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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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126
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19 import json
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121
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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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129
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23 import shlex
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121
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24 import shutil
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25 import subprocess
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26 import sys
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27 import tarfile
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28 import tempfile
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29 import time
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30
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135
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31 from bioblend import ConnectionError
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32 from bioblend import toolshed
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33
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133
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34 import galaxyxml.tool as gxt
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35 import galaxyxml.tool.parameters as gxtp
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135
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36
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133
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37 import lxml
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135
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38
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133
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39 import yaml
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121
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40
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126
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41 myversion = "V2.2 February 2021"
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121
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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 FAKEEXE = "~~~REMOVE~~~ME~~~"
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47 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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48 # with override.
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49
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50
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51 def timenow():
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52 """return current time as a string"""
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53 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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54
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55
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56 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
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57
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58
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59 def cheetah_escape(text):
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60 """Produce entities within text."""
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61 return "".join([cheetah_escape_table.get(c, c) for c in text])
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62
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63
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64 def parse_citations(citations_text):
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65 """"""
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66 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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67 citation_tuples = []
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68 for citation in citations:
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69 if citation.startswith("doi"):
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70 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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71 else:
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72 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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73 return citation_tuples
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74
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75
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76 class ScriptRunner:
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77 """Wrapper for an arbitrary script
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78 uses galaxyxml
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79
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80 """
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81
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135
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82 def __init__(self, args=None): # noqa
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121
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83 """
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84 prepare command line cl for running the tool here
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85 and prepare elements needed for galaxyxml tool generation
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86 """
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87 self.ourcwd = os.getcwd()
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126
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88 self.collections = []
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89 if len(args.collection) > 0:
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90 try:
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91 self.collections = [
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92 json.loads(x) for x in args.collection if len(x.strip()) > 1
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93 ]
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94 except Exception:
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95 print(
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96 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
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97 )
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98 try:
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99 self.infiles = [
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100 json.loads(x) for x in args.input_files if len(x.strip()) > 1
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101 ]
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102 except Exception:
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103 print(
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104 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
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105 )
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106 try:
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107 self.outfiles = [
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108 json.loads(x) for x in args.output_files if len(x.strip()) > 1
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109 ]
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110 except Exception:
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111 print(
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112 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
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113 )
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114 try:
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115 self.addpar = [
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116 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
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117 ]
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118 except Exception:
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119 print(
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120 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
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121 )
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122 try:
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123 self.selpar = [
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124 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
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125 ]
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126 except Exception:
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127 print(
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128 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
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129 )
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121
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130 self.args = args
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131 self.cleanuppar()
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132 self.lastclredirect = None
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133 self.lastxclredirect = None
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134 self.cl = []
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135 self.xmlcl = []
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136 self.is_positional = self.args.parampass == "positional"
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137 if self.args.sysexe:
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126
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138 if ' ' in self.args.sysexe:
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139 self.executeme = self.args.sysexe.split(' ')
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140 else:
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141 self.executeme = [self.args.sysexe, ]
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121
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142 else:
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143 if self.args.packages:
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126
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144 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
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121
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145 else:
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146 self.executeme = None
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147 aCL = self.cl.append
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148 aXCL = self.xmlcl.append
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149 assert args.parampass in [
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150 "0",
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151 "argparse",
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152 "positional",
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153 ], 'args.parampass must be "0","positional" or "argparse"'
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154 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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155 self.tool_id = self.tool_name
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156 self.newtool = gxt.Tool(
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157 self.tool_name,
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158 self.tool_id,
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159 self.args.tool_version,
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160 self.args.tool_desc,
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161 FAKEEXE,
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162 )
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126
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163 self.newtarpath = "%s_toolshed.gz" % self.tool_name
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121
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164 self.tooloutdir = "./tfout"
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165 self.repdir = "./TF_run_report_tempdir"
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166 self.testdir = os.path.join(self.tooloutdir, "test-data")
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167 if not os.path.exists(self.tooloutdir):
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168 os.mkdir(self.tooloutdir)
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169 if not os.path.exists(self.testdir):
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170 os.mkdir(self.testdir)
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171 if not os.path.exists(self.repdir):
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172 os.mkdir(self.repdir)
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173 self.tinputs = gxtp.Inputs()
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174 self.toutputs = gxtp.Outputs()
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175 self.testparam = []
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176 if self.args.script_path:
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177 self.prepScript()
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178 if self.args.command_override:
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179 scos = open(self.args.command_override, "r").readlines()
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180 self.command_override = [x.rstrip() for x in scos]
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181 else:
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182 self.command_override = None
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183 if self.args.test_override:
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184 stos = open(self.args.test_override, "r").readlines()
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185 self.test_override = [x.rstrip() for x in stos]
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186 else:
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187 self.test_override = None
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126
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188 if self.args.script_path:
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189 for ex in self.executeme:
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190 aCL(ex)
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191 aXCL(ex)
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192 aCL(self.sfile)
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193 aXCL("$runme")
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194 else:
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129
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195 for ex in self.executeme:
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196 aCL(ex)
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197 aXCL(ex)
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198
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126
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199 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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200 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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201 if self.args.parampass == "0":
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202 self.clsimple()
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203 else:
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204 if self.args.parampass == "positional":
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205 self.prepclpos()
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206 self.clpositional()
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207 else:
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208 self.prepargp()
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209 self.clargparse()
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129
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210 if self.args.cl_suffix: # DIY CL end
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211 clp = shlex.split(self.args.cl_suffix)
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121
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212 for c in clp:
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213 aCL(c)
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214 aXCL(c)
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126
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215
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216 def clsimple(self):
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131
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217 """no parameters or repeats - uses < and > for i/o"""
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126
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218 aCL = self.cl.append
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219 aXCL = self.xmlcl.append
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220 if len(self.infiles) > 0:
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221 aCL("<")
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222 aCL(self.infiles[0]["infilename"])
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223 aXCL("<")
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224 aXCL("$%s" % self.infiles[0]["infilename"])
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225 if len(self.outfiles) > 0:
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226 aCL(">")
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227 aCL(self.outfiles[0]["name"])
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228 aXCL(">")
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229 aXCL("$%s" % self.outfiles[0]["name"])
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121
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230
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126
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231 def prepargp(self):
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232 clsuffix = []
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233 xclsuffix = []
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234 for i, p in enumerate(self.infiles):
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135
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235 nam = p["infilename"]
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126
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236 if p["origCL"].strip().upper() == "STDIN":
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237 appendme = [
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135
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238 nam,
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239 nam,
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240 "< %s" % nam,
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126
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241 ]
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242 xappendme = [
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135
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243 nam,
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244 nam,
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245 "< $%s" % nam,
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126
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246 ]
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247 else:
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135
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248 rep = p["repeat"] == "1"
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249 over = ""
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250 if rep:
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251 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
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126
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252 appendme = [p["CL"], p["CL"], ""]
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135
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253 xappendme = [p["CL"], "$%s" % p["CL"], over]
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126
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254 clsuffix.append(appendme)
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255 xclsuffix.append(xappendme)
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256 for i, p in enumerate(self.outfiles):
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257 if p["origCL"].strip().upper() == "STDOUT":
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258 self.lastclredirect = [">", p["name"]]
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259 self.lastxclredirect = [">", "$%s" % p["name"]]
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121
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260 else:
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126
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261 clsuffix.append([p["name"], p["name"], ""])
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262 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
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263 for p in self.addpar:
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131
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264 nam = p["name"]
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265 rep = p["repeat"] == "1"
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266 if rep:
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135
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267 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
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131
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268 else:
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269 over = p["override"]
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270 clsuffix.append([p["CL"], nam, over])
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271 xclsuffix.append([p["CL"], nam, over])
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126
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272 for p in self.selpar:
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273 clsuffix.append([p["CL"], p["name"], p["override"]])
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274 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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275 self.xclsuffix = xclsuffix
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276 self.clsuffix = clsuffix
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277
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278 def prepclpos(self):
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279 clsuffix = []
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280 xclsuffix = []
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281 for i, p in enumerate(self.infiles):
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282 if p["origCL"].strip().upper() == "STDIN":
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283 appendme = [
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284 "999",
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285 p["infilename"],
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286 "< $%s" % p["infilename"],
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287 ]
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288 xappendme = [
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289 "999",
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290 p["infilename"],
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291 "< $%s" % p["infilename"],
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292 ]
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293 else:
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294 appendme = [p["CL"], p["infilename"], ""]
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295 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
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296 clsuffix.append(appendme)
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297 xclsuffix.append(xappendme)
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298 for i, p in enumerate(self.outfiles):
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299 if p["origCL"].strip().upper() == "STDOUT":
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300 self.lastclredirect = [">", p["name"]]
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301 self.lastxclredirect = [">", "$%s" % p["name"]]
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302 else:
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303 clsuffix.append([p["CL"], p["name"], ""])
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304 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
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305 for p in self.addpar:
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131
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306 nam = p["name"]
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307 rep = p["repeat"] == "1" # repeats make NO sense
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308 if rep:
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309 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
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310 over = p["override"]
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311 clsuffix.append([p["CL"], nam, over])
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133
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312 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
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126
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313 for p in self.selpar:
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133
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314 clsuffix.append([p["CL"], p["name"], p["override"]])
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134
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315 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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126
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316 clsuffix.sort()
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317 xclsuffix.sort()
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318 self.xclsuffix = xclsuffix
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319 self.clsuffix = clsuffix
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121
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320
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321 def prepScript(self):
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322 rx = open(self.args.script_path, "r").readlines()
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323 rx = [x.rstrip() for x in rx]
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324 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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325 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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326 self.script = "\n".join(rx)
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327 fhandle, self.sfile = tempfile.mkstemp(
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126
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328 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
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121
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329 )
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330 tscript = open(self.sfile, "w")
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331 tscript.write(self.script)
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332 tscript.close()
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333 self.escapedScript = [cheetah_escape(x) for x in rx]
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334 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
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126
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335 art = "%s.%s" % (self.tool_name, self.executeme[0])
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121
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336 artifact = open(art, "wb")
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337 artifact.write(bytes("\n".join(self.escapedScript), "utf8"))
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338 artifact.close()
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339
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340 def cleanuppar(self):
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341 """ positional parameters are complicated by their numeric ordinal"""
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342 if self.args.parampass == "positional":
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343 for i, p in enumerate(self.infiles):
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344 assert (
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126
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345 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
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121
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346 ), "Positional parameters must be ordinal integers - got %s for %s" % (
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126
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347 p["CL"],
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348 p["label"],
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121
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349 )
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350 for i, p in enumerate(self.outfiles):
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351 assert (
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126
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352 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
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121
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353 ), "Positional parameters must be ordinal integers - got %s for %s" % (
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126
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354 p["CL"],
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355 p["name"],
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121
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356 )
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357 for i, p in enumerate(self.addpar):
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358 assert p[
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126
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359 "CL"
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121
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360 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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126
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361 p["CL"],
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362 p["name"],
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121
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363 )
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364 for i, p in enumerate(self.infiles):
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365 infp = copy.copy(p)
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126
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366 infp["origCL"] = infp["CL"]
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367 if self.args.parampass in ["positional", "0"]:
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368 infp["infilename"] = infp["label"].replace(" ", "_")
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369 else:
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370 infp["infilename"] = infp["CL"]
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121
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371 self.infiles[i] = infp
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372 for i, p in enumerate(self.outfiles):
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126
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373 p["origCL"] = p["CL"] # keep copy
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121
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374 self.outfiles[i] = p
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375 for i, p in enumerate(self.addpar):
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126
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376 p["origCL"] = p["CL"]
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121
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377 self.addpar[i] = p
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378
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379 def clpositional(self):
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380 # inputs in order then params
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381 aCL = self.cl.append
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|
126
|
382 for (k, v, koverride) in self.clsuffix:
|
|
121
|
383 if " " in v:
|
|
|
384 aCL("%s" % v)
|
|
|
385 else:
|
|
|
386 aCL(v)
|
|
|
387 aXCL = self.xmlcl.append
|
|
126
|
388 for (k, v, koverride) in self.xclsuffix:
|
|
121
|
389 aXCL(v)
|
|
|
390 if self.lastxclredirect:
|
|
|
391 aXCL(self.lastxclredirect[0])
|
|
|
392 aXCL(self.lastxclredirect[1])
|
|
|
393
|
|
|
394 def clargparse(self):
|
|
|
395 """argparse style"""
|
|
|
396 aCL = self.cl.append
|
|
|
397 aXCL = self.xmlcl.append
|
|
|
398 # inputs then params in argparse named form
|
|
|
399
|
|
126
|
400 for (k, v, koverride) in self.xclsuffix:
|
|
121
|
401 if koverride > "":
|
|
|
402 k = koverride
|
|
131
|
403 aXCL(k)
|
|
121
|
404 else:
|
|
131
|
405 if len(k.strip()) == 1:
|
|
|
406 k = "-%s" % k
|
|
|
407 else:
|
|
|
408 k = "--%s" % k
|
|
|
409 aXCL(k)
|
|
|
410 aXCL(v)
|
|
126
|
411 for (k, v, koverride) in self.clsuffix:
|
|
121
|
412 if koverride > "":
|
|
|
413 k = koverride
|
|
|
414 elif len(k.strip()) == 1:
|
|
|
415 k = "-%s" % k
|
|
|
416 else:
|
|
|
417 k = "--%s" % k
|
|
|
418 aCL(k)
|
|
|
419 aCL(v)
|
|
129
|
420 if self.lastxclredirect:
|
|
|
421 aXCL(self.lastxclredirect[0])
|
|
|
422 aXCL(self.lastxclredirect[1])
|
|
121
|
423
|
|
|
424 def getNdash(self, newname):
|
|
|
425 if self.is_positional:
|
|
|
426 ndash = 0
|
|
|
427 else:
|
|
|
428 ndash = 2
|
|
|
429 if len(newname) < 2:
|
|
|
430 ndash = 1
|
|
|
431 return ndash
|
|
|
432
|
|
|
433 def doXMLparam(self):
|
|
135
|
434 """Add all needed elements to tool""" # noqa
|
|
121
|
435 for p in self.outfiles:
|
|
126
|
436 newname = p["name"]
|
|
|
437 newfmt = p["format"]
|
|
|
438 newcl = p["CL"]
|
|
|
439 test = p["test"]
|
|
|
440 oldcl = p["origCL"]
|
|
121
|
441 test = test.strip()
|
|
|
442 ndash = self.getNdash(newcl)
|
|
|
443 aparm = gxtp.OutputData(
|
|
124
|
444 name=newname, format=newfmt, num_dashes=ndash, label=newname
|
|
121
|
445 )
|
|
|
446 aparm.positional = self.is_positional
|
|
|
447 if self.is_positional:
|
|
|
448 if oldcl.upper() == "STDOUT":
|
|
|
449 aparm.positional = 9999999
|
|
|
450 aparm.command_line_override = "> $%s" % newname
|
|
|
451 else:
|
|
|
452 aparm.positional = int(oldcl)
|
|
|
453 aparm.command_line_override = "$%s" % newname
|
|
|
454 self.toutputs.append(aparm)
|
|
|
455 ld = None
|
|
|
456 if test.strip() > "":
|
|
|
457 if test.startswith("diff"):
|
|
|
458 c = "diff"
|
|
|
459 ld = 0
|
|
|
460 if test.split(":")[1].isdigit:
|
|
|
461 ld = int(test.split(":")[1])
|
|
|
462 tp = gxtp.TestOutput(
|
|
|
463 name=newname,
|
|
|
464 value="%s_sample" % newname,
|
|
|
465 compare=c,
|
|
|
466 lines_diff=ld,
|
|
|
467 )
|
|
|
468 elif test.startswith("sim_size"):
|
|
|
469 c = "sim_size"
|
|
|
470 tn = test.split(":")[1].strip()
|
|
|
471 if tn > "":
|
|
|
472 if "." in tn:
|
|
|
473 delta = None
|
|
|
474 delta_frac = min(1.0, float(tn))
|
|
|
475 else:
|
|
|
476 delta = int(tn)
|
|
|
477 delta_frac = None
|
|
|
478 tp = gxtp.TestOutput(
|
|
|
479 name=newname,
|
|
|
480 value="%s_sample" % newname,
|
|
|
481 compare=c,
|
|
|
482 delta=delta,
|
|
|
483 delta_frac=delta_frac,
|
|
|
484 )
|
|
126
|
485 else:
|
|
|
486 c = test
|
|
|
487 tp = gxtp.TestOutput(
|
|
|
488 name=newname,
|
|
|
489 value="%s_sample" % newname,
|
|
|
490 compare=c,
|
|
|
491 )
|
|
121
|
492 self.testparam.append(tp)
|
|
|
493 for p in self.infiles:
|
|
126
|
494 newname = p["infilename"]
|
|
|
495 newfmt = p["format"]
|
|
121
|
496 ndash = self.getNdash(newname)
|
|
135
|
497 reps = p.get("repeat", "0") == "1"
|
|
126
|
498 if not len(p["label"]) > 0:
|
|
|
499 alab = p["CL"]
|
|
121
|
500 else:
|
|
126
|
501 alab = p["label"]
|
|
121
|
502 aninput = gxtp.DataParam(
|
|
|
503 newname,
|
|
|
504 optional=False,
|
|
|
505 label=alab,
|
|
126
|
506 help=p["help"],
|
|
121
|
507 format=newfmt,
|
|
|
508 multiple=False,
|
|
|
509 num_dashes=ndash,
|
|
|
510 )
|
|
|
511 aninput.positional = self.is_positional
|
|
126
|
512 if self.is_positional:
|
|
|
513 if p["origCL"].upper() == "STDIN":
|
|
127
|
514 aninput.positional = 9999998
|
|
|
515 aninput.command_line_override = "> $%s" % newname
|
|
126
|
516 else:
|
|
127
|
517 aninput.positional = int(p["origCL"])
|
|
|
518 aninput.command_line_override = "$%s" % newname
|
|
131
|
519 if reps:
|
|
133
|
520 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {alab} as needed")
|
|
131
|
521 repe.append(aninput)
|
|
|
522 self.tinputs.append(repe)
|
|
|
523 tparm = gxtp.TestRepeat(name=f"R_{newname}")
|
|
|
524 tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
|
|
|
525 tparm.append(tparm2)
|
|
|
526 self.testparam.append(tparm)
|
|
|
527 else:
|
|
|
528 self.tinputs.append(aninput)
|
|
|
529 tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
|
|
|
530 self.testparam.append(tparm)
|
|
121
|
531 for p in self.addpar:
|
|
126
|
532 newname = p["name"]
|
|
|
533 newval = p["value"]
|
|
|
534 newlabel = p["label"]
|
|
|
535 newhelp = p["help"]
|
|
|
536 newtype = p["type"]
|
|
|
537 newcl = p["CL"]
|
|
|
538 oldcl = p["origCL"]
|
|
131
|
539 reps = p["repeat"] == "1"
|
|
121
|
540 if not len(newlabel) > 0:
|
|
|
541 newlabel = newname
|
|
|
542 ndash = self.getNdash(newname)
|
|
|
543 if newtype == "text":
|
|
|
544 aparm = gxtp.TextParam(
|
|
|
545 newname,
|
|
|
546 label=newlabel,
|
|
|
547 help=newhelp,
|
|
|
548 value=newval,
|
|
|
549 num_dashes=ndash,
|
|
|
550 )
|
|
|
551 elif newtype == "integer":
|
|
|
552 aparm = gxtp.IntegerParam(
|
|
|
553 newname,
|
|
130
|
554 label=newlabel,
|
|
121
|
555 help=newhelp,
|
|
|
556 value=newval,
|
|
|
557 num_dashes=ndash,
|
|
|
558 )
|
|
|
559 elif newtype == "float":
|
|
|
560 aparm = gxtp.FloatParam(
|
|
|
561 newname,
|
|
130
|
562 label=newlabel,
|
|
121
|
563 help=newhelp,
|
|
|
564 value=newval,
|
|
|
565 num_dashes=ndash,
|
|
|
566 )
|
|
126
|
567 elif newtype == "boolean":
|
|
|
568 aparm = gxtp.BooleanParam(
|
|
|
569 newname,
|
|
130
|
570 label=newlabel,
|
|
126
|
571 help=newhelp,
|
|
|
572 value=newval,
|
|
|
573 num_dashes=ndash,
|
|
|
574 )
|
|
121
|
575 else:
|
|
|
576 raise ValueError(
|
|
|
577 'Unrecognised parameter type "%s" for\
|
|
|
578 additional parameter %s in makeXML'
|
|
|
579 % (newtype, newname)
|
|
|
580 )
|
|
|
581 aparm.positional = self.is_positional
|
|
|
582 if self.is_positional:
|
|
|
583 aparm.positional = int(oldcl)
|
|
131
|
584 if reps:
|
|
|
585 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")
|
|
|
586 repe.append(aparm)
|
|
|
587 self.tinputs.append(repe)
|
|
|
588 tparm = gxtp.TestRepeat(name=f"R_{newname}")
|
|
|
589 tparm2 = gxtp.TestParam(newname, value=newval)
|
|
|
590 tparm.append(tparm2)
|
|
|
591 self.testparam.append(tparm)
|
|
|
592 else:
|
|
|
593 self.tinputs.append(aparm)
|
|
|
594 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
595 self.testparam.append(tparm)
|
|
126
|
596 for p in self.selpar:
|
|
|
597 newname = p["name"]
|
|
|
598 newval = p["value"]
|
|
|
599 newlabel = p["label"]
|
|
|
600 newhelp = p["help"]
|
|
|
601 newtype = p["type"]
|
|
|
602 newcl = p["CL"]
|
|
|
603 if not len(newlabel) > 0:
|
|
|
604 newlabel = newname
|
|
|
605 ndash = self.getNdash(newname)
|
|
|
606 if newtype == "selecttext":
|
|
|
607 newtext = p["texts"]
|
|
|
608 aparm = gxtp.SelectParam(
|
|
|
609 newname,
|
|
|
610 label=newlabel,
|
|
|
611 help=newhelp,
|
|
|
612 num_dashes=ndash,
|
|
|
613 )
|
|
|
614 for i in range(len(newval)):
|
|
|
615 anopt = gxtp.SelectOption(
|
|
|
616 value=newval[i],
|
|
|
617 text=newtext[i],
|
|
|
618 )
|
|
|
619 aparm.append(anopt)
|
|
|
620 aparm.positional = self.is_positional
|
|
|
621 if self.is_positional:
|
|
|
622 aparm.positional = int(newcl)
|
|
|
623 self.tinputs.append(aparm)
|
|
|
624 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
625 self.testparam.append(tparm)
|
|
|
626 else:
|
|
|
627 raise ValueError(
|
|
|
628 'Unrecognised parameter type "%s" for\
|
|
|
629 selecttext parameter %s in makeXML'
|
|
|
630 % (newtype, newname)
|
|
|
631 )
|
|
|
632 for p in self.collections:
|
|
|
633 newkind = p["kind"]
|
|
|
634 newname = p["name"]
|
|
|
635 newlabel = p["label"]
|
|
|
636 newdisc = p["discover"]
|
|
|
637 collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)
|
|
|
638 disc = gxtp.DiscoverDatasets(
|
|
|
639 pattern=newdisc, directory=f"{newname}", visible="false"
|
|
|
640 )
|
|
|
641 collect.append(disc)
|
|
|
642 self.toutputs.append(collect)
|
|
131
|
643 try:
|
|
|
644 tparm = gxtp.TestOutputCollection(newname) # broken until PR merged.
|
|
|
645 self.testparam.append(tparm)
|
|
|
646 except Exception:
|
|
|
647 print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!")
|
|
121
|
648
|
|
|
649 def doNoXMLparam(self):
|
|
|
650 """filter style package - stdin to stdout"""
|
|
|
651 if len(self.infiles) > 0:
|
|
126
|
652 alab = self.infiles[0]["label"]
|
|
121
|
653 if len(alab) == 0:
|
|
126
|
654 alab = self.infiles[0]["infilename"]
|
|
121
|
655 max1s = (
|
|
|
656 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
|
|
|
657 % str(self.infiles)
|
|
|
658 )
|
|
|
659 assert len(self.infiles) == 1, max1s
|
|
126
|
660 newname = self.infiles[0]["infilename"]
|
|
121
|
661 aninput = gxtp.DataParam(
|
|
|
662 newname,
|
|
|
663 optional=False,
|
|
|
664 label=alab,
|
|
126
|
665 help=self.infiles[0]["help"],
|
|
|
666 format=self.infiles[0]["format"],
|
|
121
|
667 multiple=False,
|
|
|
668 num_dashes=0,
|
|
|
669 )
|
|
|
670 aninput.command_line_override = "< $%s" % newname
|
|
126
|
671 aninput.positional = True
|
|
121
|
672 self.tinputs.append(aninput)
|
|
|
673 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
674 self.testparam.append(tp)
|
|
|
675 if len(self.outfiles) > 0:
|
|
126
|
676 newname = self.outfiles[0]["name"]
|
|
|
677 newfmt = self.outfiles[0]["format"]
|
|
121
|
678 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
|
|
|
679 anout.command_line_override = "> $%s" % newname
|
|
|
680 anout.positional = self.is_positional
|
|
|
681 self.toutputs.append(anout)
|
|
126
|
682 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
|
|
121
|
683 self.testparam.append(tp)
|
|
|
684
|
|
135
|
685 def makeXML(self): # noqa
|
|
121
|
686 """
|
|
|
687 Create a Galaxy xml tool wrapper for the new script
|
|
|
688 Uses galaxyhtml
|
|
|
689 Hmmm. How to get the command line into correct order...
|
|
|
690 """
|
|
|
691 if self.command_override:
|
|
|
692 self.newtool.command_override = self.command_override # config file
|
|
|
693 else:
|
|
|
694 self.newtool.command_override = self.xmlcl
|
|
|
695 cite = gxtp.Citations()
|
|
|
696 acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")
|
|
|
697 cite.append(acite)
|
|
|
698 self.newtool.citations = cite
|
|
|
699 safertext = ""
|
|
|
700 if self.args.help_text:
|
|
|
701 helptext = open(self.args.help_text, "r").readlines()
|
|
|
702 safertext = "\n".join([cheetah_escape(x) for x in helptext])
|
|
|
703 if len(safertext.strip()) == 0:
|
|
|
704 safertext = (
|
|
|
705 "Ask the tool author (%s) to rebuild with help text please\n"
|
|
|
706 % (self.args.user_email)
|
|
|
707 )
|
|
|
708 if self.args.script_path:
|
|
|
709 if len(safertext) > 0:
|
|
|
710 safertext = safertext + "\n\n------\n" # transition allowed!
|
|
|
711 scr = [x for x in self.spacedScript if x.strip() > ""]
|
|
|
712 scr.insert(0, "\n\nScript::\n")
|
|
|
713 if len(scr) > 300:
|
|
|
714 scr = (
|
|
122
|
715 scr[:100]
|
|
|
716 + [" >300 lines - stuff deleted", " ......"]
|
|
121
|
717 + scr[-100:]
|
|
|
718 )
|
|
|
719 scr.append("\n")
|
|
|
720 safertext = safertext + "\n".join(scr)
|
|
|
721 self.newtool.help = safertext
|
|
|
722 self.newtool.version_command = f'echo "{self.args.tool_version}"'
|
|
135
|
723 std = gxtp.Stdios()
|
|
|
724 std1 = gxtp.Stdio()
|
|
|
725 std.append(std1)
|
|
|
726 self.newtool.stdios = std
|
|
121
|
727 requirements = gxtp.Requirements()
|
|
|
728 if self.args.packages:
|
|
|
729 for d in self.args.packages.split(","):
|
|
|
730 ver = ""
|
|
|
731 d = d.replace("==", ":")
|
|
|
732 d = d.replace("=", ":")
|
|
|
733 if ":" in d:
|
|
|
734 packg, ver = d.split(":")
|
|
|
735 else:
|
|
|
736 packg = d
|
|
|
737 requirements.append(
|
|
|
738 gxtp.Requirement("package", packg.strip(), ver.strip())
|
|
|
739 )
|
|
135
|
740 self.newtool.requirements = requirements
|
|
121
|
741 if self.args.parampass == "0":
|
|
|
742 self.doNoXMLparam()
|
|
|
743 else:
|
|
|
744 self.doXMLparam()
|
|
|
745 self.newtool.outputs = self.toutputs
|
|
|
746 self.newtool.inputs = self.tinputs
|
|
|
747 if self.args.script_path:
|
|
|
748 configfiles = gxtp.Configfiles()
|
|
|
749 configfiles.append(
|
|
|
750 gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))
|
|
|
751 )
|
|
|
752 self.newtool.configfiles = configfiles
|
|
|
753 tests = gxtp.Tests()
|
|
|
754 test_a = gxtp.Test()
|
|
|
755 for tp in self.testparam:
|
|
|
756 test_a.append(tp)
|
|
|
757 tests.append(test_a)
|
|
|
758 self.newtool.tests = tests
|
|
|
759 self.newtool.add_comment(
|
|
|
760 "Created by %s at %s using the Galaxy Tool Factory."
|
|
|
761 % (self.args.user_email, timenow())
|
|
|
762 )
|
|
|
763 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
|
|
|
764 exml0 = self.newtool.export()
|
|
|
765 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
|
|
|
766 if (
|
|
|
767 self.test_override
|
|
|
768 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
|
|
|
769 part1 = exml.split("<tests>")[0]
|
|
|
770 part2 = exml.split("</tests>")[1]
|
|
126
|
771 fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)
|
|
121
|
772 exml = fixed
|
|
|
773 # exml = exml.replace('range="1:"', 'range="1000:"')
|
|
|
774 xf = open("%s.xml" % self.tool_name, "w")
|
|
|
775 xf.write(exml)
|
|
|
776 xf.write("\n")
|
|
|
777 xf.close()
|
|
|
778 # ready for the tarball
|
|
|
779
|
|
|
780 def run(self):
|
|
|
781 """
|
|
|
782 generate test outputs by running a command line
|
|
|
783 won't work if command or test override in play - planemo is the
|
|
|
784 easiest way to generate test outputs for that case so is
|
|
|
785 automagically selected
|
|
|
786 """
|
|
|
787 scl = " ".join(self.cl)
|
|
|
788 err = None
|
|
|
789 if self.args.parampass != "0":
|
|
|
790 if os.path.exists(self.elog):
|
|
|
791 ste = open(self.elog, "a")
|
|
|
792 else:
|
|
|
793 ste = open(self.elog, "w")
|
|
|
794 if self.lastclredirect:
|
|
|
795 sto = open(self.lastclredirect[1], "wb") # is name of an output file
|
|
|
796 else:
|
|
|
797 if os.path.exists(self.tlog):
|
|
|
798 sto = open(self.tlog, "a")
|
|
|
799 else:
|
|
|
800 sto = open(self.tlog, "w")
|
|
|
801 sto.write(
|
|
|
802 "## Executing Toolfactory generated command line = %s\n" % scl
|
|
|
803 )
|
|
|
804 sto.flush()
|
|
|
805 subp = subprocess.run(
|
|
126
|
806 self.cl, shell=False, stdout=sto, stderr=ste
|
|
121
|
807 )
|
|
|
808 sto.close()
|
|
|
809 ste.close()
|
|
|
810 retval = subp.returncode
|
|
|
811 else: # work around special case - stdin and write to stdout
|
|
|
812 if len(self.infiles) > 0:
|
|
126
|
813 sti = open(self.infiles[0]["name"], "rb")
|
|
121
|
814 else:
|
|
|
815 sti = sys.stdin
|
|
|
816 if len(self.outfiles) > 0:
|
|
126
|
817 sto = open(self.outfiles[0]["name"], "wb")
|
|
121
|
818 else:
|
|
|
819 sto = sys.stdout
|
|
|
820 subp = subprocess.run(
|
|
126
|
821 self.cl, shell=False, stdout=sto, stdin=sti
|
|
121
|
822 )
|
|
|
823 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
|
|
|
824 retval = subp.returncode
|
|
|
825 sto.close()
|
|
|
826 sti.close()
|
|
|
827 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
|
|
|
828 os.unlink(self.tlog)
|
|
|
829 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
|
|
|
830 os.unlink(self.elog)
|
|
|
831 if retval != 0 and err: # problem
|
|
|
832 sys.stderr.write(err)
|
|
|
833 logging.debug("run done")
|
|
|
834 return retval
|
|
|
835
|
|
|
836 def shedLoad(self):
|
|
|
837 """
|
|
|
838 use bioblend to create new repository
|
|
|
839 or update existing
|
|
|
840
|
|
|
841 """
|
|
|
842 if os.path.exists(self.tlog):
|
|
|
843 sto = open(self.tlog, "a")
|
|
|
844 else:
|
|
|
845 sto = open(self.tlog, "w")
|
|
|
846
|
|
|
847 ts = toolshed.ToolShedInstance(
|
|
|
848 url=self.args.toolshed_url,
|
|
|
849 key=self.args.toolshed_api_key,
|
|
|
850 verify=False,
|
|
|
851 )
|
|
|
852 repos = ts.repositories.get_repositories()
|
|
|
853 rnames = [x.get("name", "?") for x in repos]
|
|
|
854 rids = [x.get("id", "?") for x in repos]
|
|
|
855 tfcat = "ToolFactory generated tools"
|
|
|
856 if self.tool_name not in rnames:
|
|
|
857 tscat = ts.categories.get_categories()
|
|
|
858 cnames = [x.get("name", "?").strip() for x in tscat]
|
|
|
859 cids = [x.get("id", "?") for x in tscat]
|
|
|
860 catID = None
|
|
|
861 if tfcat.strip() in cnames:
|
|
|
862 ci = cnames.index(tfcat)
|
|
|
863 catID = cids[ci]
|
|
|
864 res = ts.repositories.create_repository(
|
|
|
865 name=self.args.tool_name,
|
|
|
866 synopsis="Synopsis:%s" % self.args.tool_desc,
|
|
|
867 description=self.args.tool_desc,
|
|
|
868 type="unrestricted",
|
|
|
869 remote_repository_url=self.args.toolshed_url,
|
|
|
870 homepage_url=None,
|
|
|
871 category_ids=catID,
|
|
|
872 )
|
|
|
873 tid = res.get("id", None)
|
|
|
874 sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n")
|
|
|
875 else:
|
|
|
876 i = rnames.index(self.tool_name)
|
|
|
877 tid = rids[i]
|
|
|
878 try:
|
|
|
879 res = ts.repositories.update_repository(
|
|
|
880 id=tid, tar_ball_path=self.newtarpath, commit_message=None
|
|
|
881 )
|
|
|
882 sto.write(f"#update res id {id} ={res}\n")
|
|
|
883 except ConnectionError:
|
|
|
884 sto.write(
|
|
|
885 "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
|
|
|
886 )
|
|
|
887 sto.close()
|
|
|
888
|
|
|
889 def eph_galaxy_load(self):
|
|
|
890 """
|
|
|
891 use ephemeris to load the new tool from the local toolshed after planemo uploads it
|
|
|
892 """
|
|
|
893 if os.path.exists(self.tlog):
|
|
|
894 tout = open(self.tlog, "a")
|
|
|
895 else:
|
|
|
896 tout = open(self.tlog, "w")
|
|
|
897 cll = [
|
|
|
898 "shed-tools",
|
|
|
899 "install",
|
|
|
900 "-g",
|
|
|
901 self.args.galaxy_url,
|
|
|
902 "--latest",
|
|
|
903 "-a",
|
|
|
904 self.args.galaxy_api_key,
|
|
|
905 "--name",
|
|
|
906 self.tool_name,
|
|
|
907 "--owner",
|
|
|
908 "fubar",
|
|
|
909 "--toolshed",
|
|
|
910 self.args.toolshed_url,
|
|
|
911 "--section_label",
|
|
|
912 "ToolFactory",
|
|
|
913 ]
|
|
|
914 tout.write("running\n%s\n" % " ".join(cll))
|
|
|
915 subp = subprocess.run(
|
|
|
916 cll,
|
|
|
917 cwd=self.ourcwd,
|
|
|
918 shell=False,
|
|
|
919 stderr=tout,
|
|
|
920 stdout=tout,
|
|
|
921 )
|
|
|
922 tout.write(
|
|
|
923 "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)
|
|
|
924 )
|
|
|
925 tout.close()
|
|
|
926 return subp.returncode
|
|
|
927
|
|
|
928 def writeShedyml(self):
|
|
|
929 """for planemo"""
|
|
|
930 yuser = self.args.user_email.split("@")[0]
|
|
|
931 yfname = os.path.join(self.tooloutdir, ".shed.yml")
|
|
|
932 yamlf = open(yfname, "w")
|
|
|
933 odict = {
|
|
|
934 "name": self.tool_name,
|
|
|
935 "owner": yuser,
|
|
|
936 "type": "unrestricted",
|
|
|
937 "description": self.args.tool_desc,
|
|
|
938 "synopsis": self.args.tool_desc,
|
|
|
939 "category": "TF Generated Tools",
|
|
|
940 }
|
|
|
941 yaml.dump(odict, yamlf, allow_unicode=True)
|
|
|
942 yamlf.close()
|
|
|
943
|
|
|
944 def makeTool(self):
|
|
|
945 """write xmls and input samples into place"""
|
|
126
|
946 if self.args.parampass == 0:
|
|
|
947 self.doNoXMLparam()
|
|
|
948 else:
|
|
|
949 self.makeXML()
|
|
121
|
950 if self.args.script_path:
|
|
126
|
951 stname = os.path.join(self.tooloutdir, self.sfile)
|
|
121
|
952 if not os.path.exists(stname):
|
|
|
953 shutil.copyfile(self.sfile, stname)
|
|
|
954 xreal = "%s.xml" % self.tool_name
|
|
|
955 xout = os.path.join(self.tooloutdir, xreal)
|
|
|
956 shutil.copyfile(xreal, xout)
|
|
|
957 for p in self.infiles:
|
|
126
|
958 pth = p["name"]
|
|
|
959 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
|
|
|
960 shutil.copyfile(pth, dest)
|
|
|
961 dest = os.path.join(self.repdir, "%s_sample" % p["infilename"])
|
|
121
|
962 shutil.copyfile(pth, dest)
|
|
|
963
|
|
126
|
964 def makeToolTar(self, report_fail=False):
|
|
121
|
965 """move outputs into test-data and prepare the tarball"""
|
|
|
966 excludeme = "_planemo_test_report.html"
|
|
|
967
|
|
|
968 def exclude_function(tarinfo):
|
|
|
969 filename = tarinfo.name
|
|
|
970 return None if filename.endswith(excludeme) else tarinfo
|
|
|
971
|
|
|
972 if os.path.exists(self.tlog):
|
|
|
973 tout = open(self.tlog, "a")
|
|
|
974 else:
|
|
|
975 tout = open(self.tlog, "w")
|
|
|
976 for p in self.outfiles:
|
|
126
|
977 oname = p["name"]
|
|
121
|
978 tdest = os.path.join(self.testdir, "%s_sample" % oname)
|
|
126
|
979 src = os.path.join(self.testdir, oname)
|
|
121
|
980 if not os.path.isfile(tdest):
|
|
|
981 if os.path.isfile(src):
|
|
|
982 shutil.copyfile(src, tdest)
|
|
|
983 dest = os.path.join(self.repdir, "%s.sample" % (oname))
|
|
|
984 shutil.copyfile(src, dest)
|
|
|
985 else:
|
|
126
|
986 if report_fail:
|
|
|
987 tout.write(
|
|
|
988 "###Tool may have failed - output file %s not found in testdir after planemo run %s."
|
|
|
989 % (tdest, self.testdir)
|
|
|
990 )
|
|
121
|
991 tf = tarfile.open(self.newtarpath, "w:gz")
|
|
|
992 tf.add(
|
|
|
993 name=self.tooloutdir,
|
|
|
994 arcname=self.tool_name,
|
|
|
995 filter=exclude_function,
|
|
|
996 )
|
|
|
997 tf.close()
|
|
|
998 shutil.copyfile(self.newtarpath, self.args.new_tool)
|
|
|
999
|
|
|
1000 def moveRunOutputs(self):
|
|
|
1001 """need to move planemo or run outputs into toolfactory collection"""
|
|
|
1002 with os.scandir(self.tooloutdir) as outs:
|
|
|
1003 for entry in outs:
|
|
|
1004 if not entry.is_file():
|
|
|
1005 continue
|
|
|
1006 if "." in entry.name:
|
|
126
|
1007 _, ext = os.path.splitext(entry.name)
|
|
|
1008 if ext in [".tgz", ".json"]:
|
|
|
1009 continue
|
|
|
1010 if ext in [".yml", ".xml", ".yaml"]:
|
|
|
1011 newname = f"{entry.name.replace('.','_')}.txt"
|
|
|
1012 else:
|
|
|
1013 newname = entry.name
|
|
121
|
1014 else:
|
|
126
|
1015 newname = f"{entry.name}.txt"
|
|
|
1016 dest = os.path.join(self.repdir, newname)
|
|
121
|
1017 src = os.path.join(self.tooloutdir, entry.name)
|
|
|
1018 shutil.copyfile(src, dest)
|
|
126
|
1019 if self.args.include_tests:
|
|
|
1020 with os.scandir(self.testdir) as outs:
|
|
|
1021 for entry in outs:
|
|
|
1022 if (not entry.is_file()) or entry.name.endswith(
|
|
|
1023 "_planemo_test_report.html"
|
|
|
1024 ):
|
|
|
1025 continue
|
|
|
1026 if "." in entry.name:
|
|
|
1027 _, ext = os.path.splitext(entry.name)
|
|
|
1028 if ext in [".tgz", ".json"]:
|
|
|
1029 continue
|
|
|
1030 if ext in [".yml", ".xml", ".yaml"]:
|
|
|
1031 newname = f"{entry.name.replace('.','_')}.txt"
|
|
|
1032 else:
|
|
|
1033 newname = entry.name
|
|
|
1034 else:
|
|
|
1035 newname = f"{entry.name}.txt"
|
|
|
1036 dest = os.path.join(self.repdir, newname)
|
|
|
1037 src = os.path.join(self.testdir, entry.name)
|
|
|
1038 shutil.copyfile(src, dest)
|
|
121
|
1039
|
|
126
|
1040 def planemo_test_once(self):
|
|
121
|
1041 """planemo is a requirement so is available for testing but needs a
|
|
|
1042 different call if in the biocontainer - see above
|
|
|
1043 and for generating test outputs if command or test overrides are
|
|
|
1044 supplied test outputs are sent to repdir for display
|
|
|
1045 """
|
|
137
|
1046 penv = os.environ
|
|
138
|
1047 pconfig = os.path.join(self.args.tool_dir, '.planemo.yml')
|
|
137
|
1048 penv["PLANEMO_GLOBAL_CONFIG_PATH"] = pconfig
|
|
138
|
1049 self.set_planemo_galaxy_root(self.args.galaxy_root, config_path=pconfig)
|
|
121
|
1050 xreal = "%s.xml" % self.tool_name
|
|
|
1051 tool_test_path = os.path.join(
|
|
|
1052 self.repdir, f"{self.tool_name}_planemo_test_report.html"
|
|
|
1053 )
|
|
|
1054 if os.path.exists(self.tlog):
|
|
|
1055 tout = open(self.tlog, "a")
|
|
|
1056 else:
|
|
|
1057 tout = open(self.tlog, "w")
|
|
126
|
1058 cll = [
|
|
|
1059 "planemo",
|
|
|
1060 "test",
|
|
139
|
1061 "--galaxy_python_version",
|
|
|
1062 self.args.python_version,
|
|
126
|
1063 "--conda_auto_init",
|
|
|
1064 "--test_data",
|
|
|
1065 os.path.abspath(self.testdir),
|
|
|
1066 "--test_output",
|
|
|
1067 os.path.abspath(tool_test_path),
|
|
|
1068 "--galaxy_root",
|
|
|
1069 self.args.galaxy_root,
|
|
|
1070 "--update_test_data",
|
|
|
1071 os.path.abspath(xreal),
|
|
|
1072 ]
|
|
|
1073 p = subprocess.run(
|
|
|
1074 cll,
|
|
|
1075 shell=False,
|
|
138
|
1076 env=penv,
|
|
126
|
1077 cwd=self.tooloutdir,
|
|
|
1078 stderr=tout,
|
|
|
1079 stdout=tout,
|
|
|
1080 )
|
|
121
|
1081 tout.close()
|
|
|
1082 return p.returncode
|
|
|
1083
|
|
137
|
1084 def set_planemo_galaxy_root(self, galaxyroot='/galaxy-central', config_path=".planemo.yml"):
|
|
|
1085 # bug in planemo - bogus '--dev-wheels' passed to run_tests.sh as at april 2021 - need a fiddled copy so it is ignored until fixed
|
|
138
|
1086 CONFIG_TEMPLATE = """## Planemo Global Configuration File.
|
|
137
|
1087 ## Everything in this file is completely optional - these values can all be
|
|
|
1088 ## configured via command line options for the corresponding commands.
|
|
|
1089
|
|
|
1090 ## Specify a default galaxy_root for test and server commands here.
|
|
|
1091 galaxy_root: %s
|
|
|
1092 ## Username used with toolshed(s).
|
|
|
1093 #shed_username: "<TODO>"
|
|
|
1094 sheds:
|
|
|
1095 # For each tool shed you wish to target, uncomment key or both email and
|
|
|
1096 # password.
|
|
|
1097 toolshed:
|
|
|
1098 #key: "<TODO>"
|
|
|
1099 #email: "<TODO>"
|
|
|
1100 #password: "<TODO>"
|
|
|
1101 testtoolshed:
|
|
|
1102 #key: "<TODO>"
|
|
|
1103 #email: "<TODO>"
|
|
|
1104 #password: "<TODO>"
|
|
|
1105 local:
|
|
|
1106 #key: "<TODO>"
|
|
|
1107 #email: "<TODO>"
|
|
|
1108 #password: "<TODO>"
|
|
|
1109 """
|
|
|
1110 if not os.path.exists(config_path):
|
|
|
1111 with open(config_path, "w") as f:
|
|
|
1112 f.write(CONFIG_TEMPLATE % galaxyroot)
|
|
|
1113
|
|
121
|
1114
|
|
|
1115 def main():
|
|
|
1116 """
|
|
|
1117 This is a Galaxy wrapper.
|
|
|
1118 It expects to be called by a special purpose tool.xml
|
|
|
1119
|
|
|
1120 """
|
|
|
1121 parser = argparse.ArgumentParser()
|
|
|
1122 a = parser.add_argument
|
|
|
1123 a("--script_path", default=None)
|
|
|
1124 a("--history_test", default=None)
|
|
129
|
1125 a("--cl_suffix", default=None)
|
|
121
|
1126 a("--sysexe", default=None)
|
|
|
1127 a("--packages", default=None)
|
|
|
1128 a("--tool_name", default="newtool")
|
|
|
1129 a("--tool_dir", default=None)
|
|
|
1130 a("--input_files", default=[], action="append")
|
|
|
1131 a("--output_files", default=[], action="append")
|
|
|
1132 a("--user_email", default="Unknown")
|
|
|
1133 a("--bad_user", default=None)
|
|
|
1134 a("--make_Tool", default="runonly")
|
|
|
1135 a("--help_text", default=None)
|
|
|
1136 a("--tool_desc", default=None)
|
|
|
1137 a("--tool_version", default=None)
|
|
|
1138 a("--citations", default=None)
|
|
|
1139 a("--command_override", default=None)
|
|
|
1140 a("--test_override", default=None)
|
|
|
1141 a("--additional_parameters", action="append", default=[])
|
|
126
|
1142 a("--selecttext_parameters", action="append", default=[])
|
|
121
|
1143 a("--edit_additional_parameters", action="store_true", default=False)
|
|
|
1144 a("--parampass", default="positional")
|
|
|
1145 a("--tfout", default="./tfout")
|
|
|
1146 a("--new_tool", default="new_tool")
|
|
|
1147 a("--galaxy_url", default="http://localhost:8080")
|
|
|
1148 a("--toolshed_url", default="http://localhost:9009")
|
|
|
1149 # make sure this is identical to tool_sheds_conf.xml
|
|
|
1150 # localhost != 127.0.0.1 so validation fails
|
|
|
1151 a("--toolshed_api_key", default="fakekey")
|
|
|
1152 a("--galaxy_api_key", default="fakekey")
|
|
|
1153 a("--galaxy_root", default="/galaxy-central")
|
|
|
1154 a("--galaxy_venv", default="/galaxy_venv")
|
|
126
|
1155 a("--collection", action="append", default=[])
|
|
|
1156 a("--include_tests", default=False, action="store_true")
|
|
139
|
1157 a("--python_version", default="3.9")
|
|
121
|
1158 args = parser.parse_args()
|
|
|
1159 assert not args.bad_user, (
|
|
|
1160 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
|
|
|
1161 admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
|
|
|
1162 % (args.bad_user, args.bad_user)
|
|
|
1163 )
|
|
|
1164 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
|
|
|
1165 assert (
|
|
|
1166 args.sysexe or args.packages
|
|
|
1167 ), "## Tool Factory wrapper expects an interpreter \
|
|
|
1168 or an executable package in --sysexe or --packages"
|
|
|
1169 r = ScriptRunner(args)
|
|
|
1170 r.writeShedyml()
|
|
|
1171 r.makeTool()
|
|
|
1172 if args.make_Tool == "generate":
|
|
126
|
1173 r.run()
|
|
121
|
1174 r.moveRunOutputs()
|
|
|
1175 r.makeToolTar()
|
|
|
1176 else:
|
|
126
|
1177 r.planemo_test_once()
|
|
121
|
1178 r.moveRunOutputs()
|
|
126
|
1179 r.makeToolTar(report_fail=True)
|
|
121
|
1180 if args.make_Tool == "gentestinstall":
|
|
|
1181 r.shedLoad()
|
|
|
1182 r.eph_galaxy_load()
|
|
|
1183
|
|
|
1184
|
|
|
1185 if __name__ == "__main__":
|
|
|
1186 main()
|
