annotate toolfactory/rgToolFactory2.py @ 126:def0f754ee1b draft

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author fubar
date Fri, 26 Mar 2021 09:29:58 +0000
parents f267ed4a3026
children 98c8a76b3638
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121
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1 # replace with shebang for biocontainer
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2 # see https://github.com/fubar2/toolfactory
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at
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9 # https://github.com/fubar2/toolfactory
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10 #
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11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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12 # Decided to
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13 # 1. Fix the toolfactory so it works - done for simplest case
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14 # 2. Fix planemo so the toolfactory function works
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15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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16
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17 import argparse
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18 import copy
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19 import json
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20 import logging
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21 import os
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22 import re
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23 import shutil
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24 import subprocess
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25 import sys
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26 import tarfile
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27 import tempfile
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28 import time
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29
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30 from bioblend import ConnectionError
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31 from bioblend import toolshed
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32
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33 import galaxyxml.tool as gxt
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34 import galaxyxml.tool.parameters as gxtp
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35
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36 import lxml
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37
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38 import yaml
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39
126
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40
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41 myversion = "V2.2 February 2021"
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42 verbose = True
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43 debug = True
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44 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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45 foo = len(lxml.__version__)
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46 # fug you, flake8. Say my name!
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47 FAKEEXE = "~~~REMOVE~~~ME~~~"
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48 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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49 # with override.
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50
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51
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52 def timenow():
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53 """return current time as a string"""
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54 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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55
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56
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57 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
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58
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59
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60 def cheetah_escape(text):
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61 """Produce entities within text."""
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62 return "".join([cheetah_escape_table.get(c, c) for c in text])
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63
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64
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65 def parse_citations(citations_text):
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66 """"""
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67 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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68 citation_tuples = []
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69 for citation in citations:
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70 if citation.startswith("doi"):
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71 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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72 else:
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73 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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74 return citation_tuples
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75
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76
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77 class ScriptRunner:
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78 """Wrapper for an arbitrary script
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79 uses galaxyxml
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80
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81 """
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82
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83 def __init__(self, args=None):
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84 """
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85 prepare command line cl for running the tool here
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86 and prepare elements needed for galaxyxml tool generation
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87 """
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88 self.ourcwd = os.getcwd()
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89 self.collections = []
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90 if len(args.collection) > 0:
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91 try:
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92 self.collections = [
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93 json.loads(x) for x in args.collection if len(x.strip()) > 1
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94 ]
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95 except Exception:
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96 print(
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97 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
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98 )
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99 try:
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100 self.infiles = [
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101 json.loads(x) for x in args.input_files if len(x.strip()) > 1
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102 ]
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103 except Exception:
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104 print(
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105 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
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106 )
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107 try:
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108 self.outfiles = [
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109 json.loads(x) for x in args.output_files if len(x.strip()) > 1
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110 ]
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111 except Exception:
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112 print(
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113 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
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114 )
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115 try:
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116 self.addpar = [
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117 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
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118 ]
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119 except Exception:
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120 print(
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121 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
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122 )
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123 try:
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124 self.selpar = [
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125 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
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126 ]
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127 except Exception:
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128 print(
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129 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
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130 )
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131 self.args = args
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132 self.cleanuppar()
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133 self.lastclredirect = None
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134 self.lastxclredirect = None
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135 self.cl = []
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136 self.xmlcl = []
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137 self.is_positional = self.args.parampass == "positional"
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138 if self.args.sysexe:
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139 if ' ' in self.args.sysexe:
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140 self.executeme = self.args.sysexe.split(' ')
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141 else:
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142 self.executeme = [self.args.sysexe, ]
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143 else:
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144 if self.args.packages:
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145 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
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146 else:
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147 self.executeme = None
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148 aCL = self.cl.append
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149 aXCL = self.xmlcl.append
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150 assert args.parampass in [
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151 "0",
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152 "argparse",
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153 "positional",
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154 ], 'args.parampass must be "0","positional" or "argparse"'
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155 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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156 self.tool_id = self.tool_name
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157 self.newtool = gxt.Tool(
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158 self.tool_name,
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159 self.tool_id,
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160 self.args.tool_version,
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161 self.args.tool_desc,
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162 FAKEEXE,
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163 )
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164 self.newtarpath = "%s_toolshed.gz" % self.tool_name
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165 self.tooloutdir = "./tfout"
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166 self.repdir = "./TF_run_report_tempdir"
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167 self.testdir = os.path.join(self.tooloutdir, "test-data")
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168 if not os.path.exists(self.tooloutdir):
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169 os.mkdir(self.tooloutdir)
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170 if not os.path.exists(self.testdir):
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171 os.mkdir(self.testdir)
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172 if not os.path.exists(self.repdir):
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173 os.mkdir(self.repdir)
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174 self.tinputs = gxtp.Inputs()
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175 self.toutputs = gxtp.Outputs()
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176 self.testparam = []
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177 if self.args.script_path:
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178 self.prepScript()
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179 if self.args.command_override:
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180 scos = open(self.args.command_override, "r").readlines()
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181 self.command_override = [x.rstrip() for x in scos]
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182 else:
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183 self.command_override = None
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184 if self.args.test_override:
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185 stos = open(self.args.test_override, "r").readlines()
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186 self.test_override = [x.rstrip() for x in stos]
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187 else:
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188 self.test_override = None
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189 if self.args.script_path:
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190 for ex in self.executeme:
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191 aCL(ex)
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192 aXCL(ex)
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193 aCL(self.sfile)
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194 aXCL("$runme")
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195 else:
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196 aCL(self.executeme[0])
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197 aXCL(self.executeme[0])
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198 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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199 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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200 if self.args.parampass == "0":
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201 self.clsimple()
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202 else:
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203 if self.args.parampass == "positional":
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204 self.prepclpos()
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205 self.clpositional()
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206 else:
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207 self.prepargp()
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208 self.clargparse()
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209 if self.args.cl_prefix: # DIY CL end - misnamed!
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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
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215 def clsimple(self):
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216 """no parameters - uses < and > for i/o"""
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217 aCL = self.cl.append
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218 aXCL = self.xmlcl.append
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diff changeset
219 if len(self.infiles) > 0:
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diff changeset
220 aCL("<")
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diff changeset
221 aCL(self.infiles[0]["infilename"])
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diff changeset
222 aXCL("<")
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diff changeset
223 aXCL("$%s" % self.infiles[0]["infilename"])
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diff changeset
224 if len(self.outfiles) > 0:
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diff changeset
225 aCL(">")
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diff changeset
226 aCL(self.outfiles[0]["name"])
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diff changeset
227 aXCL(">")
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diff changeset
228 aXCL("$%s" % self.outfiles[0]["name"])
121
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229
126
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230 def prepargp(self):
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diff changeset
231 clsuffix = []
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diff changeset
232 xclsuffix = []
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diff changeset
233 for i, p in enumerate(self.infiles):
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diff changeset
234 if p["origCL"].strip().upper() == "STDIN":
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diff changeset
235 appendme = [
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236 p["infilename"],
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diff changeset
237 p["infilename"],
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diff changeset
238 "< %s" % p["infilename"],
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diff changeset
239 ]
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diff changeset
240 xappendme = [
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diff changeset
241 p["infilename"],
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diff changeset
242 p["infilename"],
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diff changeset
243 "< $%s" % p["infilename"],
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diff changeset
244 ]
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245 else:
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246 appendme = [p["CL"], p["CL"], ""]
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247 xappendme = [p["CL"], "$%s" % p["CL"], ""]
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diff changeset
248 clsuffix.append(appendme)
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diff changeset
249 xclsuffix.append(xappendme)
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diff changeset
250 for i, p in enumerate(self.outfiles):
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251 if p["origCL"].strip().upper() == "STDOUT":
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diff changeset
252 self.lastclredirect = [">", p["name"]]
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diff changeset
253 self.lastxclredirect = [">", "$%s" % p["name"]]
121
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254 else:
126
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255 clsuffix.append([p["name"], p["name"], ""])
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diff changeset
256 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
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diff changeset
257 for p in self.addpar:
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258 clsuffix.append([p["CL"], p["name"], p["override"]])
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diff changeset
259 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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diff changeset
260 for p in self.selpar:
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diff changeset
261 clsuffix.append([p["CL"], p["name"], p["override"]])
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diff changeset
262 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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diff changeset
263 clsuffix.sort()
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diff changeset
264 xclsuffix.sort()
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diff changeset
265 self.xclsuffix = xclsuffix
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diff changeset
266 self.clsuffix = clsuffix
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267
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diff changeset
268 def prepclpos(self):
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269 clsuffix = []
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diff changeset
270 xclsuffix = []
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diff changeset
271 for i, p in enumerate(self.infiles):
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diff changeset
272 if p["origCL"].strip().upper() == "STDIN":
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parents: 124
diff changeset
273 appendme = [
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diff changeset
274 "999",
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parents: 124
diff changeset
275 p["infilename"],
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parents: 124
diff changeset
276 "< $%s" % p["infilename"],
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parents: 124
diff changeset
277 ]
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diff changeset
278 xappendme = [
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diff changeset
279 "999",
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diff changeset
280 p["infilename"],
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parents: 124
diff changeset
281 "< $%s" % p["infilename"],
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diff changeset
282 ]
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diff changeset
283 else:
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diff changeset
284 appendme = [p["CL"], p["infilename"], ""]
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diff changeset
285 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
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diff changeset
286 clsuffix.append(appendme)
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diff changeset
287 xclsuffix.append(xappendme)
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diff changeset
288 for i, p in enumerate(self.outfiles):
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parents: 124
diff changeset
289 if p["origCL"].strip().upper() == "STDOUT":
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diff changeset
290 self.lastclredirect = [">", p["name"]]
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diff changeset
291 self.lastxclredirect = [">", "$%s" % p["name"]]
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diff changeset
292 else:
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diff changeset
293 clsuffix.append([p["CL"], p["name"], ""])
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parents: 124
diff changeset
294 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
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parents: 124
diff changeset
295 for p in self.addpar:
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parents: 124
diff changeset
296 clsuffix.append([p["CL"], p["name"], p["override"]])
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parents: 124
diff changeset
297 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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parents: 124
diff changeset
298 for p in self.selpar:
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parents: 124
diff changeset
299 clsuffix.append([p["CL"], p["name"], p["override"]])
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parents: 124
diff changeset
300 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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parents: 124
diff changeset
301 clsuffix.sort()
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parents: 124
diff changeset
302 xclsuffix.sort()
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diff changeset
303 self.xclsuffix = xclsuffix
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diff changeset
304 self.clsuffix = clsuffix
121
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parents:
diff changeset
305
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fubar
parents:
diff changeset
306 def prepScript(self):
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fubar
parents:
diff changeset
307 rx = open(self.args.script_path, "r").readlines()
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fubar
parents:
diff changeset
308 rx = [x.rstrip() for x in rx]
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fubar
parents:
diff changeset
309 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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fubar
parents:
diff changeset
310 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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fubar
parents:
diff changeset
311 self.script = "\n".join(rx)
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fubar
parents:
diff changeset
312 fhandle, self.sfile = tempfile.mkstemp(
126
def0f754ee1b Uploaded
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diff changeset
313 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
121
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fubar
parents:
diff changeset
314 )
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fubar
parents:
diff changeset
315 tscript = open(self.sfile, "w")
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fubar
parents:
diff changeset
316 tscript.write(self.script)
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fubar
parents:
diff changeset
317 tscript.close()
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fubar
parents:
diff changeset
318 self.escapedScript = [cheetah_escape(x) for x in rx]
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fubar
parents:
diff changeset
319 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
320 art = "%s.%s" % (self.tool_name, self.executeme[0])
121
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fubar
parents:
diff changeset
321 artifact = open(art, "wb")
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fubar
parents:
diff changeset
322 artifact.write(bytes("\n".join(self.escapedScript), "utf8"))
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fubar
parents:
diff changeset
323 artifact.close()
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fubar
parents:
diff changeset
324
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fubar
parents:
diff changeset
325 def cleanuppar(self):
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fubar
parents:
diff changeset
326 """ positional parameters are complicated by their numeric ordinal"""
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fubar
parents:
diff changeset
327 if self.args.parampass == "positional":
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fubar
parents:
diff changeset
328 for i, p in enumerate(self.infiles):
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fubar
parents:
diff changeset
329 assert (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
330 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
331 ), "Positional parameters must be ordinal integers - got %s for %s" % (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
332 p["CL"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
333 p["label"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
334 )
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fubar
parents:
diff changeset
335 for i, p in enumerate(self.outfiles):
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fubar
parents:
diff changeset
336 assert (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
337 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
338 ), "Positional parameters must be ordinal integers - got %s for %s" % (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
339 p["CL"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
340 p["name"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
341 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
342 for i, p in enumerate(self.addpar):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
343 assert p[
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
344 "CL"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
345 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
346 p["CL"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
347 p["name"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
348 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
349 for i, p in enumerate(self.infiles):
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fubar
parents:
diff changeset
350 infp = copy.copy(p)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
351 infp["origCL"] = infp["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
352 if self.args.parampass in ["positional", "0"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
353 infp["infilename"] = infp["label"].replace(" ", "_")
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
354 else:
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fubar
parents: 124
diff changeset
355 infp["infilename"] = infp["CL"]
121
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fubar
parents:
diff changeset
356 self.infiles[i] = infp
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fubar
parents:
diff changeset
357 for i, p in enumerate(self.outfiles):
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
358 p["origCL"] = p["CL"] # keep copy
121
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fubar
parents:
diff changeset
359 self.outfiles[i] = p
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fubar
parents:
diff changeset
360 for i, p in enumerate(self.addpar):
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
361 p["origCL"] = p["CL"]
121
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fubar
parents:
diff changeset
362 self.addpar[i] = p
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fubar
parents:
diff changeset
363
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
364 def clpositional(self):
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fubar
parents:
diff changeset
365 # inputs in order then params
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fubar
parents:
diff changeset
366 aCL = self.cl.append
126
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fubar
parents: 124
diff changeset
367 for (k, v, koverride) in self.clsuffix:
121
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fubar
parents:
diff changeset
368 if " " in v:
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fubar
parents:
diff changeset
369 aCL("%s" % v)
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fubar
parents:
diff changeset
370 else:
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fubar
parents:
diff changeset
371 aCL(v)
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fubar
parents:
diff changeset
372 aXCL = self.xmlcl.append
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
373 for (k, v, koverride) in self.xclsuffix:
121
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fubar
parents:
diff changeset
374 aXCL(v)
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fubar
parents:
diff changeset
375 if self.lastxclredirect:
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fubar
parents:
diff changeset
376 aXCL(self.lastxclredirect[0])
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fubar
parents:
diff changeset
377 aXCL(self.lastxclredirect[1])
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fubar
parents:
diff changeset
378
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fubar
parents:
diff changeset
379 def clargparse(self):
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fubar
parents:
diff changeset
380 """argparse style"""
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fubar
parents:
diff changeset
381 aCL = self.cl.append
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fubar
parents:
diff changeset
382 aXCL = self.xmlcl.append
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fubar
parents:
diff changeset
383 # inputs then params in argparse named form
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fubar
parents:
diff changeset
384
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
385 for (k, v, koverride) in self.xclsuffix:
121
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fubar
parents:
diff changeset
386 if koverride > "":
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fubar
parents:
diff changeset
387 k = koverride
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fubar
parents:
diff changeset
388 elif len(k.strip()) == 1:
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fubar
parents:
diff changeset
389 k = "-%s" % k
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fubar
parents:
diff changeset
390 else:
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fubar
parents:
diff changeset
391 k = "--%s" % k
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fubar
parents:
diff changeset
392 aXCL(k)
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fubar
parents:
diff changeset
393 aXCL(v)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
394 for (k, v, koverride) in self.clsuffix:
121
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fubar
parents:
diff changeset
395 if koverride > "":
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fubar
parents:
diff changeset
396 k = koverride
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fubar
parents:
diff changeset
397 elif len(k.strip()) == 1:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
398 k = "-%s" % k
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fubar
parents:
diff changeset
399 else:
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fubar
parents:
diff changeset
400 k = "--%s" % k
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fubar
parents:
diff changeset
401 aCL(k)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
402 aCL(v)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
403
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
404 def getNdash(self, newname):
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fubar
parents:
diff changeset
405 if self.is_positional:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
406 ndash = 0
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
407 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
408 ndash = 2
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fubar
parents:
diff changeset
409 if len(newname) < 2:
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fubar
parents:
diff changeset
410 ndash = 1
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
411 return ndash
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
412
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
413 def doXMLparam(self):
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fubar
parents:
diff changeset
414 """flake8 made me do this..."""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
415 for p in self.outfiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
416 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
417 newfmt = p["format"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
418 newcl = p["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
419 test = p["test"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
420 oldcl = p["origCL"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
421 test = test.strip()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
422 ndash = self.getNdash(newcl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
423 aparm = gxtp.OutputData(
124
f267ed4a3026 Uploaded
fubar
parents: 122
diff changeset
424 name=newname, format=newfmt, num_dashes=ndash, label=newname
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
425 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
426 aparm.positional = self.is_positional
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
427 if self.is_positional:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
428 if oldcl.upper() == "STDOUT":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
429 aparm.positional = 9999999
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
430 aparm.command_line_override = "> $%s" % newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
431 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
432 aparm.positional = int(oldcl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
433 aparm.command_line_override = "$%s" % newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
434 self.toutputs.append(aparm)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
435 ld = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
436 if test.strip() > "":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
437 if test.startswith("diff"):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
438 c = "diff"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
439 ld = 0
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
440 if test.split(":")[1].isdigit:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
441 ld = int(test.split(":")[1])
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
442 tp = gxtp.TestOutput(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
443 name=newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
444 value="%s_sample" % newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
445 compare=c,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
446 lines_diff=ld,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
447 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
448 elif test.startswith("sim_size"):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
449 c = "sim_size"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
450 tn = test.split(":")[1].strip()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
451 if tn > "":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
452 if "." in tn:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
453 delta = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
454 delta_frac = min(1.0, float(tn))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
455 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
456 delta = int(tn)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
457 delta_frac = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
458 tp = gxtp.TestOutput(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
459 name=newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
460 value="%s_sample" % newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
461 compare=c,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
462 delta=delta,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
463 delta_frac=delta_frac,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
464 )
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
465 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
466 c = test
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
467 tp = gxtp.TestOutput(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
468 name=newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
469 value="%s_sample" % newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
470 compare=c,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
471 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
472 self.testparam.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
473 for p in self.infiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
474 newname = p["infilename"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
475 newfmt = p["format"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
476 ndash = self.getNdash(newname)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
477 if not len(p["label"]) > 0:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
478 alab = p["CL"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
479 else:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
480 alab = p["label"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
481 aninput = gxtp.DataParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
482 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
483 optional=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
484 label=alab,
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
485 help=p["help"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
486 format=newfmt,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
487 multiple=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
488 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
489 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
490 aninput.positional = self.is_positional
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
491 if self.is_positional:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
492 if p["origCL"].upper() == "STDIN":
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
493 aparm.positional = 9999998
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
494 aparm.command_line_override = "> $%s" % newname
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
495 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
496 aparm.positional = int(p["origCL"])
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
497 aparm.command_line_override = "$%s" % newname
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
498 self.tinputs.append(aninput)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
499 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
500 self.testparam.append(tparm)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
501 for p in self.addpar:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
502 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
503 newval = p["value"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
504 newlabel = p["label"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
505 newhelp = p["help"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
506 newtype = p["type"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
507 newcl = p["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
508 oldcl = p["origCL"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
509 if not len(newlabel) > 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
510 newlabel = newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
511 ndash = self.getNdash(newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
512 if newtype == "text":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
513 aparm = gxtp.TextParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
514 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
515 label=newlabel,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
516 help=newhelp,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
517 value=newval,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
518 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
519 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
520 elif newtype == "integer":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
521 aparm = gxtp.IntegerParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
522 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
523 label=newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
524 help=newhelp,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
525 value=newval,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
526 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
527 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
528 elif newtype == "float":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
529 aparm = gxtp.FloatParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
530 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
531 label=newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
532 help=newhelp,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
533 value=newval,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
534 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
535 )
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
536 elif newtype == "boolean":
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
537 aparm = gxtp.BooleanParam(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
538 newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
539 label=newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
540 help=newhelp,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
541 value=newval,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
542 num_dashes=ndash,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
543 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
544 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
545 raise ValueError(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
546 'Unrecognised parameter type "%s" for\
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
547 additional parameter %s in makeXML'
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
548 % (newtype, newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
549 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
550 aparm.positional = self.is_positional
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
551 if self.is_positional:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
552 aparm.positional = int(oldcl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
553 self.tinputs.append(aparm)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
554 tparm = gxtp.TestParam(newname, value=newval)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
555 self.testparam.append(tparm)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
556 for p in self.selpar:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
557 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
558 newval = p["value"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
559 newlabel = p["label"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
560 newhelp = p["help"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
561 newtype = p["type"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
562 newcl = p["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
563 if not len(newlabel) > 0:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
564 newlabel = newname
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
565 ndash = self.getNdash(newname)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
566 if newtype == "selecttext":
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
567 newtext = p["texts"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
568 aparm = gxtp.SelectParam(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
569 newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
570 label=newlabel,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
571 help=newhelp,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
572 num_dashes=ndash,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
573 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
574 for i in range(len(newval)):
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
575 anopt = gxtp.SelectOption(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
576 value=newval[i],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
577 text=newtext[i],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
578 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
579 aparm.append(anopt)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
580 aparm.positional = self.is_positional
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
581 if self.is_positional:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
582 aparm.positional = int(newcl)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
583 self.tinputs.append(aparm)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
584 tparm = gxtp.TestParam(newname, value=newval)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
585 self.testparam.append(tparm)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
586 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
587 raise ValueError(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
588 'Unrecognised parameter type "%s" for\
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
589 selecttext parameter %s in makeXML'
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
590 % (newtype, newname)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
591 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
592 for p in self.collections:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
593 newkind = p["kind"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
594 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
595 newlabel = p["label"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
596 newdisc = p["discover"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
597 collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
598 disc = gxtp.DiscoverDatasets(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
599 pattern=newdisc, directory=f"{newname}", visible="false"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
600 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
601 collect.append(disc)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
602 self.toutputs.append(collect)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
603 tparm = gxtp.TestOutput(newname, ftype="pdf")
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
604 self.testparam.append(tparm)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
605
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
606 def doNoXMLparam(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
607 """filter style package - stdin to stdout"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
608 if len(self.infiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
609 alab = self.infiles[0]["label"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
610 if len(alab) == 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
611 alab = self.infiles[0]["infilename"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
612 max1s = (
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
613 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
614 % str(self.infiles)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
615 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
616 assert len(self.infiles) == 1, max1s
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
617 newname = self.infiles[0]["infilename"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
618 aninput = gxtp.DataParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
619 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
620 optional=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
621 label=alab,
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
622 help=self.infiles[0]["help"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
623 format=self.infiles[0]["format"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
624 multiple=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
625 num_dashes=0,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
626 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
627 aninput.command_line_override = "< $%s" % newname
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
628 aninput.positional = True
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
629 self.tinputs.append(aninput)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
630 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
631 self.testparam.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
632 if len(self.outfiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
633 newname = self.outfiles[0]["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
634 newfmt = self.outfiles[0]["format"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
635 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
636 anout.command_line_override = "> $%s" % newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
637 anout.positional = self.is_positional
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
638 self.toutputs.append(anout)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
639 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
640 self.testparam.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
641
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
642 def makeXML(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
643 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
644 Create a Galaxy xml tool wrapper for the new script
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
645 Uses galaxyhtml
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
646 Hmmm. How to get the command line into correct order...
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
647 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
648 if self.command_override:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
649 self.newtool.command_override = self.command_override # config file
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
650 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
651 self.newtool.command_override = self.xmlcl
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
652 cite = gxtp.Citations()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
653 acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
654 cite.append(acite)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
655 self.newtool.citations = cite
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
656 safertext = ""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
657 if self.args.help_text:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
658 helptext = open(self.args.help_text, "r").readlines()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
659 safertext = "\n".join([cheetah_escape(x) for x in helptext])
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
660 if len(safertext.strip()) == 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
661 safertext = (
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
662 "Ask the tool author (%s) to rebuild with help text please\n"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
663 % (self.args.user_email)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
664 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
665 if self.args.script_path:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
666 if len(safertext) > 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
667 safertext = safertext + "\n\n------\n" # transition allowed!
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
668 scr = [x for x in self.spacedScript if x.strip() > ""]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
669 scr.insert(0, "\n\nScript::\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
670 if len(scr) > 300:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
671 scr = (
122
c763ae9237ca Uploaded
fubar
parents: 121
diff changeset
672 scr[:100]
c763ae9237ca Uploaded
fubar
parents: 121
diff changeset
673 + [" >300 lines - stuff deleted", " ......"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
674 + scr[-100:]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
675 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
676 scr.append("\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
677 safertext = safertext + "\n".join(scr)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
678 self.newtool.help = safertext
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
679 self.newtool.version_command = f'echo "{self.args.tool_version}"'
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
680 requirements = gxtp.Requirements()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
681 if self.args.packages:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
682 for d in self.args.packages.split(","):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
683 ver = ""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
684 d = d.replace("==", ":")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
685 d = d.replace("=", ":")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
686 if ":" in d:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
687 packg, ver = d.split(":")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
688 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
689 packg = d
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
690 requirements.append(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
691 gxtp.Requirement("package", packg.strip(), ver.strip())
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
692 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
693 self.newtool.requirements = requirements
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
694 if self.args.parampass == "0":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
695 self.doNoXMLparam()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
696 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
697 self.doXMLparam()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
698 self.newtool.outputs = self.toutputs
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
699 self.newtool.inputs = self.tinputs
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
700 if self.args.script_path:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
701 configfiles = gxtp.Configfiles()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
702 configfiles.append(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
703 gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
704 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
705 self.newtool.configfiles = configfiles
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
706 tests = gxtp.Tests()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
707 test_a = gxtp.Test()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
708 for tp in self.testparam:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
709 test_a.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
710 tests.append(test_a)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
711 self.newtool.tests = tests
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
712 self.newtool.add_comment(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
713 "Created by %s at %s using the Galaxy Tool Factory."
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
714 % (self.args.user_email, timenow())
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
715 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
716 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
717 exml0 = self.newtool.export()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
718 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
719 if (
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
720 self.test_override
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
721 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
722 part1 = exml.split("<tests>")[0]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
723 part2 = exml.split("</tests>")[1]
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
724 fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
725 exml = fixed
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
726 # exml = exml.replace('range="1:"', 'range="1000:"')
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
727 xf = open("%s.xml" % self.tool_name, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
728 xf.write(exml)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
729 xf.write("\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
730 xf.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
731 # ready for the tarball
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
732
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
733 def run(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
734 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
735 generate test outputs by running a command line
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
736 won't work if command or test override in play - planemo is the
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
737 easiest way to generate test outputs for that case so is
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
738 automagically selected
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
739 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
740 scl = " ".join(self.cl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
741 err = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
742 if self.args.parampass != "0":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
743 if os.path.exists(self.elog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
744 ste = open(self.elog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
745 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
746 ste = open(self.elog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
747 if self.lastclredirect:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
748 sto = open(self.lastclredirect[1], "wb") # is name of an output file
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
749 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
750 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
751 sto = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
752 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
753 sto = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
754 sto.write(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
755 "## Executing Toolfactory generated command line = %s\n" % scl
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
756 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
757 sto.flush()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
758 subp = subprocess.run(
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
759 self.cl, shell=False, stdout=sto, stderr=ste
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
760 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
761 sto.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
762 ste.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
763 retval = subp.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
764 else: # work around special case - stdin and write to stdout
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
765 if len(self.infiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
766 sti = open(self.infiles[0]["name"], "rb")
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
767 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
768 sti = sys.stdin
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
769 if len(self.outfiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
770 sto = open(self.outfiles[0]["name"], "wb")
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
771 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
772 sto = sys.stdout
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
773 subp = subprocess.run(
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
774 self.cl, shell=False, stdout=sto, stdin=sti
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
775 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
776 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
777 retval = subp.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
778 sto.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
779 sti.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
780 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
781 os.unlink(self.tlog)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
782 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
783 os.unlink(self.elog)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
784 if retval != 0 and err: # problem
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
785 sys.stderr.write(err)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
786 logging.debug("run done")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
787 return retval
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
788
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
789 def shedLoad(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
790 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
791 use bioblend to create new repository
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
792 or update existing
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
793
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
794 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
795 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
796 sto = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
797 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
798 sto = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
799
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
800 ts = toolshed.ToolShedInstance(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
801 url=self.args.toolshed_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
802 key=self.args.toolshed_api_key,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
803 verify=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
804 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
805 repos = ts.repositories.get_repositories()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
806 rnames = [x.get("name", "?") for x in repos]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
807 rids = [x.get("id", "?") for x in repos]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
808 tfcat = "ToolFactory generated tools"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
809 if self.tool_name not in rnames:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
810 tscat = ts.categories.get_categories()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
811 cnames = [x.get("name", "?").strip() for x in tscat]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
812 cids = [x.get("id", "?") for x in tscat]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
813 catID = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
814 if tfcat.strip() in cnames:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
815 ci = cnames.index(tfcat)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
816 catID = cids[ci]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
817 res = ts.repositories.create_repository(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
818 name=self.args.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
819 synopsis="Synopsis:%s" % self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
820 description=self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
821 type="unrestricted",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
822 remote_repository_url=self.args.toolshed_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
823 homepage_url=None,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
824 category_ids=catID,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
825 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
826 tid = res.get("id", None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
827 sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
828 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
829 i = rnames.index(self.tool_name)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
830 tid = rids[i]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
831 try:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
832 res = ts.repositories.update_repository(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
833 id=tid, tar_ball_path=self.newtarpath, commit_message=None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
834 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
835 sto.write(f"#update res id {id} ={res}\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
836 except ConnectionError:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
837 sto.write(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
838 "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
839 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
840 sto.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
841
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
842 def eph_galaxy_load(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
843 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
844 use ephemeris to load the new tool from the local toolshed after planemo uploads it
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
845 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
846 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
847 tout = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
848 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
849 tout = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
850 cll = [
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
851 "shed-tools",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
852 "install",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
853 "-g",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
854 self.args.galaxy_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
855 "--latest",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
856 "-a",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
857 self.args.galaxy_api_key,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
858 "--name",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
859 self.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
860 "--owner",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
861 "fubar",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
862 "--toolshed",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
863 self.args.toolshed_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
864 "--section_label",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
865 "ToolFactory",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
866 ]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
867 tout.write("running\n%s\n" % " ".join(cll))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
868 subp = subprocess.run(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
869 cll,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
870 cwd=self.ourcwd,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
871 shell=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
872 stderr=tout,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
873 stdout=tout,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
874 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
875 tout.write(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
876 "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
877 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
878 tout.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
879 return subp.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
880
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
881 def writeShedyml(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
882 """for planemo"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
883 yuser = self.args.user_email.split("@")[0]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
884 yfname = os.path.join(self.tooloutdir, ".shed.yml")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
885 yamlf = open(yfname, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
886 odict = {
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
887 "name": self.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
888 "owner": yuser,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
889 "type": "unrestricted",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
890 "description": self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
891 "synopsis": self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
892 "category": "TF Generated Tools",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
893 }
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
894 yaml.dump(odict, yamlf, allow_unicode=True)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
895 yamlf.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
896
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
897 def makeTool(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
898 """write xmls and input samples into place"""
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
899 if self.args.parampass == 0:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
900 self.doNoXMLparam()
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
901 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
902 self.makeXML()
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
903 if self.args.script_path:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
904 stname = os.path.join(self.tooloutdir, self.sfile)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
905 if not os.path.exists(stname):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
906 shutil.copyfile(self.sfile, stname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
907 xreal = "%s.xml" % self.tool_name
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
908 xout = os.path.join(self.tooloutdir, xreal)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
909 shutil.copyfile(xreal, xout)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
910 for p in self.infiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
911 pth = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
912 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
913 shutil.copyfile(pth, dest)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
914 dest = os.path.join(self.repdir, "%s_sample" % p["infilename"])
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
915 shutil.copyfile(pth, dest)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
916
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
917 def makeToolTar(self, report_fail=False):
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
918 """move outputs into test-data and prepare the tarball"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
919 excludeme = "_planemo_test_report.html"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
920
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
921 def exclude_function(tarinfo):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
922 filename = tarinfo.name
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
923 return None if filename.endswith(excludeme) else tarinfo
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
924
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
925 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
926 tout = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
927 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
928 tout = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
929 for p in self.outfiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
930 oname = p["name"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
931 tdest = os.path.join(self.testdir, "%s_sample" % oname)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
932 src = os.path.join(self.testdir, oname)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
933 if not os.path.isfile(tdest):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
934 if os.path.isfile(src):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
935 shutil.copyfile(src, tdest)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
936 dest = os.path.join(self.repdir, "%s.sample" % (oname))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
937 shutil.copyfile(src, dest)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
938 else:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
939 if report_fail:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
940 tout.write(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
941 "###Tool may have failed - output file %s not found in testdir after planemo run %s."
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
942 % (tdest, self.testdir)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
943 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
944 tf = tarfile.open(self.newtarpath, "w:gz")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
945 tf.add(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
946 name=self.tooloutdir,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
947 arcname=self.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
948 filter=exclude_function,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
949 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
950 tf.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
951 shutil.copyfile(self.newtarpath, self.args.new_tool)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
952
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
953 def moveRunOutputs(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
954 """need to move planemo or run outputs into toolfactory collection"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
955 with os.scandir(self.tooloutdir) as outs:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
956 for entry in outs:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
957 if not entry.is_file():
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
958 continue
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
959 if "." in entry.name:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
960 _, ext = os.path.splitext(entry.name)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
961 if ext in [".tgz", ".json"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
962 continue
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
963 if ext in [".yml", ".xml", ".yaml"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
964 newname = f"{entry.name.replace('.','_')}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
965 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
966 newname = entry.name
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
967 else:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
968 newname = f"{entry.name}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
969 dest = os.path.join(self.repdir, newname)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
970 src = os.path.join(self.tooloutdir, entry.name)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
971 shutil.copyfile(src, dest)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
972 if self.args.include_tests:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
973 with os.scandir(self.testdir) as outs:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
974 for entry in outs:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
975 if (not entry.is_file()) or entry.name.endswith(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
976 "_planemo_test_report.html"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
977 ):
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
978 continue
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
979 if "." in entry.name:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
980 _, ext = os.path.splitext(entry.name)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
981 if ext in [".tgz", ".json"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
982 continue
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
983 if ext in [".yml", ".xml", ".yaml"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
984 newname = f"{entry.name.replace('.','_')}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
985 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
986 newname = entry.name
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
987 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
988 newname = f"{entry.name}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
989 dest = os.path.join(self.repdir, newname)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
990 src = os.path.join(self.testdir, entry.name)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
991 shutil.copyfile(src, dest)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
992
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
993
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
994 def planemo_test_once(self):
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
995 """planemo is a requirement so is available for testing but needs a
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
996 different call if in the biocontainer - see above
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
997 and for generating test outputs if command or test overrides are
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
998 supplied test outputs are sent to repdir for display
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
999 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1000 xreal = "%s.xml" % self.tool_name
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1001 tool_test_path = os.path.join(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1002 self.repdir, f"{self.tool_name}_planemo_test_report.html"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1003 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1004 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1005 tout = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1006 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1007 tout = open(self.tlog, "w")
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1008 cll = [
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1009 "planemo",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1010 "test",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1011 "--conda_auto_init",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1012 "--test_data",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1013 os.path.abspath(self.testdir),
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1014 "--test_output",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1015 os.path.abspath(tool_test_path),
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1016 "--galaxy_root",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1017 self.args.galaxy_root,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1018 "--update_test_data",
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1019 os.path.abspath(xreal),
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1020 ]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1021 p = subprocess.run(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1022 cll,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1023 shell=False,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1024 cwd=self.tooloutdir,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1025 stderr=tout,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1026 stdout=tout,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1027 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1028 tout.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1029 return p.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1030
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1031
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1032 def main():
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1033 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1034 This is a Galaxy wrapper.
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1035 It expects to be called by a special purpose tool.xml
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1036
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1037 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1038 parser = argparse.ArgumentParser()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1039 a = parser.add_argument
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1040 a("--script_path", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1041 a("--history_test", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1042 a("--cl_prefix", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1043 a("--sysexe", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1044 a("--packages", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1045 a("--tool_name", default="newtool")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1046 a("--tool_dir", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1047 a("--input_files", default=[], action="append")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1048 a("--output_files", default=[], action="append")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1049 a("--user_email", default="Unknown")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1050 a("--bad_user", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1051 a("--make_Tool", default="runonly")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1052 a("--help_text", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1053 a("--tool_desc", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1054 a("--tool_version", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1055 a("--citations", default=None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1056 a("--command_override", default=None)
2050b2475ae5 Uploaded
fubar
parents:
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1057 a("--test_override", default=None)
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1058 a("--additional_parameters", action="append", default=[])
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1059 a("--selecttext_parameters", action="append", default=[])
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1060 a("--edit_additional_parameters", action="store_true", default=False)
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1061 a("--parampass", default="positional")
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1062 a("--tfout", default="./tfout")
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1063 a("--new_tool", default="new_tool")
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1064 a("--galaxy_url", default="http://localhost:8080")
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1065 a("--toolshed_url", default="http://localhost:9009")
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1066 # make sure this is identical to tool_sheds_conf.xml
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1067 # localhost != 127.0.0.1 so validation fails
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1068 a("--toolshed_api_key", default="fakekey")
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1069 a("--galaxy_api_key", default="fakekey")
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1070 a("--galaxy_root", default="/galaxy-central")
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1071 a("--galaxy_venv", default="/galaxy_venv")
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1072 a("--collection", action="append", default=[])
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1073 a("--include_tests", default=False, action="store_true")
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1074 args = parser.parse_args()
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1075 assert not args.bad_user, (
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1076 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
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1077 admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
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1078 % (args.bad_user, args.bad_user)
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1079 )
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1080 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
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1081 assert (
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1082 args.sysexe or args.packages
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1083 ), "## Tool Factory wrapper expects an interpreter \
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1084 or an executable package in --sysexe or --packages"
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1085 r = ScriptRunner(args)
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1086 r.writeShedyml()
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1087 r.makeTool()
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1088 if args.make_Tool == "generate":
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1089 r.run()
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1090 r.moveRunOutputs()
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1091 r.makeToolTar()
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1092 else:
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1093 # r.planemo_test(genoutputs=True) # this fails :( - see PR
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1094 # r.moveRunOutputs()
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1095 # r.makeToolTar(report_fail=False)
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1096 r.planemo_test_once()
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1097 r.moveRunOutputs()
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1098 r.makeToolTar(report_fail=True)
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1099 if args.make_Tool == "gentestinstall":
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1100 r.shedLoad()
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1101 r.eph_galaxy_load()
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1102
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1103
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1104 if __name__ == "__main__":
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1105 main()