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1
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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 # April 2021: Refactored into two tools - generate and test/install
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12 # as part of GTN tutorial development and biocontainer adoption
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13 # The tester runs planemo on a non-tested archive, creates the test outputs
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14 # and returns a new proper tool with test.
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15 # The tester was generated from the ToolFactory_tester.py script
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16
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17
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18 import argparse
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19 import copy
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20 import json
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21 import logging
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22 import os
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23 import re
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24 import shlex
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25 import shutil
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26 import subprocess
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27 import sys
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28 import tarfile
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29 import tempfile
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30 import time
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31
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32 from bioblend import ConnectionError
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33 from bioblend import galaxy
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34 from bioblend import toolshed
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35
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36 import galaxyxml.tool as gxt
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37 import galaxyxml.tool.parameters as gxtp
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38
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39 import lxml.etree as ET
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40
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41 import yaml
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42
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43 myversion = "V2.3 April 2021"
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44 verbose = True
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45 debug = True
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46 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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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 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
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57
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58 def cheetah_escape(text):
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59 """Produce entities within text."""
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60 return "".join([cheetah_escape_table.get(c, c) for c in text])
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61
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62 def parse_citations(citations_text):
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63 """"""
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64 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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65 citation_tuples = []
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66 for citation in citations:
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67 if citation.startswith("doi"):
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68 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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69 else:
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70 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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71 return citation_tuples
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72
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73 class ToolTester():
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74 # requires highly insecure docker settings - like write to tool_conf.xml and to tools !
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75 # if in a container possibly not so courageous.
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76 # Fine on your own laptop but security red flag for most production instances
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77 # uncompress passed tar, run planemo and rebuild a new tarball with tests
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78
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79 def __init__(self, report_dir, in_tool_archive, new_tool_archive, include_tests, galaxy_root):
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80 self.new_tool_archive = new_tool_archive
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81 self.include_tests = include_tests
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82 self.galaxy_root = galaxy_root
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83 self.repdir = report_dir
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84 assert in_tool_archive and tarfile.is_tarfile(in_tool_archive)
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85 # this is not going to go well with arbitrary names. TODO introspect tool xml!
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86 tff = tarfile.open(in_tool_archive, "r:*")
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87 flist = tff.getnames()
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88 ourdir = os.path.commonpath(flist) # eg pyrevpos
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89 self.tool_name = ourdir
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90 ourxmls = [x for x in flist if x.lower().endswith('.xml') and os.path.split(x)[0] == ourdir]
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91 # planemo_test/planemo_test.xml
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92 assert len(ourxmls) > 0
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93 self.ourxmls = ourxmls # [os.path.join(tool_path,x) for x in ourxmls]
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94 res = tff.extractall()
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95 tff.close()
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96 self.update_tests(ourdir)
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97 self.tooloutdir = ourdir
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98 self.testdir = os.path.join(self.tooloutdir, "test-data")
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99 if not os.path.exists(self.tooloutdir):
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100 os.mkdir(self.tooloutdir)
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101 if not os.path.exists(self.testdir):
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102 os.mkdir(self.testdir)
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103 if not os.path.exists(self.repdir):
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104 os.mkdir(self.repdir)
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105 if not os.path.exists(self.tooloutdir):
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106 os.mkdir(self.tooloutdir)
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107 if not os.path.exists(self.testdir):
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108 os.mkdir(self.testdir)
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109 if not os.path.exists(self.repdir):
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110 os.mkdir(self.repdir)
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111 self.moveRunOutputs()
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112 self.makeToolTar()
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113
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114 def call_planemo(self,xmlpath,ourdir):
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115 penv = os.environ
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116 penv['HOME'] = os.path.join(self.galaxy_root,'planemo')
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117 #penv["GALAXY_VIRTUAL_ENV"] = os.path.join(penv['HOME'],'.planemo','gx_venv_3.9')
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118 penv["PIP_CACHE_DIR"] = os.path.join(self.galaxy_root,'pipcache')
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119 toolfile = os.path.split(xmlpath)[1]
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120 tool_name = self.tool_name
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121 tool_test_output = os.path.join(self.repdir, f"{tool_name}_planemo_test_report.html")
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122 cll = ["planemo",
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123 "test",
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124 #"--job_config_file",
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125 # os.path.join(self.galaxy_root,"config","job_conf.xml"),
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126 #"--galaxy_python_version",
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127 #"3.9",
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128 "--test_output",
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129 os.path.abspath(tool_test_output),
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130 "--galaxy_root",
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131 self.galaxy_root,
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132 "--update_test_data",
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133 os.path.abspath(xmlpath),
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134 ]
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135 print("Call planemo cl =", cll)
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136 p = subprocess.run(
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137 cll,
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138 capture_output=True,
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139 encoding='utf8',
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140 env = penv,
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141 shell=False,
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142 )
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143 return p
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144
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145 def makeToolTar(self):
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146 """move outputs into test-data and prepare the tarball"""
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147 excludeme = "_planemo_test_report.html"
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148
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149 def exclude_function(tarinfo):
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150 filename = tarinfo.name
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151 return None if filename.endswith(excludeme) else tarinfo
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152
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153 newtar = 'new_%s_toolshed.gz' % self.tool_name
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154 ttf = tarfile.open(newtar, "w:gz")
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155 ttf.add(name=self.tooloutdir,
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156 arcname=self.tool_name,
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157 filter=exclude_function)
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158 ttf.close()
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159 shutil.copyfile(newtar, self.new_tool_archive)
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160
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161 def move_One(self,scandir):
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162 with os.scandir('.') as outs:
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163 for entry in outs:
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164 newname = entry.name
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165 if not entry.is_file() or entry.name.endswith('_sample'):
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166 continue
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167 if not (entry.name.endswith('.html') or entry.name.endswith('.gz') or entry.name.endswith(".tgz")):
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168 fname, ext = os.path.splitext(entry.name)
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169 if len(ext) > 1:
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170 newname = f"{fname}_{ext[1:]}.txt"
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171 else:
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172 newname = f"{fname}.txt"
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173 dest = os.path.join(self.repdir, newname)
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174 src = entry.name
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175 shutil.copyfile(src, dest)
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176
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177 def moveRunOutputs(self):
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178 """need to move planemo or run outputs into toolfactory collection"""
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179 self.move_One(self.tooloutdir)
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180 self.move_One('.')
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181 if self.include_tests:
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182 self.move_One(self.testdir)
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183
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184 def update_tests(self,ourdir):
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185 for xmlf in self.ourxmls:
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186 capture = self.call_planemo(xmlf,ourdir)
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187 logf = open(f"%s_run_report" % (self.tool_name),'w')
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188 logf.write("stdout:")
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189 logf.write(capture.stdout)
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190 logf.write("stderr:")
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191 logf.write(capture.stderr)
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192
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193
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194 class ToolConfUpdater():
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195 # update config/tool_conf.xml with a new tool unpacked in /tools
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196 # requires highly insecure docker settings - like write to tool_conf.xml and to tools !
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197 # if in a container possibly not so courageous.
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198 # Fine on your own laptop but security red flag for most production instances
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199
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200 def __init__(self, args, tool_conf_path, new_tool_archive_path, new_tool_name, tool_dir):
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201 self.args = args
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202 self.tool_conf_path = tool_conf_path
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203 self.our_name = 'ToolFactory'
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204 tff = tarfile.open(new_tool_archive_path, "r:*")
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205 flist = tff.getnames()
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206 ourdir = os.path.commonpath(flist) # eg pyrevpos
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207 self.tool_id = ourdir # they are the same for TF tools
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208 ourxml = [x for x in flist if x.lower().endswith('.xml')]
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209 res = tff.extractall(tool_dir)
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210 tff.close()
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211 self.update_toolconf(ourdir,ourxml)
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212
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213 def install_deps(self):
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214 gi = galaxy.GalaxyInstance(url=self.args.galaxy_url, key=self.args.galaxy_api_key)
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215 x = gi.tools.install_dependencies(self.tool_id)
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216 print(f"Called install_dependencies on {self.tool_id} - got {x}")
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217
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218 def update_toolconf(self,ourdir,ourxml): # path is relative to tools
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219 updated = False
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220 tree = ET.parse(self.tool_conf_path)
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221 root = tree.getroot()
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222 hasTF = False
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223 TFsection = None
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224 for e in root.findall('section'):
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225 if e.attrib['name'] == self.our_name:
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226 hasTF = True
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227 TFsection = e
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228 if not hasTF:
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229 TFsection = ET.Element('section')
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230 root.insert(0,TFsection) # at the top!
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231 our_tools = TFsection.findall('tool')
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232 conf_tools = [x.attrib['file'] for x in our_tools]
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233 for xml in ourxml: # may be > 1
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234 if not xml in conf_tools: # new
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235 updated = True
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236 ET.SubElement(TFsection, 'tool', {'file':xml})
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237 ET.indent(tree)
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238 tree.write(self.tool_conf_path, pretty_print=True)
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239 if False and self.args.packages and self.args.packages > '':
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240 self.install_deps()
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241
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242 class ScriptRunner:
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243 """Wrapper for an arbitrary script
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244 uses galaxyxml
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245
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246 """
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247
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248 def __init__(self, args=None): # noqa
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249 """
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250 prepare command line cl for running the tool here
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251 and prepare elements needed for galaxyxml tool generation
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252 """
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253 self.ourcwd = os.getcwd()
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254 self.collections = []
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255 if len(args.collection) > 0:
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256 try:
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257 self.collections = [
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258 json.loads(x) for x in args.collection if len(x.strip()) > 1
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259 ]
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260 except Exception:
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261 print(
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262 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
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263 )
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264 try:
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265 self.infiles = [
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266 json.loads(x) for x in args.input_files if len(x.strip()) > 1
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267 ]
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268 except Exception:
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269 print(
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270 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
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271 )
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272 try:
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273 self.outfiles = [
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274 json.loads(x) for x in args.output_files if len(x.strip()) > 1
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275 ]
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276 except Exception:
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277 print(
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278 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
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279 )
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280 try:
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281 self.addpar = [
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282 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
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283 ]
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284 except Exception:
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285 print(
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286 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
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287 )
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288 try:
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289 self.selpar = [
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290 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
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291 ]
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292 except Exception:
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293 print(
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294 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
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295 )
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296 self.args = args
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297 self.cleanuppar()
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298 self.lastclredirect = None
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299 self.lastxclredirect = None
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300 self.cl = []
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301 self.xmlcl = []
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302 self.is_positional = self.args.parampass == "positional"
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303 if self.args.sysexe:
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304 if ' ' in self.args.sysexe:
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305 self.executeme = self.args.sysexe.split(' ')
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306 else:
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307 self.executeme = [self.args.sysexe, ]
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308 else:
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309 if self.args.packages:
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310 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
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311 else:
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312 self.executeme = None
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313 aCL = self.cl.append
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314 aXCL = self.xmlcl.append
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315 assert args.parampass in [
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316 "0",
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317 "argparse",
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318 "positional",
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319 ], 'args.parampass must be "0","positional" or "argparse"'
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320 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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321 self.tool_id = self.tool_name
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322 self.newtool = gxt.Tool(
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323 self.tool_name,
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324 self.tool_id,
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325 self.args.tool_version,
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326 self.args.tool_desc,
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327 FAKEEXE,
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328 )
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329 self.newtarpath = "%s_toolshed.gz" % self.tool_name
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330 self.tooloutdir = "./tfout"
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331 self.repdir = "./TF_run_report"
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332 self.testdir = os.path.join(self.tooloutdir, "test-data")
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333 if not os.path.exists(self.tooloutdir):
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334 os.mkdir(self.tooloutdir)
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335 if not os.path.exists(self.testdir):
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336 os.mkdir(self.testdir)
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337 if not os.path.exists(self.repdir):
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338 os.mkdir(self.repdir)
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339 self.tinputs = gxtp.Inputs()
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340 self.toutputs = gxtp.Outputs()
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341 self.testparam = []
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342 if self.args.script_path:
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343 self.prepScript()
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344 if self.args.command_override:
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345 scos = open(self.args.command_override, "r").readlines()
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346 self.command_override = [x.rstrip() for x in scos]
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347 else:
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348 self.command_override = None
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349 if self.args.test_override:
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350 stos = open(self.args.test_override, "r").readlines()
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351 self.test_override = [x.rstrip() for x in stos]
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352 else:
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353 self.test_override = None
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354 if self.args.script_path:
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355 for ex in self.executeme:
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356 aCL(ex)
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357 aXCL(ex)
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358 aCL(self.sfile)
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359 aXCL("$runme")
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360 else:
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361 for ex in self.executeme:
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362 aCL(ex)
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363 aXCL(ex)
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364
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365 if self.args.parampass == "0":
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366 self.clsimple()
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367 else:
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368 if self.args.parampass == "positional":
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369 self.prepclpos()
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370 self.clpositional()
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371 else:
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372 self.prepargp()
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373 self.clargparse()
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374
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375 def clsimple(self):
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376 """no parameters or repeats - uses < and > for i/o"""
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377 aCL = self.cl.append
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378 aXCL = self.xmlcl.append
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379 if len(self.infiles) > 0:
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380 aCL("<")
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381 aCL(self.infiles[0]["infilename"])
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382 aXCL("<")
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383 aXCL("$%s" % self.infiles[0]["infilename"])
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384 if len(self.outfiles) > 0:
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385 aCL(">")
|
|
|
386 aCL(self.outfiles[0]["name"])
|
|
|
387 aXCL(">")
|
|
|
388 aXCL("$%s" % self.outfiles[0]["name"])
|
|
|
389 if self.args.cl_user_suffix: # DIY CL end
|
|
|
390 clp = shlex.split(self.args.cl_user_suffix)
|
|
|
391 for c in clp:
|
|
|
392 aCL(c)
|
|
|
393 aXCL(c)
|
|
|
394
|
|
|
395 def prepargp(self):
|
|
|
396 clsuffix = []
|
|
|
397 xclsuffix = []
|
|
|
398 for i, p in enumerate(self.infiles):
|
|
|
399 nam = p["infilename"]
|
|
|
400 if p["origCL"].strip().upper() == "STDIN":
|
|
|
401 appendme = [
|
|
|
402 nam,
|
|
|
403 nam,
|
|
|
404 "< %s" % nam,
|
|
|
405 ]
|
|
|
406 xappendme = [
|
|
|
407 nam,
|
|
|
408 nam,
|
|
|
409 "< $%s" % nam,
|
|
|
410 ]
|
|
|
411 else:
|
|
|
412 rep = p["repeat"] == "1"
|
|
|
413 over = ""
|
|
|
414 if rep:
|
|
|
415 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
|
|
|
416 appendme = [p["CL"], p["CL"], ""]
|
|
|
417 xappendme = [p["CL"], "$%s" % p["CL"], over]
|
|
|
418 clsuffix.append(appendme)
|
|
|
419 xclsuffix.append(xappendme)
|
|
|
420 for i, p in enumerate(self.outfiles):
|
|
|
421 if p["origCL"].strip().upper() == "STDOUT":
|
|
|
422 self.lastclredirect = [">", p["name"]]
|
|
|
423 self.lastxclredirect = [">", "$%s" % p["name"]]
|
|
|
424 else:
|
|
|
425 clsuffix.append([p["name"], p["name"], ""])
|
|
|
426 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
|
|
|
427 for p in self.addpar:
|
|
|
428 nam = p["name"]
|
|
|
429 rep = p["repeat"] == "1"
|
|
|
430 if rep:
|
|
|
431 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
|
|
|
432 else:
|
|
|
433 over = p["override"]
|
|
|
434 clsuffix.append([p["CL"], nam, over])
|
|
|
435 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
|
|
|
436 for p in self.selpar:
|
|
|
437 clsuffix.append([p["CL"], p["name"], p["override"]])
|
|
|
438 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
|
|
|
439 self.xclsuffix = xclsuffix
|
|
|
440 self.clsuffix = clsuffix
|
|
|
441
|
|
|
442 def prepclpos(self):
|
|
|
443 clsuffix = []
|
|
|
444 xclsuffix = []
|
|
|
445 for i, p in enumerate(self.infiles):
|
|
|
446 if p["origCL"].strip().upper() == "STDIN":
|
|
|
447 appendme = [
|
|
|
448 "999",
|
|
|
449 p["infilename"],
|
|
|
450 "< $%s" % p["infilename"],
|
|
|
451 ]
|
|
|
452 xappendme = [
|
|
|
453 "999",
|
|
|
454 p["infilename"],
|
|
|
455 "< $%s" % p["infilename"],
|
|
|
456 ]
|
|
|
457 else:
|
|
|
458 appendme = [p["CL"], p["infilename"], ""]
|
|
|
459 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
|
|
|
460 clsuffix.append(appendme)
|
|
|
461 xclsuffix.append(xappendme)
|
|
|
462 for i, p in enumerate(self.outfiles):
|
|
|
463 if p["origCL"].strip().upper() == "STDOUT":
|
|
|
464 self.lastclredirect = [">", p["name"]]
|
|
|
465 self.lastxclredirect = [">", "$%s" % p["name"]]
|
|
|
466 else:
|
|
|
467 clsuffix.append([p["CL"], p["name"], ""])
|
|
|
468 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
|
|
|
469 for p in self.addpar:
|
|
|
470 nam = p["name"]
|
|
|
471 rep = p["repeat"] == "1" # repeats make NO sense
|
|
|
472 if rep:
|
|
|
473 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
|
|
|
474 over = p["override"]
|
|
|
475 clsuffix.append([p["CL"], nam, over])
|
|
|
476 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
|
|
|
477 for p in self.selpar:
|
|
|
478 clsuffix.append([p["CL"], p["name"], p["override"]])
|
|
|
479 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
|
|
|
480 clsuffix.sort()
|
|
|
481 xclsuffix.sort()
|
|
|
482 self.xclsuffix = xclsuffix
|
|
|
483 self.clsuffix = clsuffix
|
|
|
484
|
|
|
485 def prepScript(self):
|
|
|
486 rx = open(self.args.script_path, "r").readlines()
|
|
|
487 rx = [x.rstrip() for x in rx]
|
|
|
488 rxcheck = [x.strip() for x in rx if x.strip() > ""]
|
|
|
489 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
|
|
|
490 self.script = "\n".join(rx)
|
|
|
491 fhandle, self.sfile = tempfile.mkstemp(
|
|
|
492 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
|
|
|
493 )
|
|
|
494 tscript = open(self.sfile, "w")
|
|
|
495 tscript.write(self.script)
|
|
|
496 tscript.close()
|
|
|
497 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
|
|
|
498 rx.insert(0,'#raw')
|
|
|
499 rx.append('#end raw')
|
|
|
500 self.escapedScript = rx
|
|
|
501 art = "%s.%s" % (self.tool_name, self.executeme[0])
|
|
|
502 artifact = open(art, "wb")
|
|
|
503 artifact.write(bytes(self.script, "utf8"))
|
|
|
504 artifact.close()
|
|
|
505
|
|
|
506 def cleanuppar(self):
|
|
|
507 """ positional parameters are complicated by their numeric ordinal"""
|
|
|
508 if self.args.parampass == "positional":
|
|
|
509 for i, p in enumerate(self.infiles):
|
|
|
510 assert (
|
|
|
511 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
|
|
|
512 ), "Positional parameters must be ordinal integers - got %s for %s" % (
|
|
|
513 p["CL"],
|
|
|
514 p["label"],
|
|
|
515 )
|
|
|
516 for i, p in enumerate(self.outfiles):
|
|
|
517 assert (
|
|
|
518 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
|
|
|
519 ), "Positional parameters must be ordinal integers - got %s for %s" % (
|
|
|
520 p["CL"],
|
|
|
521 p["name"],
|
|
|
522 )
|
|
|
523 for i, p in enumerate(self.addpar):
|
|
|
524 assert p[
|
|
|
525 "CL"
|
|
|
526 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
|
|
|
527 p["CL"],
|
|
|
528 p["name"],
|
|
|
529 )
|
|
|
530 for i, p in enumerate(self.infiles):
|
|
|
531 infp = copy.copy(p)
|
|
|
532 infp["origCL"] = infp["CL"]
|
|
|
533 if self.args.parampass in ["positional", "0"]:
|
|
|
534 infp["infilename"] = infp["label"].replace(" ", "_")
|
|
|
535 else:
|
|
|
536 infp["infilename"] = infp["CL"]
|
|
|
537 self.infiles[i] = infp
|
|
|
538 for i, p in enumerate(self.outfiles):
|
|
|
539 p["origCL"] = p["CL"] # keep copy
|
|
|
540 self.outfiles[i] = p
|
|
|
541 for i, p in enumerate(self.addpar):
|
|
|
542 p["origCL"] = p["CL"]
|
|
|
543 self.addpar[i] = p
|
|
|
544
|
|
|
545 def clpositional(self):
|
|
|
546 # inputs in order then params
|
|
|
547 aCL = self.cl.append
|
|
|
548 for (k, v, koverride) in self.clsuffix:
|
|
|
549 if " " in v:
|
|
|
550 aCL("%s" % v)
|
|
|
551 else:
|
|
|
552 aCL(v)
|
|
|
553 aXCL = self.xmlcl.append
|
|
|
554 for (k, v, koverride) in self.xclsuffix:
|
|
|
555 aXCL(v)
|
|
|
556 if self.lastxclredirect:
|
|
|
557 aXCL(self.lastxclredirect[0])
|
|
|
558 aXCL(self.lastxclredirect[1])
|
|
|
559 if self.args.cl_user_suffix: # DIY CL end
|
|
|
560 clp = shlex.split(self.args.cl_user_suffix)
|
|
|
561 for c in clp:
|
|
|
562 aCL(c)
|
|
|
563 aXCL(c)
|
|
|
564
|
|
|
565
|
|
|
566 def clargparse(self):
|
|
|
567 """argparse style"""
|
|
|
568 aCL = self.cl.append
|
|
|
569 aXCL = self.xmlcl.append
|
|
|
570 # inputs then params in argparse named form
|
|
|
571
|
|
|
572 for (k, v, koverride) in self.xclsuffix:
|
|
|
573 if koverride > "":
|
|
|
574 k = koverride
|
|
|
575 aXCL(k)
|
|
|
576 else:
|
|
|
577 if len(k.strip()) == 1:
|
|
|
578 k = "-%s" % k
|
|
|
579 else:
|
|
|
580 k = "--%s" % k
|
|
|
581 aXCL(k)
|
|
|
582 aXCL(v)
|
|
|
583 for (k, v, koverride) in self.clsuffix:
|
|
|
584 if koverride > "":
|
|
|
585 k = koverride
|
|
|
586 elif len(k.strip()) == 1:
|
|
|
587 k = "-%s" % k
|
|
|
588 else:
|
|
|
589 k = "--%s" % k
|
|
|
590 aCL(k)
|
|
|
591 aCL(v)
|
|
|
592 if self.lastxclredirect:
|
|
|
593 aXCL(self.lastxclredirect[0])
|
|
|
594 aXCL(self.lastxclredirect[1])
|
|
|
595 if self.args.cl_user_suffix: # DIY CL end
|
|
|
596 clp = shlex.split(self.args.cl_user_suffix)
|
|
|
597 for c in clp:
|
|
|
598 aCL(c)
|
|
|
599 aXCL(c)
|
|
|
600
|
|
|
601 def getNdash(self, newname):
|
|
|
602 if self.is_positional:
|
|
|
603 ndash = 0
|
|
|
604 else:
|
|
|
605 ndash = 2
|
|
|
606 if len(newname) < 2:
|
|
|
607 ndash = 1
|
|
|
608 return ndash
|
|
|
609
|
|
|
610 def doXMLparam(self): # noqa
|
|
|
611 """Add all needed elements to tool"""
|
|
|
612 for p in self.outfiles:
|
|
|
613 newname = p["name"]
|
|
|
614 newfmt = p["format"]
|
|
|
615 newcl = p["CL"]
|
|
|
616 test = p["test"]
|
|
|
617 oldcl = p["origCL"]
|
|
|
618 test = test.strip()
|
|
|
619 ndash = self.getNdash(newcl)
|
|
|
620 aparm = gxtp.OutputData(
|
|
|
621 name=newname, format=newfmt, num_dashes=ndash, label=newname
|
|
|
622 )
|
|
|
623 aparm.positional = self.is_positional
|
|
|
624 if self.is_positional:
|
|
|
625 if oldcl.upper() == "STDOUT":
|
|
|
626 aparm.positional = 9999999
|
|
|
627 aparm.command_line_override = "> $%s" % newname
|
|
|
628 else:
|
|
|
629 aparm.positional = int(oldcl)
|
|
|
630 aparm.command_line_override = "$%s" % newname
|
|
|
631 self.toutputs.append(aparm)
|
|
|
632 ld = None
|
|
|
633 if test.strip() > "":
|
|
|
634 if test.startswith("diff"):
|
|
|
635 c = "diff"
|
|
|
636 ld = 0
|
|
|
637 if test.split(":")[1].isdigit:
|
|
|
638 ld = int(test.split(":")[1])
|
|
|
639 tp = gxtp.TestOutput(
|
|
|
640 name=newname,
|
|
|
641 value="%s_sample" % newname,
|
|
|
642 compare=c,
|
|
|
643 lines_diff=ld,
|
|
|
644 )
|
|
|
645 elif test.startswith("sim_size"):
|
|
|
646 c = "sim_size"
|
|
|
647 tn = test.split(":")[1].strip()
|
|
|
648 if tn > "":
|
|
|
649 if "." in tn:
|
|
|
650 delta = None
|
|
|
651 delta_frac = min(1.0, float(tn))
|
|
|
652 else:
|
|
|
653 delta = int(tn)
|
|
|
654 delta_frac = None
|
|
|
655 tp = gxtp.TestOutput(
|
|
|
656 name=newname,
|
|
|
657 value="%s_sample" % newname,
|
|
|
658 compare=c,
|
|
|
659 delta=delta,
|
|
|
660 delta_frac=delta_frac,
|
|
|
661 )
|
|
|
662 else:
|
|
|
663 c = test
|
|
|
664 tp = gxtp.TestOutput(
|
|
|
665 name=newname,
|
|
|
666 value="%s_sample" % newname,
|
|
|
667 compare=c,
|
|
|
668 )
|
|
|
669 self.testparam.append(tp)
|
|
|
670 for p in self.infiles:
|
|
|
671 newname = p["infilename"]
|
|
|
672 newfmt = p["format"]
|
|
|
673 ndash = self.getNdash(newname)
|
|
|
674 reps = p.get("repeat", "0") == "1"
|
|
|
675 if not len(p["label"]) > 0:
|
|
|
676 alab = p["CL"]
|
|
|
677 else:
|
|
|
678 alab = p["label"]
|
|
|
679 aninput = gxtp.DataParam(
|
|
|
680 newname,
|
|
|
681 optional=False,
|
|
|
682 label=alab,
|
|
|
683 help=p["help"],
|
|
|
684 format=newfmt,
|
|
|
685 multiple=False,
|
|
|
686 num_dashes=ndash,
|
|
|
687 )
|
|
|
688 aninput.positional = self.is_positional
|
|
|
689 if self.is_positional:
|
|
|
690 if p["origCL"].upper() == "STDIN":
|
|
|
691 aninput.positional = 9999998
|
|
|
692 aninput.command_line_override = "> $%s" % newname
|
|
|
693 else:
|
|
|
694 aninput.positional = int(p["origCL"])
|
|
|
695 aninput.command_line_override = "$%s" % newname
|
|
|
696 if reps:
|
|
|
697 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {alab} as needed")
|
|
|
698 repe.append(aninput)
|
|
|
699 self.tinputs.append(repe)
|
|
|
700 tparm = gxtp.TestRepeat(name=f"R_{newname}")
|
|
|
701 tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
|
|
|
702 tparm.append(tparm2)
|
|
|
703 self.testparam.append(tparm)
|
|
|
704 else:
|
|
|
705 self.tinputs.append(aninput)
|
|
|
706 tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
|
|
|
707 self.testparam.append(tparm)
|
|
|
708 for p in self.addpar:
|
|
|
709 newname = p["name"]
|
|
|
710 newval = p["value"]
|
|
|
711 newlabel = p["label"]
|
|
|
712 newhelp = p["help"]
|
|
|
713 newtype = p["type"]
|
|
|
714 newcl = p["CL"]
|
|
|
715 oldcl = p["origCL"]
|
|
|
716 reps = p["repeat"] == "1"
|
|
|
717 if not len(newlabel) > 0:
|
|
|
718 newlabel = newname
|
|
|
719 ndash = self.getNdash(newname)
|
|
|
720 if newtype == "text":
|
|
|
721 aparm = gxtp.TextParam(
|
|
|
722 newname,
|
|
|
723 label=newlabel,
|
|
|
724 help=newhelp,
|
|
|
725 value=newval,
|
|
|
726 num_dashes=ndash,
|
|
|
727 )
|
|
|
728 elif newtype == "integer":
|
|
|
729 aparm = gxtp.IntegerParam(
|
|
|
730 newname,
|
|
|
731 label=newlabel,
|
|
|
732 help=newhelp,
|
|
|
733 value=newval,
|
|
|
734 num_dashes=ndash,
|
|
|
735 )
|
|
|
736 elif newtype == "float":
|
|
|
737 aparm = gxtp.FloatParam(
|
|
|
738 newname,
|
|
|
739 label=newlabel,
|
|
|
740 help=newhelp,
|
|
|
741 value=newval,
|
|
|
742 num_dashes=ndash,
|
|
|
743 )
|
|
|
744 elif newtype == "boolean":
|
|
|
745 aparm = gxtp.BooleanParam(
|
|
|
746 newname,
|
|
|
747 label=newlabel,
|
|
|
748 help=newhelp,
|
|
|
749 value=newval,
|
|
|
750 num_dashes=ndash,
|
|
|
751 )
|
|
|
752 else:
|
|
|
753 raise ValueError(
|
|
|
754 'Unrecognised parameter type "%s" for\
|
|
|
755 additional parameter %s in makeXML'
|
|
|
756 % (newtype, newname)
|
|
|
757 )
|
|
|
758 aparm.positional = self.is_positional
|
|
|
759 if self.is_positional:
|
|
|
760 aparm.positional = int(oldcl)
|
|
|
761 if reps:
|
|
|
762 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")
|
|
|
763 repe.append(aparm)
|
|
|
764 self.tinputs.append(repe)
|
|
|
765 tparm = gxtp.TestRepeat(name=f"R_{newname}")
|
|
|
766 tparm2 = gxtp.TestParam(newname, value=newval)
|
|
|
767 tparm.append(tparm2)
|
|
|
768 self.testparam.append(tparm)
|
|
|
769 else:
|
|
|
770 self.tinputs.append(aparm)
|
|
|
771 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
772 self.testparam.append(tparm)
|
|
|
773 for p in self.selpar:
|
|
|
774 newname = p["name"]
|
|
|
775 newval = p["value"]
|
|
|
776 newlabel = p["label"]
|
|
|
777 newhelp = p["help"]
|
|
|
778 newtype = p["type"]
|
|
|
779 newcl = p["CL"]
|
|
|
780 if not len(newlabel) > 0:
|
|
|
781 newlabel = newname
|
|
|
782 ndash = self.getNdash(newname)
|
|
|
783 if newtype == "selecttext":
|
|
|
784 newtext = p["texts"]
|
|
|
785 aparm = gxtp.SelectParam(
|
|
|
786 newname,
|
|
|
787 label=newlabel,
|
|
|
788 help=newhelp,
|
|
|
789 num_dashes=ndash,
|
|
|
790 )
|
|
|
791 for i in range(len(newval)):
|
|
|
792 anopt = gxtp.SelectOption(
|
|
|
793 value=newval[i],
|
|
|
794 text=newtext[i],
|
|
|
795 )
|
|
|
796 aparm.append(anopt)
|
|
|
797 aparm.positional = self.is_positional
|
|
|
798 if self.is_positional:
|
|
|
799 aparm.positional = int(newcl)
|
|
|
800 self.tinputs.append(aparm)
|
|
|
801 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
802 self.testparam.append(tparm)
|
|
|
803 else:
|
|
|
804 raise ValueError(
|
|
|
805 'Unrecognised parameter type "%s" for\
|
|
|
806 selecttext parameter %s in makeXML'
|
|
|
807 % (newtype, newname)
|
|
|
808 )
|
|
|
809 for p in self.collections:
|
|
|
810 newkind = p["kind"]
|
|
|
811 newname = p["name"]
|
|
|
812 newlabel = p["label"]
|
|
|
813 newdisc = p["discover"]
|
|
|
814 collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)
|
|
|
815 disc = gxtp.DiscoverDatasets(
|
|
|
816 pattern=newdisc, directory=f"{newname}", visible="false"
|
|
|
817 )
|
|
|
818 collect.append(disc)
|
|
|
819 self.toutputs.append(collect)
|
|
|
820 try:
|
|
|
821 tparm = gxtp.TestOutputCollection(newname) # broken until PR merged.
|
|
|
822 self.testparam.append(tparm)
|
|
|
823 except Exception:
|
|
|
824 print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!")
|
|
|
825
|
|
|
826 def doNoXMLparam(self):
|
|
|
827 """filter style package - stdin to stdout"""
|
|
|
828 if len(self.infiles) > 0:
|
|
|
829 alab = self.infiles[0]["label"]
|
|
|
830 if len(alab) == 0:
|
|
|
831 alab = self.infiles[0]["infilename"]
|
|
|
832 max1s = (
|
|
|
833 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
|
|
|
834 % str(self.infiles)
|
|
|
835 )
|
|
|
836 assert len(self.infiles) == 1, max1s
|
|
|
837 newname = self.infiles[0]["infilename"]
|
|
|
838 aninput = gxtp.DataParam(
|
|
|
839 newname,
|
|
|
840 optional=False,
|
|
|
841 label=alab,
|
|
|
842 help=self.infiles[0]["help"],
|
|
|
843 format=self.infiles[0]["format"],
|
|
|
844 multiple=False,
|
|
|
845 num_dashes=0,
|
|
|
846 )
|
|
|
847 aninput.command_line_override = "< $%s" % newname
|
|
|
848 aninput.positional = True
|
|
|
849 self.tinputs.append(aninput)
|
|
|
850 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
851 self.testparam.append(tp)
|
|
|
852 if len(self.outfiles) > 0:
|
|
|
853 newname = self.outfiles[0]["name"]
|
|
|
854 newfmt = self.outfiles[0]["format"]
|
|
|
855 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
|
|
|
856 anout.command_line_override = "> $%s" % newname
|
|
|
857 anout.positional = self.is_positional
|
|
|
858 self.toutputs.append(anout)
|
|
|
859 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
|
|
|
860 self.testparam.append(tp)
|
|
|
861
|
|
|
862 def makeXML(self): # noqa
|
|
|
863 """
|
|
|
864 Create a Galaxy xml tool wrapper for the new script
|
|
|
865 Uses galaxyhtml
|
|
|
866 Hmmm. How to get the command line into correct order...
|
|
|
867 """
|
|
|
868 if self.command_override:
|
|
|
869 self.newtool.command_override = self.command_override # config file
|
|
|
870 else:
|
|
|
871 self.newtool.command_override = self.xmlcl
|
|
|
872 cite = gxtp.Citations()
|
|
|
873 acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")
|
|
|
874 cite.append(acite)
|
|
|
875 self.newtool.citations = cite
|
|
|
876 safertext = ""
|
|
|
877 if self.args.help_text:
|
|
|
878 helptext = open(self.args.help_text, "r").readlines()
|
|
|
879 safertext = "\n".join([cheetah_escape(x) for x in helptext])
|
|
|
880 if len(safertext.strip()) == 0:
|
|
|
881 safertext = (
|
|
|
882 "Ask the tool author (%s) to rebuild with help text please\n"
|
|
|
883 % (self.args.user_email)
|
|
|
884 )
|
|
|
885 if self.args.script_path:
|
|
|
886 if len(safertext) > 0:
|
|
|
887 safertext = safertext + "\n\n------\n" # transition allowed!
|
|
|
888 scr = [x for x in self.spacedScript if x.strip() > ""]
|
|
|
889 scr.insert(0, "\n\nScript::\n")
|
|
|
890 if len(scr) > 300:
|
|
|
891 scr = (
|
|
|
892 scr[:100]
|
|
|
893 + [" >300 lines - stuff deleted", " ......"]
|
|
|
894 + scr[-100:]
|
|
|
895 )
|
|
|
896 scr.append("\n")
|
|
|
897 safertext = safertext + "\n".join(scr)
|
|
|
898 self.newtool.help = safertext
|
|
|
899 self.newtool.version_command = f'echo "{self.args.tool_version}"'
|
|
|
900 std = gxtp.Stdios()
|
|
|
901 std1 = gxtp.Stdio()
|
|
|
902 std.append(std1)
|
|
|
903 self.newtool.stdios = std
|
|
|
904 requirements = gxtp.Requirements()
|
|
|
905 if self.args.packages:
|
|
|
906 try:
|
|
|
907 for d in self.args.packages.split(","):
|
|
|
908 ver = ""
|
|
|
909 d = d.replace("==", ":")
|
|
|
910 d = d.replace("=", ":")
|
|
|
911 if ":" in d:
|
|
|
912 packg, ver = d.split(":")
|
|
|
913 else:
|
|
|
914 packg = d
|
|
|
915 requirements.append(
|
|
|
916 gxtp.Requirement("package", packg.strip(), ver.strip())
|
|
|
917 )
|
|
|
918 except Exception:
|
|
|
919 print('### malformed packages string supplied - cannot parse =',self.args.packages)
|
|
|
920 sys.exit(2)
|
|
|
921 self.newtool.requirements = requirements
|
|
|
922 if self.args.parampass == "0":
|
|
|
923 self.doNoXMLparam()
|
|
|
924 else:
|
|
|
925 self.doXMLparam()
|
|
|
926 self.newtool.outputs = self.toutputs
|
|
|
927 self.newtool.inputs = self.tinputs
|
|
|
928 if self.args.script_path:
|
|
|
929 configfiles = gxtp.Configfiles()
|
|
|
930 configfiles.append(
|
|
|
931 gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))
|
|
|
932 )
|
|
|
933 self.newtool.configfiles = configfiles
|
|
|
934 tests = gxtp.Tests()
|
|
|
935 test_a = gxtp.Test()
|
|
|
936 for tp in self.testparam:
|
|
|
937 test_a.append(tp)
|
|
|
938 tests.append(test_a)
|
|
|
939 self.newtool.tests = tests
|
|
|
940 self.newtool.add_comment(
|
|
|
941 "Created by %s at %s using the Galaxy Tool Factory."
|
|
|
942 % (self.args.user_email, timenow())
|
|
|
943 )
|
|
|
944 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
|
|
|
945 exml0 = self.newtool.export()
|
|
|
946 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
|
|
|
947 if (
|
|
|
948 self.test_override
|
|
|
949 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
|
|
|
950 part1 = exml.split("<tests>")[0]
|
|
|
951 part2 = exml.split("</tests>")[1]
|
|
|
952 fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)
|
|
|
953 exml = fixed
|
|
|
954 # exml = exml.replace('range="1:"', 'range="1000:"')
|
|
|
955 xf = open("%s.xml" % self.tool_name, "w")
|
|
|
956 xf.write(exml)
|
|
|
957 xf.write("\n")
|
|
|
958 xf.close()
|
|
|
959 # ready for the tarball
|
|
|
960
|
|
|
961 def run(self): #noqa
|
|
|
962 """
|
|
|
963 generate test outputs by running a command line
|
|
|
964 won't work if command or test override in play - planemo is the
|
|
|
965 easiest way to generate test outputs for that case so is
|
|
|
966 automagically selected
|
|
|
967 """
|
|
|
968 scl = " ".join(self.cl)
|
|
|
969 err = None
|
|
|
970 logname = f"{self.tool_name}_runner_log"
|
|
|
971 if self.args.parampass != "0":
|
|
|
972 if self.lastclredirect:
|
|
|
973 logf = open(self.lastclredirect[1], "wb") # is name of an output file
|
|
|
974 else:
|
|
|
975 logf = open(logname,'w')
|
|
|
976 logf.write("No dependencies so sending CL = '%s' to the fast direct runner instead of planemo to generate tests" % scl)
|
|
|
977 subp = subprocess.run(
|
|
|
978 self.cl, shell=False, stdout=logf, stderr=logf
|
|
|
979 )
|
|
|
980 logf.close()
|
|
|
981 retval = subp.returncode
|
|
|
982 else: # work around special case - stdin and write to stdout
|
|
|
983 if len(self.infiles) > 0:
|
|
|
984 sti = open(self.infiles[0]["name"], "rb")
|
|
|
985 else:
|
|
|
986 sti = sys.stdin
|
|
|
987 if len(self.outfiles) > 0:
|
|
|
988 sto = open(self.outfiles[0]["name"], "wb")
|
|
|
989 else:
|
|
|
990 sto = sys.stdout
|
|
|
991 subp = subprocess.run(
|
|
|
992 self.cl, shell=False, stdout=sto, stdin=sti
|
|
|
993 )
|
|
|
994 retval = subp.returncode
|
|
|
995 sto.close()
|
|
|
996 sti.close()
|
|
|
997 if retval != 0 and err: # problem
|
|
|
998 sys.stderr.write(err)
|
|
|
999 for p in self.outfiles:
|
|
|
1000 oname = p["name"]
|
|
|
1001 tdest = os.path.join(self.testdir, "%s_sample" % oname)
|
|
|
1002 if not os.path.isfile(tdest):
|
|
|
1003 if os.path.isfile(oname):
|
|
|
1004 shutil.copyfile(oname, tdest)
|
|
|
1005 dest = os.path.join(self.repdir, "%s.sample.%s" % (oname,p['format']))
|
|
|
1006 shutil.copyfile(oname, dest)
|
|
|
1007 else:
|
|
|
1008 if report_fail:
|
|
|
1009 tout.write(
|
|
|
1010 "###Tool may have failed - output file %s not found in testdir after planemo run %s."
|
|
|
1011 % (oname, self.testdir)
|
|
|
1012 )
|
|
|
1013 for p in self.infiles:
|
|
|
1014 pth = p["name"]
|
|
|
1015 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
|
|
|
1016 shutil.copyfile(pth, dest)
|
|
|
1017 dest = os.path.join(self.repdir, "%s_sample.%s" % (p["infilename"],p["format"]))
|
|
|
1018 shutil.copyfile(pth, dest)
|
|
|
1019 with os.scandir('.') as outs:
|
|
|
1020 for entry in outs:
|
|
|
1021 newname = entry.name
|
|
|
1022 if not entry.is_file() or entry.name.endswith('_sample'):
|
|
|
1023 continue
|
|
|
1024 if not (entry.name.endswith('.html') or entry.name.endswith('.gz') or entry.name.endswith(".tgz")):
|
|
|
1025 fname, ext = os.path.splitext(entry.name)
|
|
|
1026 if len(ext) > 1:
|
|
|
1027 newname = f"{fname}_{ext[1:]}.txt"
|
|
|
1028 else:
|
|
|
1029 newname = f"{fname}.txt"
|
|
|
1030 dest = os.path.join(self.repdir, newname)
|
|
|
1031 src = entry.name
|
|
|
1032 shutil.copyfile(src, dest)
|
|
|
1033 return retval
|
|
|
1034
|
|
|
1035 def writeShedyml(self):
|
|
|
1036 """for planemo"""
|
|
|
1037 yuser = self.args.user_email.split("@")[0]
|
|
|
1038 yfname = os.path.join(self.tooloutdir, ".shed.yml")
|
|
|
1039 yamlf = open(yfname, "w")
|
|
|
1040 odict = {
|
|
|
1041 "name": self.tool_name,
|
|
|
1042 "owner": yuser,
|
|
|
1043 "type": "unrestricted",
|
|
|
1044 "description": self.args.tool_desc,
|
|
|
1045 "synopsis": self.args.tool_desc,
|
|
|
1046 "category": "TF Generated Tools",
|
|
|
1047 }
|
|
|
1048 yaml.dump(odict, yamlf, allow_unicode=True)
|
|
|
1049 yamlf.close()
|
|
|
1050
|
|
|
1051 def makeTool(self):
|
|
|
1052 """write xmls and input samples into place"""
|
|
|
1053 if self.args.parampass == 0:
|
|
|
1054 self.doNoXMLparam()
|
|
|
1055 else:
|
|
|
1056 self.makeXML()
|
|
|
1057 if self.args.script_path:
|
|
|
1058 stname = os.path.join(self.tooloutdir, self.sfile)
|
|
|
1059 if not os.path.exists(stname):
|
|
|
1060 shutil.copyfile(self.sfile, stname)
|
|
|
1061 xreal = "%s.xml" % self.tool_name
|
|
|
1062 xout = os.path.join(self.tooloutdir, xreal)
|
|
|
1063 shutil.copyfile(xreal, xout)
|
|
|
1064 for p in self.infiles:
|
|
|
1065 pth = p["name"]
|
|
|
1066 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
|
|
|
1067 shutil.copyfile(pth, dest)
|
|
|
1068 dest = os.path.join(self.repdir, "%s_sample.%s" % (p["infilename"],p["format"]))
|
|
|
1069 shutil.copyfile(pth, dest)
|
|
|
1070
|
|
|
1071 def makeToolTar(self, report_fail=False):
|
|
|
1072 """move outputs into test-data and prepare the tarball"""
|
|
|
1073 excludeme = "_planemo_test_report.html"
|
|
|
1074
|
|
|
1075 def exclude_function(tarinfo):
|
|
|
1076 filename = tarinfo.name
|
|
|
1077 return None if filename.endswith(excludeme) else tarinfo
|
|
|
1078
|
|
|
1079 for p in self.outfiles:
|
|
|
1080 oname = p["name"]
|
|
|
1081 tdest = os.path.join(self.testdir, "%s_sample" % oname)
|
|
|
1082 src = os.path.join(self.testdir, oname)
|
|
|
1083 if not os.path.isfile(tdest):
|
|
|
1084 if os.path.isfile(src):
|
|
|
1085 shutil.copyfile(src, tdest)
|
|
|
1086 dest = os.path.join(self.repdir, "%s.sample" % (oname))
|
|
|
1087 shutil.copyfile(src, dest)
|
|
|
1088 else:
|
|
|
1089 if report_fail:
|
|
|
1090 print(
|
|
|
1091 "###Tool may have failed - output file %s not found in testdir after planemo run %s."
|
|
|
1092 % (tdest, self.testdir)
|
|
|
1093 )
|
|
|
1094 tf = tarfile.open(self.newtarpath, "w:gz")
|
|
|
1095 tf.add(
|
|
|
1096 name=self.tooloutdir,
|
|
|
1097 arcname=self.tool_name,
|
|
|
1098 filter=exclude_function,
|
|
|
1099 )
|
|
|
1100 tf.close()
|
|
|
1101 shutil.copyfile(self.newtarpath, self.args.new_tool)
|
|
|
1102
|
|
|
1103 def moveRunOutputs(self):
|
|
|
1104 """need to move planemo or run outputs into toolfactory collection"""
|
|
|
1105 with os.scandir(self.tooloutdir) as outs:
|
|
|
1106 for entry in outs:
|
|
|
1107 if not entry.is_file():
|
|
|
1108 continue
|
|
|
1109 if not entry.name.endswith('.html'):
|
|
|
1110 _, ext = os.path.splitext(entry.name)
|
|
|
1111 newname = f"{entry.name.replace('.','_')}.txt"
|
|
|
1112 dest = os.path.join(self.repdir, newname)
|
|
|
1113 src = os.path.join(self.tooloutdir, entry.name)
|
|
|
1114 shutil.copyfile(src, dest)
|
|
|
1115 if self.args.include_tests:
|
|
|
1116 with os.scandir(self.testdir) as outs:
|
|
|
1117 for entry in outs:
|
|
|
1118 if (not entry.is_file()) or entry.name.endswith(
|
|
|
1119 "_planemo_test_report.html"
|
|
|
1120 ):
|
|
|
1121 continue
|
|
|
1122 if "." in entry.name:
|
|
|
1123 _, ext = os.path.splitext(entry.name)
|
|
|
1124 if ext in [".tgz", ".json"]:
|
|
|
1125 continue
|
|
|
1126 if ext in [".yml", ".xml", ".yaml"]:
|
|
|
1127 newname = f"{entry.name.replace('.','_')}.txt"
|
|
|
1128 else:
|
|
|
1129 newname = entry.name
|
|
|
1130 else:
|
|
|
1131 newname = f"{entry.name}.txt"
|
|
|
1132 dest = os.path.join(self.repdir, newname)
|
|
|
1133 src = os.path.join(self.testdir, entry.name)
|
|
|
1134 shutil.copyfile(src, dest)
|
|
|
1135
|
|
|
1136
|
|
|
1137 def main():
|
|
|
1138 """
|
|
|
1139 This is a Galaxy wrapper.
|
|
|
1140 It expects to be called by a special purpose tool.xml
|
|
|
1141
|
|
|
1142 """
|
|
|
1143 parser = argparse.ArgumentParser()
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|
|
1144 a = parser.add_argument
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|
|
1145 a("--script_path", default=None)
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|
|
1146 a("--history_test", default=None)
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|
|
1147 a("--cl_user_suffix", default=None)
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|
|
1148 a("--sysexe", default=None)
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|
|
1149 a("--packages", default=None)
|
|
|
1150 a("--tool_name", default="newtool")
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|
|
1151 a("--tool_dir", default=None)
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|
|
1152 a("--input_files", default=[], action="append")
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|
|
1153 a("--output_files", default=[], action="append")
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|
|
1154 a("--user_email", default="Unknown")
|
|
|
1155 a("--bad_user", default=None)
|
|
|
1156 a("--help_text", default=None)
|
|
|
1157 a("--tool_desc", default=None)
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|
|
1158 a("--tool_version", default=None)
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|
|
1159 a("--citations", default=None)
|
|
|
1160 a("--command_override", default=None)
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|
|
1161 a("--test_override", default=None)
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|
|
1162 a("--additional_parameters", action="append", default=[])
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|
|
1163 a("--selecttext_parameters", action="append", default=[])
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|
|
1164 a("--edit_additional_parameters", action="store_true", default=False)
|
|
|
1165 a("--parampass", default="positional")
|
|
|
1166 a("--tfout", default="./tfout")
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|
|
1167 a("--new_tool", default="new_tool")
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|
|
1168 a("--galaxy_root", default="/galaxy-central")
|
|
|
1169 a("--galaxy_venv", default="/galaxy_venv")
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|
|
1170 a("--collection", action="append", default=[])
|
|
|
1171 a("--include_tests", default=False, action="store_true")
|
|
|
1172 a("--install", default=False, action="store_true")
|
|
|
1173 a("--run_test", default=False, action="store_true")
|
|
|
1174 a("--local_tools", default='tools') # relative to galaxy_root
|
|
|
1175 a("--tool_conf_path", default='/galaxy_root/config/tool_conf.xml')
|
|
|
1176 a("--galaxy_url", default="http://localhost:8080")
|
|
|
1177 a("--toolshed_url", default="http://localhost:9009")
|
|
|
1178 # make sure this is identical to tool_sheds_conf.xml
|
|
|
1179 # localhost != 127.0.0.1 so validation fails
|
|
|
1180 a("--toolshed_api_key", default="fakekey")
|
|
|
1181 a("--galaxy_api_key", default="8993d65865e6d6d1773c2c34a1cc207d")
|
|
|
1182 args = parser.parse_args()
|
|
|
1183 assert not args.bad_user, (
|
|
|
1184 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
|
|
|
1185 admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
|
|
|
1186 % (args.bad_user, args.bad_user)
|
|
|
1187 )
|
|
|
1188 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
|
|
|
1189 assert (
|
|
|
1190 args.sysexe or args.packages
|
|
|
1191 ), "## Tool Factory wrapper expects an interpreter \
|
|
|
1192 or an executable package in --sysexe or --packages"
|
|
|
1193 print('Hello from',os.getcwd())
|
|
|
1194 r = ScriptRunner(args)
|
|
|
1195 r.writeShedyml()
|
|
|
1196 r.makeTool()
|
|
|
1197 r.makeToolTar()
|
|
|
1198 if args.run_test:
|
|
|
1199 if not args.packages or args.packages.strip() == "bash":
|
|
|
1200 r.run()
|
|
|
1201 r.makeToolTar()
|
|
|
1202 else:
|
|
|
1203 tt = ToolTester(report_dir=r.repdir, in_tool_archive=r.newtarpath, new_tool_archive=r.args.new_tool, galaxy_root=args.galaxy_root, include_tests=False)
|
|
|
1204 if args.install:
|
|
|
1205 #try:
|
|
|
1206 tcu = ToolConfUpdater(args=args, tool_dir=os.path.join(args.galaxy_root,args.local_tools),
|
|
|
1207 new_tool_archive_path=r.newtarpath, tool_conf_path=os.path.join(args.galaxy_root,'config','tool_conf.xml'),
|
|
|
1208 new_tool_name=r.tool_name)
|
|
|
1209 #except Exception:
|
|
|
1210 # print("### Unable to install the new tool. Are you sure you have all the required special settings?")
|
|
|
1211
|
|
|
1212 if __name__ == "__main__":
|
|
|
1213 main()
|
|
|
1214
|
