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
721
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
722 def eph_galaxy_load(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
723 """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
724 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
725 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
726 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
727 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
728 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
729 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
730 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
731 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
732 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
733 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
734 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
735 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
736 "--name",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
737 self.args.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
738 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
739 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
740 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
741 self.args.toolshed_url,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
742 "--section_label",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
743 "ToolFactory",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
744 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
745 tout.write("running\n%s\n" % " ".join(cll))
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
746 p = subprocess.run(cll, shell=False, stderr=tout, stdout=tout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
747 tout.write(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
748 "installed %s - got retcode %d\n" % (self.args.tool_name, p.returncode)
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
749 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
750 tout.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
751 return p.returncode
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
752
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
753 def planemo_shedload(self):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
754 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
755 planemo shed_create --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
756 planemo shed_init --name=<name>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
757 --owner=<shed_username>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
758 --description=<short description>
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
759 [--remote_repository_url=<URL to .shed.yml on github>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
760 [--homepage_url=<Homepage for tool.>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
761 [--long_description=<long description>]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
762 [--category=<category name>]*
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
763
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
764
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
765 planemo shed_update --check_diff --shed_target testtoolshed
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
766 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
767 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
768 tout = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
769 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
770 tout = open(self.tlog, "w")
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
771 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
772 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
773 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
774 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
775 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
776 rids = [x.get("id", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
777 #cat = "ToolFactory generated tools"
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
778 if self.args.tool_name not in rnames:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
779 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
780 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
781 "shed_create",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
782 "--shed_target",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
783 "local",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
784 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
785 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
786 "--name",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
787 self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
788 "--shed_key",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
789 self.args.toolshed_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
790 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
791 try:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
792 p = subprocess.run(
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
793 cll, shell=False, cwd=self.tooloutdir, stdout=tout, stderr=tout
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
794 )
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
795 except:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
796 pass
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
797 if p.returncode != 0:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
798 tout.write("Repository %s exists\n" % self.args.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
799 else:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
800 tout.write("initiated %s\n" % self.args.tool_name)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
801 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
802 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
803 "shed_upload",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
804 "--shed_target",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
805 "local",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
806 "--owner",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
807 "fubar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
808 "--name",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
809 self.args.tool_name,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
810 "--shed_key",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
811 self.args.toolshed_api_key,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
812 "--tar",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
813 self.newtarpath,
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
814 ]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
815 p = subprocess.run(cll, shell=False, stdout=tout, stderr=tout)
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
816 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
817 tout.close()
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
818 return p.returncode
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
819
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
820 def eph_test(self, genoutputs=True):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
821 """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
822 """
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
823 if os.path.exists(self.tlog):
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
824 tout = open(self.tlog, "a")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
825 else:
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
826 tout = open(self.tlog, "w")
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
827 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
828 "shed-tools",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
829 "test",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
830 "-g",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
831 self.args.galaxy_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
832 "-a",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
833 self.args.galaxy_api_key,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
834 "--name",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
835 self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
836 "--owner",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
837 "fubar",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
838 ]
76
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
839 if genoutputs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
840 dummy, tfile = tempfile.mkstemp()
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
841 p = subprocess.run(
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
842 cll, shell=False, stderr=dummy, stdout=dummy
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
843 )
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
844
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
845 with open('tool_test_output.json','rb') as f:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
846 s = json.loads(f.read())
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
847 print('read %s' % s)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
848 cl = s['tests'][0]['data']['job']['command_line'].split()
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
849 n = cl.index('--script_path')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
850 jobdir = cl[n+1]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
851 jobdir = jobdir.replace('"','')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
852 jobdir = jobdir.split('/configs')[0]
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
853 print('jobdir=%s' % jobdir)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
854
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
855 #"/home/ross/galthrow/database/jobs_directory/000/649/configs/tmptfxu51gs\"
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
856 src = os.path.join(jobdir,'working',self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
857 if os.path.exists(src):
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
858 dest = os.path.join(self.testdir, self.newtarpath)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
859 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
860 else:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
861 tout.write('No toolshed archive found after first ephemeris test - not a good sign')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
862 ephouts = os.path.join(jobdir,'working','tfout','test-data')
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
863 with os.scandir(ephouts) as outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
864 for entry in outs:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
865 if not entry.is_file():
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
866 continue
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
867 dest = os.path.join(self.tooloutdir, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
868 src = os.path.join(ephouts, entry.name)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
869 shutil.copyfile(src, dest)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
870 else:
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
871 p = subprocess.run(
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
872 cll, shell=False, stderr=tout, stdout=tout)
46db8143adb7 Uploaded
fubar
parents: 75
diff changeset
873 tout.write("eph_test Ran %s got %d" % (" ".join(cll), p.returncode))
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
874 tout.close()
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
875 return p.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
876
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
877 def planemo_test(self, genoutputs=True):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
878 """planemo is a requirement so is available for testing
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
879 and for generating test outputs if command or test overrides are supplied
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
880 test outputs are sent to repdir for display
67
2cb06a59d84b Uploaded
fubar
parents: 66
diff changeset
881 planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
882 """
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
883 xreal = "%s.xml" % self.tool_name
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
884 tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html")
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
885 if os.path.exists(self.tlog):
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
886 tout = open(self.tlog, "a")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
887 else:
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
888 tout = open(self.tlog, "w")
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
889 if genoutputs:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
890 dummy, tfile = tempfile.mkstemp()
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
891 cll = [
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
892 "planemo",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
893 "test",
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
894 "--test_data", os.path.abspath(self.testdir),
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
895 "--test_output", os.path.abspath(tool_test_path),
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
896 "--galaxy_root",
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
897 self.args.galaxy_root,
74
3d4324df911b Uploaded
fubar
parents: 72
diff changeset
898 "--update_test_data",
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
899 os.path.abspath(xreal),
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
900 ]
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
901 p = subprocess.run(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
902 cll,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
903 shell=False,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
904 cwd=self.tooloutdir,
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
905 stderr=dummy,
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
906 stdout=dummy,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
907 )
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
908
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
909 else:
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
910 cll = [
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
911 "planemo",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
912 "test",
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
913 "--test_data", os.path.abspath(self.testdir),
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
914 "--test_output", os.path.abspath(tool_test_path),
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
915 "--galaxy_root",
74
3d4324df911b Uploaded
fubar
parents: 72
diff changeset
916 self.args.galaxy_root,
78
89aca6c67405 Uploaded
fubar
parents: 76
diff changeset
917 os.path.abspath(xreal),
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
918 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
919 p = subprocess.run(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
920 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
921 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
922 tout.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
923 return p.returncode
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
924
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
925 def writeShedyml(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
926 """for planemo"""
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
927 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
928 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
929 yamlf = open(yfname, "w")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
930 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
931 "name": self.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
932 "owner": yuser,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
933 "type": "unrestricted",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
934 "description": self.args.tool_desc,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
935 "synopsis": self.args.tool_desc,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
936 "category": "TF Generated Tools",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
937 }
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
938 yaml.dump(odict, yamlf, allow_unicode=True)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
939 yamlf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
940
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
941 def makeTool(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
942 """write xmls and input samples into place"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
943 self.makeXML()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
944 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
945 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
946 if not os.path.exists(stname):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
947 shutil.copyfile(self.sfile, stname)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
948 xreal = "%s.xml" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
949 xout = os.path.join(self.tooloutdir, xreal)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
950 shutil.copyfile(xreal, xout)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
951 for p in self.infiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
952 pth = p[IPATHPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
953 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
954 shutil.copyfile(pth, dest)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
955
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
956 def makeToolTar(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
957 """move outputs into test-data and prepare the tarball"""
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
958 excludeme = "tool_test_output"
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
959
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
960 def exclude_function(tarinfo):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
961 filename = tarinfo.name
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
962 return (
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
963 None
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
964 if filename.startswith(excludeme)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
965 else tarinfo
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
966 )
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
967
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
968 for p in self.outfiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
969 src = p[ONAMEPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
970 if os.path.isfile(src):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
971 dest = os.path.join(self.testdir, "%s_sample" % src)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
972 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
973 dest = os.path.join(self.repdir, "%s.%s" % (src, p[OFMTPOS]))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
974 shutil.copyfile(src, dest)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
975 else:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
976 print(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
977 "### problem - output file %s not found in tooloutdir %s"
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
978 % (src, self.tooloutdir)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
979 )
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
980 tf = tarfile.open(self.newtarpath, "w:gz")
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
981 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
982 tf.close()
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983 shutil.copyfile(self.newtarpath, self.args.new_tool)
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984
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985 def moveRunOutputs(self):
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986 """need to move planemo or run outputs into toolfactory collection"""
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987 with os.scandir(self.tooloutdir) as outs:
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988 for entry in outs:
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989 if not entry.is_file():
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990 continue
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991 if "." in entry.name:
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992 nayme, ext = os.path.splitext(entry.name)
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993 if ext in ['.yml','.xml','.json','.yaml']:
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994 ext = f'{ext}.txt'
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995 else:
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996 ext = ".txt"
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997 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
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998 dest = os.path.join(self.repdir, ofn)
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999 src = os.path.join(self.tooloutdir, entry.name)
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1000 shutil.copyfile(src, dest)
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1001 with os.scandir(self.testdir) as outs:
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1002 for entry in outs:
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1003 if not entry.is_file():
50
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1004 continue
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1005 if "." in entry.name:
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diff changeset
1006 nayme, ext = os.path.splitext(entry.name)
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1007 else:
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1008 ext = ".txt"
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1009 newname = f"{entry.name}{ext}"
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1010 dest = os.path.join(self.repdir, newname)
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1011 src = os.path.join(self.testdir, entry.name)
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1012 shutil.copyfile(src, dest)
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1013
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1014
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1015
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1016 def main():
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1017 """
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1018 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
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1019 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
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1020 --tool_name "foo" --interpreter "Rscript"
48
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1021 </command>
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1022 """
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1023 parser = argparse.ArgumentParser()
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1024 a = parser.add_argument
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1025 a("--script_path", default=None)
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diff changeset
1026 a("--history_test", default=None)
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diff changeset
1027 a("--cl_prefix", default=None)
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diff changeset
1028 a("--sysexe", default=None)
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diff changeset
1029 a("--packages", default=None)
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diff changeset
1030 a("--tool_name", default="newtool")
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diff changeset
1031 a("--tool_dir", default=None)
48
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1032 a("--input_files", default=[], action="append")
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diff changeset
1033 a("--output_files", default=[], action="append")
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1034 a("--user_email", default="Unknown")
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diff changeset
1035 a("--bad_user", default=None)
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1036 a("--make_Tool", default="runonly")
48
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1037 a("--help_text", default=None)
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1038 a("--tool_desc", default=None)
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parents:
diff changeset
1039 a("--tool_version", default=None)
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diff changeset
1040 a("--citations", default=None)
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1041 a("--command_override", default=None)
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1042 a("--test_override", default=None)
48
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1043 a("--additional_parameters", action="append", default=[])
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diff changeset
1044 a("--edit_additional_parameters", action="store_true", default=False)
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1045 a("--parampass", default="positional")
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1046 a("--tfout", default="./tfout")
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diff changeset
1047 a("--new_tool", default="new_tool")
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1048 a("--galaxy_url", default="http://localhost:8080")
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1049 a(
76
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1050 "--toolshed_url", default="http://localhost:9009")
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1051 # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails
63
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1052 a("--toolshed_api_key", default="fakekey")
50
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diff changeset
1053 a("--galaxy_api_key", default="fakekey")
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diff changeset
1054 a("--galaxy_root", default="/galaxy-central")
48
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1055 args = parser.parse_args()
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1056 assert not args.bad_user, (
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diff changeset
1057 '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
1058 % (args.bad_user, args.bad_user)
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diff changeset
1059 )
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1060 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
48
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diff changeset
1061 assert (
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1062 args.sysexe or args.packages
48
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diff changeset
1063 ), "## Tool Factory wrapper expects an interpreter or an executable package"
49
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1064 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
48
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1065 # remove quotes we need to deal with spaces in CL params
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1066 for i, x in enumerate(args.additional_parameters):
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1067 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
48
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1068 r = ScriptRunner(args)
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1069 r.writeShedyml()
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1070 r.makeTool()
66
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1071 if args.make_Tool == "generate":
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1072 retcode = r.run()
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diff changeset
1073 r.moveRunOutputs()
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diff changeset
1074 r.makeToolTar()
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1075 else:
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1076 retcode = r.planemo_test(genoutputs=True) # this fails :( - see PR
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diff changeset
1077 r.moveRunOutputs()
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1078 r.makeToolTar()
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1079 retcode = r.planemo_test(genoutputs=False)
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diff changeset
1080 r.moveRunOutputs()
80
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1081 r.makeToolTar()
76
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1082 print(f"second planemo_test returned {retcode}")
66
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diff changeset
1083 if args.make_Tool == "gentestinstall":
80
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1084 r.shedLoad()
66
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diff changeset
1085 r.eph_galaxy_load()
63
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diff changeset
1086
48
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1087
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1088 if __name__ == "__main__":
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1089 main()