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1 # see https://github.com/fubar2/toolfactory
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2 #
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3 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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4 #
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5 # all rights reserved
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6 # Licensed under the LGPL
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7 # suggestions for improvement and bug fixes welcome at
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8 # https://github.com/fubar2/toolfactory
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9 #
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10 # April 2021: Refactored into two tools - generate and test/install
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11 # as part of GTN tutorial development and biocontainer adoption
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12 # The tester runs planemo on a non-tested archive, creates the test outputs
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13 # and returns a new proper tool with test.
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14
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15
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16
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17 import argparse
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18 import copy
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19 import fcntl
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20 import json
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21 import os
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22 import re
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23 import shlex
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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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31 from bioblend import galaxy
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32
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33 import galaxyxml.tool as gxt
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34 import galaxyxml.tool.parameters as gxtp
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35
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36 import lxml.etree as ET
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37
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38 import yaml
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39
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40 myversion = "V2.3 April 2021"
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41 verbose = True
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42 debug = True
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43 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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44 FAKEEXE = "~~~REMOVE~~~ME~~~"
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45 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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46 # with override.
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47
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48
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49 def timenow():
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50 """return current time as a string"""
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51 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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52
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53
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54 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
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55
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56
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57 def cheetah_escape(text):
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58 """Produce entities within text."""
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59 return "".join([cheetah_escape_table.get(c, c) for c in text])
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60
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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 Locker:
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74 """
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75 multiple instances of the TF may try to update tool_conf.xml so use a simple lockfile
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76 to prevent overwriting mix ups.
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77 """
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78 def __enter__ (self):
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79 lockfile = "/tmp/.toolfactory_lockfile.lck"
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80 if not os.path.exists(lockfile):
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81 try:
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82 os.utime(lockfile, None)
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83 except OSError:
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84 open(lockfile, 'a').close()
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85 self.fp = open(lockfile)
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86 fcntl.flock(self.fp.fileno(), fcntl.LOCK_EX)
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87
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88 def __exit__ (self, _type, value, tb):
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89 fcntl.flock(self.fp.fileno(), fcntl.LOCK_UN)
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90 self.fp.close()
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91
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92
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93 class Tool_Conf_Updater:
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94
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95 """# update config/tool_conf.xml with a new tool unpacked in /tools
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96 # requires highly insecure docker settings - like write to tool_conf.xml and to tools !
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97 # if in a container possibly not so courageous.
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98 # Fine on your own laptop but security red flag for most production instances
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99 Note potential race condition for tool_conf.xml update - uses a file lock.
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100 """
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101
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102 def __init__(
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103 self, args, tool_conf_path, new_tool_archive_path, new_tool_name, local_tool_dir, run_test
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104 ):
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105 self.args = args
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106 self.tool_conf_path = os.path.join(args.galaxy_root, tool_conf_path)
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107 self.tool_dir = os.path.join(args.galaxy_root, local_tool_dir,'TFtools')
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108 self.out_section = "ToolFactory Generated Tools"
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109 tff = tarfile.open(new_tool_archive_path, "r:*")
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110 flist = tff.getnames()
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111 ourdir = os.path.commonpath(flist) # eg pyrevpos
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112 self.tool_id = ourdir # they are the same for TF tools
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113 ourxml = [x for x in flist if x.lower().endswith(".xml")]
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114 tff.extractall()
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115 tff.close()
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116 self.run_rsync(ourdir, self.tool_dir)
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117 with Locker():
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118 self.update_toolconf(ourdir, ourxml)
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119
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120 def run_rsync(self, srcf, dstf):
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121 src = os.path.abspath(srcf)
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122 dst = os.path.abspath(dstf)
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123 if os.path.isdir(src):
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124 cll = ["rsync", "-r", src, dst]
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125 else:
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126 cll = ["rsync", src, dst]
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127 subprocess.run(
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128 cll,
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129 capture_output=False,
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130 encoding="utf8",
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131 shell=False,
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132 )
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133
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134 def update_toolconf(self, ourdir, ourxml): # path is relative to tools
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135 localconf = "./local_tool_conf.xml"
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136 self.run_rsync(self.tool_conf_path, localconf)
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137 tree = ET.parse(localconf)
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138 root = tree.getroot()
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139 hasTF = False
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140 TFsection = None
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141 for e in root.findall("section"):
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142 if e.attrib["name"] == self.out_section:
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143 hasTF = True
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144 TFsection = e
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145 if not hasTF:
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146 TFsection = ET.Element("section", {"id":self.out_section, "name":self.out_section})
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147 root.insert(0, TFsection) # at the top!
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148 our_tools = TFsection.findall("tool")
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149 conf_tools = [x.attrib["file"] for x in our_tools]
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150 for xml in ourxml: # may be > 1
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151 if xml not in conf_tools: # new
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152 ET.SubElement(TFsection, "tool", {"file": os.path.join('TFtools', xml)})
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153 newconf = f"{self.tool_id}_conf"
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154 tree.write(newconf, pretty_print=True)
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155 self.run_rsync(newconf, self.tool_conf_path)
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156
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157
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158
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159
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160 class Tool_Factory:
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161 """Wrapper for an arbitrary script
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162 uses galaxyxml
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163
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164 """
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165
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166 def __init__(self, args=None): # noqa
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167 """
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168 prepare command line cl for running the tool here
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169 and prepare elements needed for galaxyxml tool generation
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170 """
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171 self.ourcwd = os.getcwd()
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172 self.collections = []
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173 if len(args.collection) > 0:
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174 try:
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175 self.collections = [
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176 json.loads(x) for x in args.collection if len(x.strip()) > 1
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177 ]
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178 except Exception:
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179 print(
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180 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
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181 )
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182 try:
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183 self.infiles = [
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184 json.loads(x) for x in args.input_files if len(x.strip()) > 1
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185 ]
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186 except Exception:
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187 print(
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188 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
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189 )
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190 try:
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191 self.outfiles = [
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192 json.loads(x) for x in args.output_files if len(x.strip()) > 1
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193 ]
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194 except Exception:
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195 print(
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196 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
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197 )
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198 try:
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199 self.addpar = [
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200 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
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201 ]
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202 except Exception:
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203 print(
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204 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
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205 )
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206 try:
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207 self.selpar = [
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208 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
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209 ]
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210 except Exception:
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211 print(
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212 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
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213 )
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214 self.args = args
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215 self.cleanuppar()
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216 self.lastxclredirect = None
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217 self.xmlcl = []
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218 self.is_positional = self.args.parampass == "positional"
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219 if self.args.sysexe:
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220 if " " in self.args.sysexe:
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221 self.executeme = self.args.sysexe.split(" ")
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222 else:
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223 self.executeme = [
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224 self.args.sysexe,
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225 ]
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226 else:
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227 if self.args.packages:
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228 self.executeme = [
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229 self.args.packages.split(",")[0].split(":")[0].strip(),
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230 ]
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231 else:
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232 self.executeme = None
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233 aXCL = self.xmlcl.append
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234 assert args.parampass in [
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235 "0",
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236 "argparse",
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237 "positional",
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238 ], 'args.parampass must be "0","positional" or "argparse"'
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239 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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240 self.tool_id = self.tool_name
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241 self.newtool = gxt.Tool(
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242 self.tool_name,
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243 self.tool_id,
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244 self.args.tool_version,
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245 self.args.tool_desc,
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246 FAKEEXE,
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247 )
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248 self.tooloutdir = "./tfout"
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249 self.repdir = "./toolgen"
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250 self.newtarpath = os.path.join(self.tooloutdir, "%s_not_tested.toolshed.gz" % self.tool_name)
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251 self.testdir = os.path.join(self.tooloutdir, "test-data")
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252 if not os.path.exists(self.tooloutdir):
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253 os.mkdir(self.tooloutdir)
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254 if not os.path.exists(self.testdir):
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255 os.mkdir(self.testdir)
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256 if not os.path.exists(self.repdir):
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257 os.mkdir(self.repdir)
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258 self.tinputs = gxtp.Inputs()
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259 self.toutputs = gxtp.Outputs()
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260 self.testparam = []
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261 if self.args.script_path:
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262 self.prepScript()
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263 if self.args.command_override:
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264 scos = open(self.args.command_override, "r").readlines()
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265 self.command_override = [x.rstrip() for x in scos]
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266 else:
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267 self.command_override = None
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268 if self.args.test_override:
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269 stos = open(self.args.test_override, "r").readlines()
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270 self.test_override = [x.rstrip() for x in stos]
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271 else:
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272 self.test_override = None
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273 if self.args.script_path:
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274 for ex in self.executeme:
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275 aXCL(ex)
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276 aXCL("$runme")
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277 else:
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278 for ex in self.executeme:
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279 aXCL(ex)
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280
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281 if self.args.parampass == "0":
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282 self.clsimple()
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283 else:
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284 if self.args.parampass == "positional":
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285 self.prepclpos()
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286 self.clpositional()
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287 else:
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288 self.prepargp()
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289 self.clargparse()
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290
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291 def clsimple(self):
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292 """no parameters or repeats - uses < and > for i/o"""
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293 aXCL = self.xmlcl.append
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294 if len(self.infiles) > 0:
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295 aXCL("<")
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296 aXCL("$%s" % self.infiles[0]["infilename"])
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297 if len(self.outfiles) > 0:
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298 aXCL(">")
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299 aXCL("$%s" % self.outfiles[0]["name"])
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300 if self.args.cl_user_suffix: # DIY CL end
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301 clp = shlex.split(self.args.cl_user_suffix)
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302 for c in clp:
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303 aXCL(c)
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304
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305 def prepargp(self):
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306 xclsuffix = []
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307 for i, p in enumerate(self.infiles):
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308 nam = p["infilename"]
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309 if p["origCL"].strip().upper() == "STDIN":
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310 xappendme = [
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311 nam,
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312 nam,
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313 "< $%s" % nam,
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314 ]
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315 else:
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316 rep = p["repeat"] == "1"
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317 over = ""
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318 if rep:
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319 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
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320 xappendme = [p["CL"], "$%s" % p["CL"], over]
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321 xclsuffix.append(xappendme)
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322 for i, p in enumerate(self.outfiles):
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323 if p["origCL"].strip().upper() == "STDOUT":
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324 self.lastxclredirect = [">", "$%s" % p["name"]]
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325 else:
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326 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
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327 for p in self.addpar:
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328 nam = p["name"]
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329 rep = p["repeat"] == "1"
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330 if rep:
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331 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
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332 else:
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333 over = p["override"]
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334 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
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335 for p in self.selpar:
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336 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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337 self.xclsuffix = xclsuffix
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338
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339 def prepclpos(self):
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340 xclsuffix = []
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341 for i, p in enumerate(self.infiles):
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342 if p["origCL"].strip().upper() == "STDIN":
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343 xappendme = [
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344 "999",
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345 p["infilename"],
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346 "< $%s" % p["infilename"],
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347 ]
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348 else:
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349 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
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350 xclsuffix.append(xappendme)
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351 for i, p in enumerate(self.outfiles):
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352 if p["origCL"].strip().upper() == "STDOUT":
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353 self.lastxclredirect = [">", "$%s" % p["name"]]
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354 else:
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355 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
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356 for p in self.addpar:
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357 nam = p["name"]
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358 rep = p["repeat"] == "1" # repeats make NO sense
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359 if rep:
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360 print(
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361 f"### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!"
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362 )
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363 over = p["override"]
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364 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
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365 for p in self.selpar:
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366 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
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367 xclsuffix.sort()
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368 self.xclsuffix = xclsuffix
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369
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370 def prepScript(self):
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371 rx = open(self.args.script_path, "r").readlines()
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372 rx = [x.rstrip() for x in rx]
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373 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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374 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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375 self.script = "\n".join(rx)
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376 fhandle, self.sfile = tempfile.mkstemp(
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377 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
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378 )
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379 tscript = open(self.sfile, "w")
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380 tscript.write(self.script)
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381 tscript.close()
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382 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
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383 rx.insert(0, "#raw")
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384 rx.append("#end raw")
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385 self.escapedScript = rx
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386 art = "%s.%s" % (self.tool_name, self.executeme[0])
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387 artifact = open(art, "wb")
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388 artifact.write(bytes(self.script, "utf8"))
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389 artifact.close()
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390
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391 def cleanuppar(self):
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392 """ positional parameters are complicated by their numeric ordinal"""
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393 if self.args.parampass == "positional":
|
|
|
394 for i, p in enumerate(self.infiles):
|
|
|
395 assert (
|
|
|
396 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
|
|
|
397 ), "Positional parameters must be ordinal integers - got %s for %s" % (
|
|
|
398 p["CL"],
|
|
|
399 p["label"],
|
|
|
400 )
|
|
|
401 for i, p in enumerate(self.outfiles):
|
|
|
402 assert (
|
|
|
403 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
|
|
|
404 ), "Positional parameters must be ordinal integers - got %s for %s" % (
|
|
|
405 p["CL"],
|
|
|
406 p["name"],
|
|
|
407 )
|
|
|
408 for i, p in enumerate(self.addpar):
|
|
|
409 assert p[
|
|
|
410 "CL"
|
|
|
411 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
|
|
|
412 p["CL"],
|
|
|
413 p["name"],
|
|
|
414 )
|
|
|
415 for i, p in enumerate(self.infiles):
|
|
|
416 infp = copy.copy(p)
|
|
|
417 infp["origCL"] = infp["CL"]
|
|
|
418 if self.args.parampass in ["positional", "0"]:
|
|
|
419 infp["infilename"] = infp["label"].replace(" ", "_")
|
|
|
420 else:
|
|
|
421 infp["infilename"] = infp["CL"]
|
|
|
422 self.infiles[i] = infp
|
|
|
423 for i, p in enumerate(self.outfiles):
|
|
|
424 outfp = copy.copy(p)
|
|
|
425 outfp["origCL"] = outfp["CL"] # keep copy
|
|
|
426 self.outfiles[i] = outfp
|
|
|
427 for i, p in enumerate(self.addpar):
|
|
|
428 addp = copy.copy(p)
|
|
|
429 addp["origCL"] = addp["CL"]
|
|
|
430 self.addpar[i] = addp
|
|
|
431
|
|
|
432 def clpositional(self):
|
|
|
433 # inputs in order then params
|
|
|
434 aXCL = self.xmlcl.append
|
|
|
435 for (k, v, koverride) in self.xclsuffix:
|
|
|
436 aXCL(v)
|
|
|
437 if self.lastxclredirect:
|
|
|
438 for cl in self.lastxclredirect:
|
|
|
439 aXCL(cl)
|
|
|
440 if self.args.cl_user_suffix: # DIY CL end
|
|
|
441 clp = shlex.split(self.args.cl_user_suffix)
|
|
|
442 for c in clp:
|
|
|
443 aXCL(c)
|
|
|
444
|
|
|
445 def clargparse(self):
|
|
|
446 """argparse style"""
|
|
|
447 aXCL = self.xmlcl.append
|
|
|
448 # inputs then params in argparse named form
|
|
|
449
|
|
|
450 for (k, v, koverride) in self.xclsuffix:
|
|
|
451 if koverride > "":
|
|
|
452 k = koverride
|
|
|
453 aXCL(k)
|
|
|
454 else:
|
|
|
455 if len(k.strip()) == 1:
|
|
|
456 k = "-%s" % k
|
|
|
457 else:
|
|
|
458 k = "--%s" % k
|
|
|
459 aXCL(k)
|
|
|
460 aXCL(v)
|
|
|
461 if self.lastxclredirect:
|
|
|
462 for cl in self.lastxclredirect:
|
|
|
463 aXCL(cl)
|
|
|
464 if self.args.cl_user_suffix: # DIY CL end
|
|
|
465 clp = shlex.split(self.args.cl_user_suffix)
|
|
|
466 for c in clp:
|
|
|
467 aXCL(c)
|
|
|
468
|
|
|
469 def getNdash(self, newname):
|
|
|
470 if self.is_positional:
|
|
|
471 ndash = 0
|
|
|
472 else:
|
|
|
473 ndash = 2
|
|
|
474 if len(newname) < 2:
|
|
|
475 ndash = 1
|
|
|
476 return ndash
|
|
|
477
|
|
|
478 def doXMLparam(self): # noqa
|
|
|
479 """Add all needed elements to tool"""
|
|
|
480 for p in self.outfiles:
|
|
|
481 newname = p["name"]
|
|
|
482 newfmt = p["format"]
|
|
|
483 newcl = p["CL"]
|
|
|
484 test = p["test"]
|
|
|
485 oldcl = p["origCL"]
|
|
|
486 test = test.strip()
|
|
|
487 ndash = self.getNdash(newcl)
|
|
|
488 aparm = gxtp.OutputData(
|
|
|
489 name=newname, format=newfmt, num_dashes=ndash, label=newname
|
|
|
490 )
|
|
|
491 aparm.positional = self.is_positional
|
|
|
492 if self.is_positional:
|
|
|
493 if oldcl.upper() == "STDOUT":
|
|
|
494 aparm.positional = 9999999
|
|
|
495 aparm.command_line_override = "> $%s" % newname
|
|
|
496 else:
|
|
|
497 aparm.positional = int(oldcl)
|
|
|
498 aparm.command_line_override = "$%s" % newname
|
|
|
499 self.toutputs.append(aparm)
|
|
|
500 ld = None
|
|
|
501 if test.strip() > "":
|
|
|
502 if test.startswith("diff"):
|
|
|
503 c = "diff"
|
|
|
504 ld = 0
|
|
|
505 if test.split(":")[1].isdigit:
|
|
|
506 ld = int(test.split(":")[1])
|
|
|
507 tp = gxtp.TestOutput(
|
|
|
508 name=newname,
|
|
|
509 value="%s_sample" % newname,
|
|
|
510 compare=c,
|
|
|
511 lines_diff=ld,
|
|
|
512 )
|
|
|
513 elif test.startswith("sim_size"):
|
|
|
514 c = "sim_size"
|
|
|
515 tn = test.split(":")[1].strip()
|
|
|
516 if tn > "":
|
|
|
517 if "." in tn:
|
|
|
518 delta = None
|
|
|
519 delta_frac = min(1.0, float(tn))
|
|
|
520 else:
|
|
|
521 delta = int(tn)
|
|
|
522 delta_frac = None
|
|
|
523 tp = gxtp.TestOutput(
|
|
|
524 name=newname,
|
|
|
525 value="%s_sample" % newname,
|
|
|
526 compare=c,
|
|
|
527 delta=delta,
|
|
|
528 delta_frac=delta_frac,
|
|
|
529 )
|
|
|
530 else:
|
|
|
531 c = test
|
|
|
532 tp = gxtp.TestOutput(
|
|
|
533 name=newname,
|
|
|
534 value="%s_sample" % newname,
|
|
|
535 compare=c,
|
|
|
536 )
|
|
|
537 self.testparam.append(tp)
|
|
|
538 for p in self.infiles:
|
|
|
539 newname = p["infilename"]
|
|
|
540 newfmt = p["format"]
|
|
|
541 ndash = self.getNdash(newname)
|
|
|
542 reps = p.get("repeat", "0") == "1"
|
|
|
543 if not len(p["label"]) > 0:
|
|
|
544 alab = p["CL"]
|
|
|
545 else:
|
|
|
546 alab = p["label"]
|
|
|
547 aninput = gxtp.DataParam(
|
|
|
548 newname,
|
|
|
549 optional=False,
|
|
|
550 label=alab,
|
|
|
551 help=p["help"],
|
|
|
552 format=newfmt,
|
|
|
553 multiple=False,
|
|
|
554 num_dashes=ndash,
|
|
|
555 )
|
|
|
556 aninput.positional = self.is_positional
|
|
|
557 if self.is_positional:
|
|
|
558 if p["origCL"].upper() == "STDIN":
|
|
|
559 aninput.positional = 9999998
|
|
|
560 aninput.command_line_override = "> $%s" % newname
|
|
|
561 else:
|
|
|
562 aninput.positional = int(p["origCL"])
|
|
|
563 aninput.command_line_override = "$%s" % newname
|
|
|
564 if reps:
|
|
|
565 repe = gxtp.Repeat(
|
|
|
566 name=f"R_{newname}", title=f"Add as many {alab} as needed"
|
|
|
567 )
|
|
|
568 repe.append(aninput)
|
|
|
569 self.tinputs.append(repe)
|
|
|
570 tparm = gxtp.TestRepeat(name=f"R_{newname}")
|
|
|
571 tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
|
|
|
572 tparm.append(tparm2)
|
|
|
573 self.testparam.append(tparm)
|
|
|
574 else:
|
|
|
575 self.tinputs.append(aninput)
|
|
|
576 tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
|
|
|
577 self.testparam.append(tparm)
|
|
|
578 for p in self.addpar:
|
|
|
579 newname = p["name"]
|
|
|
580 newval = p["value"]
|
|
|
581 newlabel = p["label"]
|
|
|
582 newhelp = p["help"]
|
|
|
583 newtype = p["type"]
|
|
|
584 newcl = p["CL"]
|
|
|
585 oldcl = p["origCL"]
|
|
|
586 reps = p["repeat"] == "1"
|
|
|
587 if not len(newlabel) > 0:
|
|
|
588 newlabel = newname
|
|
|
589 ndash = self.getNdash(newname)
|
|
|
590 if newtype == "text":
|
|
|
591 aparm = gxtp.TextParam(
|
|
|
592 newname,
|
|
|
593 label=newlabel,
|
|
|
594 help=newhelp,
|
|
|
595 value=newval,
|
|
|
596 num_dashes=ndash,
|
|
|
597 )
|
|
|
598 elif newtype == "integer":
|
|
|
599 aparm = gxtp.IntegerParam(
|
|
|
600 newname,
|
|
|
601 label=newlabel,
|
|
|
602 help=newhelp,
|
|
|
603 value=newval,
|
|
|
604 num_dashes=ndash,
|
|
|
605 )
|
|
|
606 elif newtype == "float":
|
|
|
607 aparm = gxtp.FloatParam(
|
|
|
608 newname,
|
|
|
609 label=newlabel,
|
|
|
610 help=newhelp,
|
|
|
611 value=newval,
|
|
|
612 num_dashes=ndash,
|
|
|
613 )
|
|
|
614 elif newtype == "boolean":
|
|
|
615 aparm = gxtp.BooleanParam(
|
|
|
616 newname,
|
|
|
617 label=newlabel,
|
|
|
618 help=newhelp,
|
|
|
619 value=newval,
|
|
|
620 num_dashes=ndash,
|
|
|
621 )
|
|
|
622 else:
|
|
|
623 raise ValueError(
|
|
|
624 'Unrecognised parameter type "%s" for\
|
|
|
625 additional parameter %s in makeXML'
|
|
|
626 % (newtype, newname)
|
|
|
627 )
|
|
|
628 aparm.positional = self.is_positional
|
|
|
629 if self.is_positional:
|
|
|
630 aparm.positional = int(oldcl)
|
|
|
631 if reps:
|
|
|
632 repe = gxtp.Repeat(
|
|
|
633 name=f"R_{newname}", title=f"Add as many {newlabel} as needed"
|
|
|
634 )
|
|
|
635 repe.append(aparm)
|
|
|
636 self.tinputs.append(repe)
|
|
|
637 tparm = gxtp.TestRepeat(name=f"R_{newname}")
|
|
|
638 tparm2 = gxtp.TestParam(newname, value=newval)
|
|
|
639 tparm.append(tparm2)
|
|
|
640 self.testparam.append(tparm)
|
|
|
641 else:
|
|
|
642 self.tinputs.append(aparm)
|
|
|
643 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
644 self.testparam.append(tparm)
|
|
|
645 for p in self.selpar:
|
|
|
646 newname = p["name"]
|
|
|
647 newval = p["value"]
|
|
|
648 newlabel = p["label"]
|
|
|
649 newhelp = p["help"]
|
|
|
650 newtype = p["type"]
|
|
|
651 newcl = p["CL"]
|
|
|
652 if not len(newlabel) > 0:
|
|
|
653 newlabel = newname
|
|
|
654 ndash = self.getNdash(newname)
|
|
|
655 if newtype == "selecttext":
|
|
|
656 newtext = p["texts"]
|
|
|
657 aparm = gxtp.SelectParam(
|
|
|
658 newname,
|
|
|
659 label=newlabel,
|
|
|
660 help=newhelp,
|
|
|
661 num_dashes=ndash,
|
|
|
662 )
|
|
|
663 for i in range(len(newval)):
|
|
|
664 anopt = gxtp.SelectOption(
|
|
|
665 value=newval[i],
|
|
|
666 text=newtext[i],
|
|
|
667 )
|
|
|
668 aparm.append(anopt)
|
|
|
669 aparm.positional = self.is_positional
|
|
|
670 if self.is_positional:
|
|
|
671 aparm.positional = int(newcl)
|
|
|
672 self.tinputs.append(aparm)
|
|
|
673 tparm = gxtp.TestParam(newname, value=newval)
|
|
|
674 self.testparam.append(tparm)
|
|
|
675 else:
|
|
|
676 raise ValueError(
|
|
|
677 'Unrecognised parameter type "%s" for\
|
|
|
678 selecttext parameter %s in makeXML'
|
|
|
679 % (newtype, newname)
|
|
|
680 )
|
|
|
681 for p in self.collections:
|
|
|
682 newkind = p["kind"]
|
|
|
683 newname = p["name"]
|
|
|
684 newlabel = p["label"]
|
|
|
685 newdisc = p["discover"]
|
|
|
686 collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)
|
|
|
687 disc = gxtp.DiscoverDatasets(
|
|
|
688 pattern=newdisc, directory=f"{newname}", visible="false"
|
|
|
689 )
|
|
|
690 collect.append(disc)
|
|
|
691 self.toutputs.append(collect)
|
|
|
692 try:
|
|
|
693 tparm = gxtp.TestOutputCollection(newname) # broken until PR merged.
|
|
|
694 self.testparam.append(tparm)
|
|
|
695 except Exception:
|
|
|
696 print(
|
|
|
697 "#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!"
|
|
|
698 )
|
|
|
699
|
|
|
700 def doNoXMLparam(self):
|
|
|
701 """filter style package - stdin to stdout"""
|
|
|
702 if len(self.infiles) > 0:
|
|
|
703 alab = self.infiles[0]["label"]
|
|
|
704 if len(alab) == 0:
|
|
|
705 alab = self.infiles[0]["infilename"]
|
|
|
706 max1s = (
|
|
|
707 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
|
|
|
708 % str(self.infiles)
|
|
|
709 )
|
|
|
710 assert len(self.infiles) == 1, max1s
|
|
|
711 newname = self.infiles[0]["infilename"]
|
|
|
712 aninput = gxtp.DataParam(
|
|
|
713 newname,
|
|
|
714 optional=False,
|
|
|
715 label=alab,
|
|
|
716 help=self.infiles[0]["help"],
|
|
|
717 format=self.infiles[0]["format"],
|
|
|
718 multiple=False,
|
|
|
719 num_dashes=0,
|
|
|
720 )
|
|
|
721 aninput.command_line_override = "< $%s" % newname
|
|
|
722 aninput.positional = True
|
|
|
723 self.tinputs.append(aninput)
|
|
|
724 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
|
|
|
725 self.testparam.append(tp)
|
|
|
726 if len(self.outfiles) > 0:
|
|
|
727 newname = self.outfiles[0]["name"]
|
|
|
728 newfmt = self.outfiles[0]["format"]
|
|
|
729 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
|
|
|
730 anout.command_line_override = "> $%s" % newname
|
|
|
731 anout.positional = self.is_positional
|
|
|
732 self.toutputs.append(anout)
|
|
|
733 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
|
|
|
734 self.testparam.append(tp)
|
|
|
735
|
|
|
736 def makeXML(self): # noqa
|
|
|
737 """
|
|
|
738 Create a Galaxy xml tool wrapper for the new script
|
|
|
739 Uses galaxyhtml
|
|
|
740 Hmmm. How to get the command line into correct order...
|
|
|
741 """
|
|
|
742 if self.command_override:
|
|
|
743 self.newtool.command_override = self.command_override # config file
|
|
|
744 else:
|
|
|
745 self.newtool.command_override = self.xmlcl
|
|
|
746 cite = gxtp.Citations()
|
|
|
747 acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")
|
|
|
748 cite.append(acite)
|
|
|
749 self.newtool.citations = cite
|
|
|
750 safertext = ""
|
|
|
751 if self.args.help_text:
|
|
|
752 helptext = open(self.args.help_text, "r").readlines()
|
|
|
753 safertext = "\n".join([cheetah_escape(x) for x in helptext])
|
|
|
754 if len(safertext.strip()) == 0:
|
|
|
755 safertext = (
|
|
|
756 "Ask the tool author (%s) to rebuild with help text please\n"
|
|
|
757 % (self.args.user_email)
|
|
|
758 )
|
|
|
759 if self.args.script_path:
|
|
|
760 if len(safertext) > 0:
|
|
|
761 safertext = safertext + "\n\n------\n" # transition allowed!
|
|
|
762 scr = [x for x in self.spacedScript if x.strip() > ""]
|
|
|
763 scr.insert(0, "\n\nScript::\n")
|
|
|
764 if len(scr) > 300:
|
|
|
765 scr = (
|
|
|
766 scr[:100]
|
|
|
767 + [" >300 lines - stuff deleted", " ......"]
|
|
|
768 + scr[-100:]
|
|
|
769 )
|
|
|
770 scr.append("\n")
|
|
|
771 safertext = safertext + "\n".join(scr)
|
|
|
772 self.newtool.help = safertext
|
|
|
773 self.newtool.version_command = f'echo "{self.args.tool_version}"'
|
|
|
774 std = gxtp.Stdios()
|
|
|
775 std1 = gxtp.Stdio()
|
|
|
776 std.append(std1)
|
|
|
777 self.newtool.stdios = std
|
|
|
778 requirements = gxtp.Requirements()
|
|
|
779 if self.args.packages:
|
|
|
780 try:
|
|
|
781 for d in self.args.packages.split(","):
|
|
|
782 ver = None
|
|
|
783 packg = None
|
|
|
784 d = d.replace("==", ":")
|
|
|
785 d = d.replace("=", ":")
|
|
|
786 if ":" in d:
|
|
|
787 packg, ver = d.split(":")
|
|
|
788 ver = ver.strip()
|
|
|
789 packg = packg.strip()
|
|
|
790 else:
|
|
|
791 packg = d.strip()
|
|
|
792 ver = None
|
|
|
793 if ver == "":
|
|
|
794 ver = None
|
|
|
795 if packg:
|
|
|
796 requirements.append(
|
|
|
797 gxtp.Requirement("package", packg.strip(), ver)
|
|
|
798 )
|
|
|
799 except Exception:
|
|
|
800 print(
|
|
|
801 "### malformed packages string supplied - cannot parse =",
|
|
|
802 self.args.packages,
|
|
|
803 )
|
|
|
804 sys.exit(2)
|
|
|
805 self.newtool.requirements = requirements
|
|
|
806 if self.args.parampass == "0":
|
|
|
807 self.doNoXMLparam()
|
|
|
808 else:
|
|
|
809 self.doXMLparam()
|
|
|
810 self.newtool.outputs = self.toutputs
|
|
|
811 self.newtool.inputs = self.tinputs
|
|
|
812 if self.args.script_path:
|
|
|
813 configfiles = gxtp.Configfiles()
|
|
|
814 configfiles.append(
|
|
|
815 gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))
|
|
|
816 )
|
|
|
817 self.newtool.configfiles = configfiles
|
|
|
818 tests = gxtp.Tests()
|
|
|
819 test_a = gxtp.Test()
|
|
|
820 for tp in self.testparam:
|
|
|
821 test_a.append(tp)
|
|
|
822 tests.append(test_a)
|
|
|
823 self.newtool.tests = tests
|
|
|
824 self.newtool.add_comment(
|
|
|
825 "Created by %s at %s using the Galaxy Tool Factory."
|
|
|
826 % (self.args.user_email, timenow())
|
|
|
827 )
|
|
|
828 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
|
|
|
829 exml0 = self.newtool.export()
|
|
|
830 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
|
|
|
831 if (
|
|
|
832 self.test_override
|
|
|
833 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
|
|
|
834 part1 = exml.split("<tests>")[0]
|
|
|
835 part2 = exml.split("</tests>")[1]
|
|
|
836 fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)
|
|
|
837 exml = fixed
|
|
|
838 # exml = exml.replace('range="1:"', 'range="1000:"')
|
|
|
839 with open("%s.xml" % self.tool_name, "w") as xf:
|
|
|
840 xf.write(exml)
|
|
|
841 xf.write("\n")
|
|
|
842 with open(self.args.untested_tool_out, 'w') as outf:
|
|
|
843 outf.write(exml)
|
|
|
844 outf.write('\n')
|
|
|
845 # ready for the tarball
|
|
|
846
|
|
|
847 def writeShedyml(self):
|
|
|
848 """for planemo"""
|
|
|
849 yuser = self.args.user_email.split("@")[0]
|
|
|
850 yfname = os.path.join(self.tooloutdir, ".shed.yml")
|
|
|
851 yamlf = open(yfname, "w")
|
|
|
852 odict = {
|
|
|
853 "name": self.tool_name,
|
|
|
854 "owner": yuser,
|
|
|
855 "type": "unrestricted",
|
|
|
856 "description": self.args.tool_desc,
|
|
|
857 "synopsis": self.args.tool_desc,
|
|
|
858 "category": "TF Generated Tools",
|
|
|
859 }
|
|
|
860 yaml.dump(odict, yamlf, allow_unicode=True)
|
|
|
861 yamlf.close()
|
|
|
862
|
|
|
863 def makeTool(self):
|
|
|
864 """write xmls and input samples into place"""
|
|
|
865 if self.args.parampass == 0:
|
|
|
866 self.doNoXMLparam()
|
|
|
867 else:
|
|
|
868 self.makeXML()
|
|
|
869 if self.args.script_path:
|
|
|
870 stname = os.path.join(self.tooloutdir, self.sfile)
|
|
|
871 if not os.path.exists(stname):
|
|
|
872 shutil.copyfile(self.sfile, stname)
|
|
|
873 xreal = "%s.xml" % self.tool_name
|
|
|
874 xout = os.path.join(self.tooloutdir, xreal)
|
|
|
875 shutil.copyfile(xreal, xout)
|
|
|
876 #xout = os.path.join(self.repdir, xreal)
|
|
|
877 #shutil.copyfile(xreal, xout)
|
|
|
878 for p in self.infiles:
|
|
|
879 pth = p["name"]
|
|
|
880 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
|
|
|
881 shutil.copyfile(pth, dest)
|
|
|
882 dest = os.path.join(
|
|
|
883 self.repdir, "%s_sample.%s" % (p["infilename"], p["format"])
|
|
|
884 )
|
|
|
885 shutil.copyfile(pth, dest)
|
|
|
886
|
|
|
887 def makeToolTar(self, report_fail=False):
|
|
|
888 """move outputs into test-data and prepare the tarball"""
|
|
|
889 excludeme = "_planemo_test_report.html"
|
|
|
890
|
|
|
891 def exclude_function(tarinfo):
|
|
|
892 filename = tarinfo.name
|
|
|
893 return None if filename.endswith(excludeme) else tarinfo
|
|
|
894
|
|
|
895 for p in self.outfiles:
|
|
|
896 oname = p["name"]
|
|
|
897 tdest = os.path.join(self.testdir, "%s_sample" % oname)
|
|
|
898 src = os.path.join(self.testdir, oname)
|
|
|
899 if not os.path.isfile(tdest):
|
|
|
900 if os.path.isfile(src):
|
|
|
901 shutil.copyfile(src, tdest)
|
|
|
902 dest = os.path.join(self.repdir, "%s.sample.%s" % (oname,p['format']))
|
|
|
903 shutil.copyfile(src, dest)
|
|
|
904 else:
|
|
|
905 if report_fail:
|
|
|
906 print(
|
|
|
907 "###Tool may have failed - output file %s not found in testdir after planemo run %s."
|
|
|
908 % (tdest, self.testdir)
|
|
|
909 )
|
|
|
910 tf = tarfile.open(self.newtarpath, "w:gz")
|
|
|
911 tf.add(
|
|
|
912 name=self.tooloutdir,
|
|
|
913 arcname=self.tool_name,
|
|
|
914 filter=exclude_function,
|
|
|
915 )
|
|
|
916 shutil.copy(self.newtarpath, os.path.join(self.tooloutdir, f"{self.tool_name}_untested.toolshed.gz"))
|
|
|
917 tf.close()
|
|
|
918
|
|
|
919
|
|
|
920 def main():
|
|
|
921 """
|
|
|
922 This is a Galaxy wrapper.
|
|
|
923 It expects to be called by a special purpose tool.xml
|
|
|
924
|
|
|
925 """
|
|
|
926 parser = argparse.ArgumentParser()
|
|
|
927 a = parser.add_argument
|
|
|
928 a("--script_path", default=None)
|
|
|
929 a("--history_test", default=None)
|
|
|
930 a("--cl_user_suffix", default=None)
|
|
|
931 a("--sysexe", default=None)
|
|
|
932 a("--packages", default=None)
|
|
|
933 a("--tool_name", default="newtool")
|
|
|
934 a("--tool_dir", default=None)
|
|
|
935 a("--input_files", default=[], action="append")
|
|
|
936 a("--output_files", default=[], action="append")
|
|
|
937 a("--user_email", default="Unknown")
|
|
|
938 a("--bad_user", default=None)
|
|
|
939 a("--help_text", default=None)
|
|
|
940 a("--tool_desc", default=None)
|
|
|
941 a("--tool_version", default=None)
|
|
|
942 a("--citations", default=None)
|
|
|
943 a("--command_override", default=None)
|
|
|
944 a("--test_override", default=None)
|
|
|
945 a("--additional_parameters", action="append", default=[])
|
|
|
946 a("--selecttext_parameters", action="append", default=[])
|
|
|
947 a("--edit_additional_parameters", action="store_true", default=False)
|
|
|
948 a("--parampass", default="positional")
|
|
|
949 a("--tfout", default="./tfout")
|
|
|
950 a("--galaxy_root", default="/galaxy-central")
|
|
|
951 a("--galaxy_venv", default="/galaxy_venv")
|
|
|
952 a("--collection", action="append", default=[])
|
|
|
953 a("--include_tests", default=False, action="store_true")
|
|
|
954 a("--install", default="1")
|
|
|
955 a("--admin_only", default=False, action="store_true")
|
|
|
956 a("--untested_tool_out", default=None)
|
|
|
957 a("--local_tools", default="tools") # relative to $__root_dir__
|
|
|
958 a("--tool_conf_path", default="config/tool_conf.xml") # relative to $__root_dir__
|
|
|
959 args = parser.parse_args()
|
|
|
960 if args.admin_only:
|
|
|
961 assert not args.bad_user, (
|
|
|
962 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
|
|
|
963 admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
|
|
|
964 % (args.bad_user, args.bad_user)
|
|
|
965 )
|
|
|
966 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
|
|
|
967 r = Tool_Factory(args)
|
|
|
968 r.writeShedyml()
|
|
|
969 r.makeTool()
|
|
|
970 r.makeToolTar()
|
|
|
971 if args.install == "1":
|
|
|
972 TCU = Tool_Conf_Updater(
|
|
|
973 args=args,
|
|
|
974 local_tool_dir=args.local_tools,
|
|
|
975 new_tool_archive_path=r.newtarpath,
|
|
|
976 tool_conf_path=args.tool_conf_path,
|
|
|
977 new_tool_name=r.tool_name,
|
|
|
978 run_test = args.run_test
|
|
|
979 )
|
|
|
980
|
|
|
981 if __name__ == "__main__":
|
|
|
982 main()
|
