annotate toolfactory/rgToolFactory2.py @ 115:bf7b4b603bf9 draft

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author fubar
date Sat, 05 Dec 2020 04:02:18 +0000
parents e0cf315853cf
children b1a29d3d50d6
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1 # replace with shebang for biocontainer
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2 # see https://github.com/fubar2/toolfactory
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3 #
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4 # copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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5 #
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6 # all rights reserved
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7 # Licensed under the LGPL
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8 # suggestions for improvement and bug fixes welcome at
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9 # https://github.com/fubar2/toolfactory
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10 #
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11 # July 2020: BCC was fun and I feel like rip van winkle after 5 years.
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12 # Decided to
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13 # 1. Fix the toolfactory so it works - done for simplest case
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14 # 2. Fix planemo so the toolfactory function works
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15 # 3. Rewrite bits using galaxyxml functions where that makes sense - done
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16 #
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17 # uses planemo in a biodocker sort of image as a requirement
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18 # otherwise planemo seems to leak dependencies back into the
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19 # calling venv. Hilarity ensues.
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22
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23 import argparse
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24 import copy
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25 import datetime
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26 import grp
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27 import json
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28 import logging
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29 import os
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30 import re
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31 import shutil
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32 import subprocess
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33 import sys
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34 import tarfile
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35 import tempfile
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36 import time
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39 from bioblend import ConnectionError
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40 from bioblend import toolshed
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41
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42 import docker
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43
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44 import galaxyxml.tool as gxt
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45 import galaxyxml.tool.parameters as gxtp
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46
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47 import lxml
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49 import yaml
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51 myversion = "V2.1 July 2020"
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52 verbose = True
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53 debug = True
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54 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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55 ourdelim = "~~~"
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56
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57 # --input_files="$intab.input_files~~~$intab.input_CL~~~$intab.input_formats\
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58 #~~~$intab.input_label~~~$intab.input_help"
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59 IPATHPOS = 0
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60 ICLPOS = 1
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61 IFMTPOS = 2
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62 ILABPOS = 3
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63 IHELPOS = 4
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64 IOCLPOS = 5
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66 # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
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67 ONAMEPOS = 0
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68 OFMTPOS = 1
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69 OCLPOS = 2
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70 OTESTPOS = 3
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71 OOCLPOS = 4
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74 # --additional_parameters="$i.param_name~~~$i.param_value~~~
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75 # $i.param_label~~~$i.param_help~~~$i.param_type~~~$i.CL~~~i$.param_CLoverride"
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76 ANAMEPOS = 0
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77 AVALPOS = 1
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78 ALABPOS = 2
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79 AHELPPOS = 3
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80 ATYPEPOS = 4
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81 ACLPOS = 5
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82 AOVERPOS = 6
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83 AOCLPOS = 7
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86 foo = len(lxml.__version__)
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87 # fug you, flake8. Say my name!
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88 FAKEEXE = "~~~REMOVE~~~ME~~~"
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89 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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90 # with override.
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93 def timenow():
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94 """return current time as a string"""
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95 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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98 def quote_non_numeric(s):
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99 """return a prequoted string for non-numerics
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100 useful for perl and Rscript parameter passing?
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101 """
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102 try:
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103 _ = float(s)
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104 return s
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105 except ValueError:
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106 return '"%s"' % s
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109 html_escape_table = {"&": "&amp;", ">": "&gt;", "<": "&lt;", "$": r"\$","#":"&#35;", "$":"&#36;"}
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110 cheetah_escape_table = {"$": "\$","#":"\#"}
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112 def html_escape(text):
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113 """Produce entities within text."""
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114 return "".join([html_escape_table.get(c, c) for c in text])
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115
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116 def cheetah_escape(text):
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117 """Produce entities within text."""
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118 return "".join([cheetah_escape_table.get(c, c) for c in text])
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119
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121 def html_unescape(text):
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122 """Revert entities within text. Multiple character targets so use replace"""
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123 t = text.replace("&amp;", "&")
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124 t = t.replace("&gt;", ">")
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125 t = t.replace("&lt;", "<")
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126 t = t.replace("\\$", "$")
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127 t = t.replace("&#36;","$")
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128 t = t.replace("&#35;","#")
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129 return t
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131
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132 def parse_citations(citations_text):
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133 """"""
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134 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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135 citation_tuples = []
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136 for citation in citations:
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137 if citation.startswith("doi"):
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138 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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139 else:
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140 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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141 return citation_tuples
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142
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143
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144 class ScriptRunner:
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145 """Wrapper for an arbitrary script
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146 uses galaxyxml
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147
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148 """
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149
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150 def __init__(self, args=None):
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151 """
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152 prepare command line cl for running the tool here
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153 and prepare elements needed for galaxyxml tool generation
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154 """
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155 self.ourcwd = os.getcwd()
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156 self.ourenv = copy.deepcopy(os.environ)
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157 self.infiles = [x.split(ourdelim) for x in args.input_files]
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158 self.outfiles = [x.split(ourdelim) for x in args.output_files]
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159 self.addpar = [x.split(ourdelim) for x in args.additional_parameters]
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160 self.args = args
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161 self.cleanuppar()
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162 self.lastclredirect = None
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163 self.lastxclredirect = None
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164 self.cl = []
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165 self.xmlcl = []
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166 self.is_positional = self.args.parampass == "positional"
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167 if self.args.sysexe:
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168 self.executeme = self.args.sysexe
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169 else:
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170 if self.args.packages:
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171 self.executeme = self.args.packages.split(",")[0].split(":")[0]
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172 else:
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173 self.executeme = None
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174 aCL = self.cl.append
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175 aXCL = self.xmlcl.append
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176 assert args.parampass in [
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177 "0",
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178 "argparse",
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179 "positional",
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180 ], 'args.parampass must be "0","positional" or "argparse"'
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181 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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182 self.tool_id = self.tool_name
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183 self.newtool = gxt.Tool(
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184 self.tool_name,
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185 self.tool_id,
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186 self.args.tool_version,
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187 self.args.tool_desc,
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188 FAKEEXE,
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189 )
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190 self.newtarpath = "toolfactory_%s.tgz" % self.tool_name
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191 self.tooloutdir = "./tfout"
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192 self.repdir = "./TF_run_report_tempdir"
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193 self.testdir = os.path.join(self.tooloutdir, "test-data")
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194 if not os.path.exists(self.tooloutdir):
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195 os.mkdir(self.tooloutdir)
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196 if not os.path.exists(self.testdir):
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197 os.mkdir(self.testdir)
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198 if not os.path.exists(self.repdir):
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199 os.mkdir(self.repdir)
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200 self.tinputs = gxtp.Inputs()
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201 self.toutputs = gxtp.Outputs()
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202 self.testparam = []
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203 if self.args.script_path:
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204 self.prepScript()
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205 if self.args.command_override:
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206 scos = open(self.args.command_override, "r").readlines()
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207 self.command_override = [x.rstrip() for x in scos]
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208 else:
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209 self.command_override = None
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210 if self.args.test_override:
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211 stos = open(self.args.test_override, "r").readlines()
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212 self.test_override = [x.rstrip() for x in stos]
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213 else:
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214 self.test_override = None
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215 if self.args.cl_prefix: # DIY CL start
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216 clp = self.args.cl_prefix.split(" ")
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217 for c in clp:
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218 aCL(c)
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219 aXCL(c)
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220 else:
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221 if self.args.script_path:
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222 aCL(self.executeme)
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223 aCL(self.sfile)
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224 aXCL(self.executeme)
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225 aXCL("$runme")
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226 else:
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227 aCL(self.executeme)
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228 aXCL(self.executeme)
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229 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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230 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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231
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232 if self.args.parampass == "0":
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233 self.clsimple()
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234 else:
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235 clsuffix = []
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236 xclsuffix = []
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237 for i, p in enumerate(self.infiles):
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238 if p[IOCLPOS] == "STDIN":
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239 appendme = [
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240 p[IOCLPOS],
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241 p[ICLPOS],
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242 p[IPATHPOS],
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243 "< %s" % p[IPATHPOS],
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244 ]
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245 xappendme = [
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246 p[IOCLPOS],
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247 p[ICLPOS],
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248 p[IPATHPOS],
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249 "< $%s" % p[ICLPOS],
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250 ]
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251 else:
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252 appendme = [p[IOCLPOS], p[ICLPOS], p[IPATHPOS], ""]
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253 xappendme = [p[IOCLPOS], p[ICLPOS], "$%s" % p[ICLPOS], ""]
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254 clsuffix.append(appendme)
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255 xclsuffix.append(xappendme)
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256 for i, p in enumerate(self.outfiles):
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257 if p[OOCLPOS] == "STDOUT":
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258 self.lastclredirect = [">", p[ONAMEPOS]]
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259 self.lastxclredirect = [">", "$%s" % p[OCLPOS]]
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260 else:
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261 clsuffix.append([p[ONAMEPOS], p[ONAMEPOS], p[ONAMEPOS], ""])
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262 xclsuffix.append([p[ONAMEPOS], p[ONAMEPOS], "$%s" % p[ONAMEPOS], ""])
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263 for p in self.addpar:
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264 clsuffix.append([p[AOCLPOS], p[ACLPOS], p[AVALPOS], p[AOVERPOS]])
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265 xclsuffix.append(
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266 [p[AOCLPOS], p[ACLPOS], '"$%s"' % p[ANAMEPOS], p[AOVERPOS]]
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267 )
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268 clsuffix.sort()
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269 xclsuffix.sort()
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270 self.xclsuffix = xclsuffix
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271 self.clsuffix = clsuffix
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272 if self.args.parampass == "positional":
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273 self.clpositional()
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274 else:
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275 self.clargparse()
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276
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277 def prepScript(self):
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278 rx = open(self.args.script_path, "r").readlines()
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279 rx = [x.rstrip() for x in rx]
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280 rxcheck = [x.strip() for x in rx if x.strip() > ""]
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281 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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282 self.script = "\n".join(rx)
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283 fhandle, self.sfile = tempfile.mkstemp(
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284 prefix=self.tool_name, suffix="_%s" % (self.executeme)
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285 )
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286 tscript = open(self.sfile, "w")
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287 tscript.write(self.script)
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288 tscript.close()
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289 self.escapedScript = [cheetah_escape(x) for x in rx]
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290 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
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291 art = "%s.%s" % (self.tool_name, self.executeme)
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292 artifact = open(art, "wb")
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293 artifact.write(bytes('\n'.join(self.escapedScript),'utf8'))
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294 artifact.close()
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295
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296 def cleanuppar(self):
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297 """ positional parameters are complicated by their numeric ordinal"""
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298 for i, p in enumerate(self.infiles):
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299 infp = copy.copy(p)
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300 if self.args.parampass == "positional":
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301 assert infp[
75
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302 ICLPOS
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303 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
111
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304 infp[ICLPOS],
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diff changeset
305 infp[ILABPOS],
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306 )
111
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307 icl = infp[ICLPOS]
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308 infp.append(icl)
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309 if infp[ICLPOS].isdigit() or self.args.parampass == "0":
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310 scl = "input%d" % (i + 1)
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311 infp[ICLPOS] = scl
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312 self.infiles[i] = infp
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313 for i, p in enumerate(
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314 self.outfiles
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315 ):
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316 if self.args.parampass == "positional" and p[OCLPOS].upper() != "STDOUT":
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317 assert p[
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318 OCLPOS
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319 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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320 p[OCLPOS],
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321 p[ONAMEPOS],
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322 )
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323 p.append(p[OCLPOS]) # keep copy
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324 if p[OOCLPOS].isdigit() or p[OOCLPOS].upper() == "STDOUT":
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325 scl = p[ONAMEPOS]
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326 p[OCLPOS] = scl
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327 self.outfiles[i] = p
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328 for i, p in enumerate(self.addpar):
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329 if self.args.parampass == "positional":
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330 assert p[
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331 ACLPOS
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332 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
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parents: 74
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333 p[ACLPOS],
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334 p[ANAMEPOS],
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335 )
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336 p.append(p[ACLPOS])
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337 if p[ACLPOS].isdigit():
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338 scl = "input%s" % p[ACLPOS]
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339 p[ACLPOS] = scl
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340 self.addpar[i] = p
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341
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342 def clsimple(self):
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343 """no parameters - uses < and > for i/o"""
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344 aCL = self.cl.append
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345 aXCL = self.xmlcl.append
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346
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347 if len(self.infiles) > 0:
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348 aCL("<")
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349 aCL(self.infiles[0][IPATHPOS])
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350 aXCL("<")
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351 aXCL("$%s" % self.infiles[0][ICLPOS])
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352 if len(self.outfiles) > 0:
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353 aCL(">")
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354 aCL(self.outfiles[0][OCLPOS])
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355 aXCL(">")
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356 aXCL("$%s" % self.outfiles[0][ONAMEPOS])
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357
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358 def clpositional(self):
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359 # inputs in order then params
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360 aCL = self.cl.append
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361 for (o_v, k, v, koverride) in self.clsuffix:
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parents:
diff changeset
362 if " " in v:
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parents:
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363 aCL("%s" % v)
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parents:
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364 else:
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365 aCL(v)
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366 aXCL = self.xmlcl.append
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367 for (o_v, k, v, koverride) in self.xclsuffix:
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368 aXCL(v)
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369 if self.lastxclredirect:
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370 aXCL(self.lastxclredirect[0])
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371 aXCL(self.lastxclredirect[1])
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372
48
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373
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374 def clargparse(self):
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diff changeset
375 """argparse style"""
48
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376 aCL = self.cl.append
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377 aXCL = self.xmlcl.append
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378 # inputs then params in argparse named form
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379
48
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380 for (o_v, k, v, koverride) in self.xclsuffix:
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parents:
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381 if koverride > "":
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parents:
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382 k = koverride
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parents:
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383 elif len(k.strip()) == 1:
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384 k = "-%s" % k
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parents:
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385 else:
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386 k = "--%s" % k
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parents:
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387 aXCL(k)
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parents:
diff changeset
388 aXCL(v)
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diff changeset
389 for (o_v, k, v, koverride) in self.clsuffix:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
390 if koverride > "":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
391 k = koverride
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
392 elif len(k.strip()) == 1:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
393 k = "-%s" % k
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fubar
parents:
diff changeset
394 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
395 k = "--%s" % k
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fubar
parents:
diff changeset
396 aCL(k)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
397 aCL(v)
112
5509dc4c1cf2 Uploaded
fubar
parents: 111
diff changeset
398
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
399
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
400 def getNdash(self, newname):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
401 if self.is_positional:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
402 ndash = 0
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
403 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
404 ndash = 2
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
405 if len(newname) < 2:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
406 ndash = 1
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
407 return ndash
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
408
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fubar
parents:
diff changeset
409 def doXMLparam(self):
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fubar
parents:
diff changeset
410 """flake8 made me do this..."""
111
223b78754735 Uploaded
fubar
parents: 110
diff changeset
411 for p in self.outfiles: # --output_files "$otab.history_name~~~$otab.history_format~~~$otab.history_CL~~~$otab.history_test"
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
412 newname, newfmt, newcl, test, oldcl = p
108
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
413 test = test.strip()
48
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fubar
parents:
diff changeset
414 ndash = self.getNdash(newcl)
111
223b78754735 Uploaded
fubar
parents: 110
diff changeset
415 aparm = gxtp.OutputData(name=newname, format=newfmt, num_dashes=ndash, label=newcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
416 aparm.positional = self.is_positional
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fubar
parents:
diff changeset
417 if self.is_positional:
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
418 if oldcl.upper() == "STDOUT":
48
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fubar
parents:
diff changeset
419 aparm.positional = 9999999
111
223b78754735 Uploaded
fubar
parents: 110
diff changeset
420 aparm.command_line_override = "> $%s" % newname
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
421 else:
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fubar
parents:
diff changeset
422 aparm.positional = int(oldcl)
111
223b78754735 Uploaded
fubar
parents: 110
diff changeset
423 aparm.command_line_override = "$%s" % newname
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
424 self.toutputs.append(aparm)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
425 ld = None
108
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
426 if test.strip() > "":
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
427 if test.startswith("diff"):
108
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
428 c = "diff"
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
429 ld = 0
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
430 if test.split(":")[1].isdigit:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
431 ld = int(test.split(":")[1])
108
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
432 tp = gxtp.TestOutput(
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
433 name=newcl,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
434 value="%s_sample" % newcl,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
435 format=newfmt,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
436 compare= c,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
437 lines_diff=ld,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
438 )
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
439 elif test.startswith("sim_size"):
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
440 c = "sim_size"
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
441 tn = test.split(":")[1].strip()
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
442 if tn > '':
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
443 if '.' in tn:
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
444 delta = None
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
445 delta_frac = min(1.0,float(tn))
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
446 else:
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
447 delta = int(tn)
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
448 delta_frac = None
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
449 tp = gxtp.TestOutput(
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
450 name=newcl,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
451 value="%s_sample" % newcl,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
452 format=newfmt,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
453 compare= c,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
454 delta = delta,
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
455 delta_frac = delta_frac
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
456 )
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
457 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
458 for p in self.infiles:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
459 newname = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
460 newfmt = p[IFMTPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
461 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
462 if not len(p[ILABPOS]) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
463 alab = p[ICLPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
464 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
465 alab = p[ILABPOS]
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
466 aninput = gxtp.DataParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
467 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
468 optional=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
469 label=alab,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
470 help=p[IHELPOS],
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
471 format=newfmt,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
472 multiple=False,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
473 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
474 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
475 aninput.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
476 self.tinputs.append(aninput)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
477 tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
478 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
479 for p in self.addpar:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
480 newname, newval, newlabel, newhelp, newtype, newcl, override, oldcl = p
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
481 if not len(newlabel) > 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
482 newlabel = newname
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
483 ndash = self.getNdash(newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
484 if newtype == "text":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
485 aparm = gxtp.TextParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
486 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
487 label=newlabel,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
488 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
489 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
490 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
491 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
492 elif newtype == "integer":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
493 aparm = gxtp.IntegerParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
494 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
495 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
496 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
497 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
498 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
499 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
500 elif newtype == "float":
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
501 aparm = gxtp.FloatParam(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
502 newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
503 label=newname,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
504 help=newhelp,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
505 value=newval,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
506 num_dashes=ndash,
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
507 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
508 else:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
509 raise ValueError(
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
510 'Unrecognised parameter type "%s" for\
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
511 additional parameter %s in makeXML'
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
512 % (newtype, newname)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
513 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
514 aparm.positional = self.is_positional
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
515 if self.is_positional:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
516 aparm.positional = int(oldcl)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
517 self.tinputs.append(aparm)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
518 tparm = gxtp.TestParam(newname, value=newval)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
519 self.testparam.append(tparm)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
520
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
521 def doNoXMLparam(self):
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
522 """filter style package - stdin to stdout"""
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
523 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
524 alab = self.infiles[0][ILABPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
525 if len(alab) == 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
526 alab = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
527 max1s = (
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
528 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
529 % str(self.infiles)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
530 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
531 assert len(self.infiles) == 1, max1s
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
532 newname = self.infiles[0][ICLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
533 aninput = gxtp.DataParam(
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
534 newname,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
535 optional=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
536 label=alab,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
537 help=self.infiles[0][IHELPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
538 format=self.infiles[0][IFMTPOS],
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
539 multiple=False,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
540 num_dashes=0,
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
541 )
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
542 aninput.command_line_override = "< $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
543 aninput.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
544 self.tinputs.append(aninput)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
545 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
546 self.testparam.append(tp)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
547 if len(self.outfiles) > 0:
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
548 newname = self.outfiles[0][OCLPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
549 newfmt = self.outfiles[0][OFMTPOS]
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
550 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
551 anout.command_line_override = "> $%s" % newname
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
552 anout.positional = self.is_positional
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
553 self.toutputs.append(anout)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
554 tp = gxtp.TestOutput(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
555 name=newname, value="%s_sample" % newname, format=newfmt
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
556 )
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
557 self.testparam.append(tp)
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
558
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
559 def makeXML(self):
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
560 """
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
561 Create a Galaxy xml tool wrapper for the new script
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
562 Uses galaxyhtml
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
563 Hmmm. How to get the command line into correct order...
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
564 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
565 if self.command_override:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
566 self.newtool.command_override = self.command_override # config file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
567 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
568 self.newtool.command_override = self.xmlcl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
569 if self.args.help_text:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
570 helptext = open(self.args.help_text, "r").readlines()
108
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
571 safertext = "\n".join([cheetah_escape(x) for x in helptext])
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
572 if self.args.script_path:
110
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
573 scr = [x for x in self.spacedScript if x.strip() > ""]
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
574 scr.insert(0,'\n------\n\nScript::\n')
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
575 if len(scr) > 300:
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
576 scr = (
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
577 scr[:100]
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
578 + [">300 lines - stuff deleted", "......"]
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
579 + scr[-100:]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
580 )
111
223b78754735 Uploaded
fubar
parents: 110
diff changeset
581 scr.append('\n')
110
ab2474035f81 Uploaded
fubar
parents: 109
diff changeset
582 safertext = safertext + "\n".join(scr)
108
e878bfc6b80c Uploaded
fubar
parents: 107
diff changeset
583 self.newtool.help = safertext
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
584 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
585 self.newtool.help = (
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
586 "Please ask the tool author (%s) for help \
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
587 as none was supplied at tool generation\n"
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
588 % (self.args.user_email)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
589 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
590 self.newtool.version_command = None # do not want
48
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parents:
diff changeset
591 requirements = gxtp.Requirements()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
592 if self.args.packages:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
593 for d in self.args.packages.split(","):
113
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fubar
parents: 112
diff changeset
594 ver = ''
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parents: 112
diff changeset
595 d = d.replace('==',':')
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parents: 112
diff changeset
596 d = d.replace('=',':')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
597 if ":" in d:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
598 packg, ver = d.split(":")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
599 else:
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
600 packg = d
50
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fubar
parents: 49
diff changeset
601 requirements.append(
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
602 gxtp.Requirement("package", packg.strip(), ver.strip())
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
603 )
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fubar
parents: 49
diff changeset
604 self.newtool.requirements = requirements
48
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fubar
parents:
diff changeset
605 if self.args.parampass == "0":
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fubar
parents:
diff changeset
606 self.doNoXMLparam()
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fubar
parents:
diff changeset
607 else:
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parents:
diff changeset
608 self.doXMLparam()
50
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fubar
parents: 49
diff changeset
609 self.newtool.outputs = self.toutputs
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fubar
parents: 49
diff changeset
610 self.newtool.inputs = self.tinputs
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fubar
parents: 49
diff changeset
611 if self.args.script_path:
48
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parents:
diff changeset
612 configfiles = gxtp.Configfiles()
109
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parents: 108
diff changeset
613 configfiles.append(gxtp.Configfile(name="runme", text="\n".join(self.escapedScript)))
50
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fubar
parents: 49
diff changeset
614 self.newtool.configfiles = configfiles
48
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fubar
parents:
diff changeset
615 tests = gxtp.Tests()
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parents:
diff changeset
616 test_a = gxtp.Test()
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fubar
parents:
diff changeset
617 for tp in self.testparam:
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parents:
diff changeset
618 test_a.append(tp)
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parents:
diff changeset
619 tests.append(test_a)
50
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fubar
parents: 49
diff changeset
620 self.newtool.tests = tests
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fubar
parents: 49
diff changeset
621 self.newtool.add_comment(
48
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fubar
parents:
diff changeset
622 "Created by %s at %s using the Galaxy Tool Factory."
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
623 % (self.args.user_email, timenow())
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parents:
diff changeset
624 )
50
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fubar
parents: 49
diff changeset
625 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
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fubar
parents: 49
diff changeset
626 self.newtool.add_comment(
108
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parents: 107
diff changeset
627 "Cite: Creating re-usable tools from scripts doi:10.1093/bioinformatics/bts573"
48
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fubar
parents:
diff changeset
628 )
50
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fubar
parents: 49
diff changeset
629 exml0 = self.newtool.export()
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
630 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
631 if (
bf432f4486c7 Uploaded
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parents: 49
diff changeset
632 self.test_override
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fubar
parents: 49
diff changeset
633 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
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fubar
parents: 49
diff changeset
634 part1 = exml.split("<tests>")[0]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
635 part2 = exml.split("</tests>")[1]
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parents: 49
diff changeset
636 fixed = "%s\n%s\n%s" % (part1, self.test_override, part2)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
637 exml = fixed
63
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parents: 62
diff changeset
638 exml = exml.replace('range="1:"', 'range="1000:"')
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
639 xf = open("%s.xml" % self.tool_name, "w")
48
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fubar
parents:
diff changeset
640 xf.write(exml)
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fubar
parents:
diff changeset
641 xf.write("\n")
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fubar
parents:
diff changeset
642 xf.close()
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fubar
parents:
diff changeset
643 # ready for the tarball
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fubar
parents:
diff changeset
644
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fubar
parents:
diff changeset
645 def run(self):
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fubar
parents:
diff changeset
646 """
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
647 generate test outputs by running a command line
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
648 won't work if command or test override in play - planemo is the
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
649 easiest way to generate test outputs for that case so is
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
650 automagically selected
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
651 """
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fubar
parents:
diff changeset
652 scl = " ".join(self.cl)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
653 err = None
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
654 if self.args.parampass != "0":
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
655 if os.path.exists(self.elog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
656 ste = open(self.elog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
657 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
658 ste = open(self.elog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
659 if self.lastclredirect:
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
660 sto = open(self.lastclredirect[1], "wb") # is name of an output file
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
661 else:
56
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
662 if os.path.exists(self.tlog):
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
663 sto = open(self.tlog, "a")
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
664 else:
68fbdbe35f08 Uploaded
fubar
parents: 51
diff changeset
665 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
666 sto.write(
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
667 "## Executing Toolfactory generated command line = %s\n" % scl
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
668 )
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
669 sto.flush()
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
670 subp = subprocess.run(
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
671 self.cl, env=self.ourenv, shell=False, stdout=sto, stderr=ste
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
672 )
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
673 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
674 ste.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
675 retval = subp.returncode
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
676 else: # work around special case - stdin and write to stdout
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
677 if len(self.infiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
678 sti = open(self.infiles[0][IPATHPOS], "rb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
679 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
680 sti = sys.stdin
62
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
681 if len(self.outfiles) > 0:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
682 sto = open(self.outfiles[0][ONAMEPOS], "wb")
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
683 else:
881bd8c81ac9 Uploaded
fubar
parents: 57
diff changeset
684 sto = sys.stdout
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
685 subp = subprocess.run(
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
686 self.cl, env=self.ourenv, shell=False, stdout=sto, stdin=sti
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
687 )
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
688 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
689 retval = subp.returncode
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
690 sto.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
691 sti.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
692 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
693 os.unlink(self.tlog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
694 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
695 os.unlink(self.elog)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
696 if retval != 0 and err: # problem
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
697 sys.stderr.write(err)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
698 logging.debug("run done")
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
699 return retval
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
700
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
701 def copy_to_container(self, src, dest, container):
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
702 """Recreate the src directory tree at dest - full path included"""
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
703 idir = os.getcwd()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
704 workdir = os.path.dirname(src)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
705 os.chdir(workdir)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
706 _, tfname = tempfile.mkstemp(suffix=".tar")
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
707 tar = tarfile.open(tfname, mode="w")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
708 srcb = os.path.basename(src)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
709 tar.add(srcb)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
710 tar.close()
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
711 data = open(tfname, "rb").read()
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
712 container.put_archive(dest, data)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
713 os.unlink(tfname)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
714 os.chdir(idir)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
715
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
716 def copy_from_container(self, src, dest, container):
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
717 """recreate the src directory tree at dest using docker sdk"""
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
718 os.makedirs(dest, exist_ok=True)
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
719 _, tfname = tempfile.mkstemp(suffix=".tar")
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
720 tf = open(tfname, "wb")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
721 bits, stat = container.get_archive(src)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
722 for chunk in bits:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
723 tf.write(chunk)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
724 tf.close()
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
725 tar = tarfile.open(tfname, "r")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
726 tar.extractall(dest)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
727 tar.close()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
728 os.unlink(tfname)
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
729
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
730 def planemo_biodocker_test(self):
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
731 """planemo currently leaks dependencies if used in the same container and gets unhappy after a
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
732 first successful run. https://github.com/galaxyproject/planemo/issues/1078#issuecomment-731476930
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
733
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
734 Docker biocontainer has planemo with caches filled to save repeated downloads
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
735
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
736
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
737 """
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
738
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
739 def prun(container, tout, cl, user="biodocker"):
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
740 rlog = container.exec_run(cl, user=user)
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
741 slogl = str(rlog).split("\\n")
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
742 slog = "\n".join(slogl)
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
743 tout.write(f"## got rlog {slog} from {cl}\n")
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
744
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
745 if os.path.exists(self.tlog):
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
746 tout = open(self.tlog, "a")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
747 else:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
748 tout = open(self.tlog, "w")
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
749 planemoimage = "quay.io/fubar2/planemo-biocontainer"
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
750 xreal = "%s.xml" % self.tool_name
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
751 repname = f"{self.tool_name}_planemo_test_report.html"
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
752 ptestrep_path = os.path.join(self.repdir, repname)
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
753 tool_name = self.tool_name
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
754 client = docker.from_env()
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
755 tvol = client.volumes.create()
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
756 tvolname = tvol.name
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
757 destdir = "/toolfactory/ptest"
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
758 imrep = os.path.join(destdir, repname)
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
759 # need to keep the container running so keep it open with tail -f.
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
760 # will stop and destroy it when we are done
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
761 container = client.containers.run(
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
762 planemoimage,
114
e0cf315853cf Uploaded
fubar
parents: 113
diff changeset
763 "sleep 120m",
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
764 detach=True,
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
765 user="biodocker",
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
766 volumes={f"{tvolname}": {"bind": "/toolfactory", "mode": "rw"}},
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
767 )
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
768 cl = f"mkdir -p {destdir}"
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
769 prun(container, tout, cl, user="root")
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
770 # that's how hard it is to get root on a biodocker container :(
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
771 cl = f"rm -rf {destdir}/*"
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
772 prun(container, tout, cl, user="root")
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
773 ptestpath = os.path.join(destdir, "tfout", xreal)
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
774 self.copy_to_container(self.tooloutdir, destdir, container)
107
18e616939a91 Uploaded
fubar
parents: 106
diff changeset
775 cl = "chown -R biodocker /toolfactory"
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
776 prun(container, tout, cl, user="root")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
777 rlog = container.exec_run(f"ls -la {destdir}")
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
778 ptestcl = f"planemo test --update_test_data --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
779 try:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
780 rlog = container.exec_run(ptestcl)
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
781 # fails because test outputs missing but updates the test-data directory
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
782 except:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
783 e = sys.exc_info()[0]
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
784 tout.write(f"#### error: {e} from {ptestcl}\n")
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
785 cl = f"planemo test --test_output {imrep} --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
786 try:
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
787 prun(container, tout, cl)
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
788 except:
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
789 pass
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
790 testouts = tempfile.mkdtemp(suffix=None, prefix="tftemp", dir=".")
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
791 self.copy_from_container(destdir, testouts, container)
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
792 src = os.path.join(testouts, "ptest")
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
793 if os.path.isdir(src):
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
794 shutil.copytree(src, ".", dirs_exist_ok=True)
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
795 src = repname
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
796 if os.path.isfile(repname):
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
797 shutil.copyfile(src, ptestrep_path)
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
798 else:
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
799 tout.write(f"No output from run to shutil.copytree in {src}\n")
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
800 tout.close()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
801 container.stop()
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
802 container.remove()
103
2ca51677d6d1 Uploaded
fubar
parents: 102
diff changeset
803 tvol.remove()
115
bf7b4b603bf9 Uploaded
fubar
parents: 114
diff changeset
804 shutil.rmtree(testouts) # leave for debugging
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
805
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
806 def shedLoad(self):
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
807 """
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
808 use bioblend to create new repository
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
809 or update existing
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
810
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
811 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
812 if os.path.exists(self.tlog):
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
813 sto = open(self.tlog, "a")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
814 else:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
815 sto = open(self.tlog, "w")
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
816
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
817 ts = toolshed.ToolShedInstance(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
818 url=self.args.toolshed_url, key=self.args.toolshed_api_key, verify=False
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
819 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
820 repos = ts.repositories.get_repositories()
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
821 rnames = [x.get("name", "?") for x in repos]
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
822 rids = [x.get("id", "?") for x in repos]
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
823 tfcat = "ToolFactory generated tools"
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
824 if self.tool_name not in rnames:
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
825 tscat = ts.categories.get_categories()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
826 cnames = [x.get("name", "?").strip() for x in tscat]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
827 cids = [x.get("id", "?") for x in tscat]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
828 catID = None
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
829 if tfcat.strip() in cnames:
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
830 ci = cnames.index(tfcat)
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
831 catID = cids[ci]
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
832 res = ts.repositories.create_repository(
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
833 name=self.args.tool_name,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
834 synopsis="Synopsis:%s" % self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
835 description=self.args.tool_desc,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
836 type="unrestricted",
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
837 remote_repository_url=self.args.toolshed_url,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
838 homepage_url=None,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
839 category_ids=catID,
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
840 )
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
841 tid = res.get("id", None)
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
842 sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
843 else:
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
844 i = rnames.index(self.tool_name)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
845 tid = rids[i]
100
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
846 try:
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
847 res = ts.repositories.update_repository(
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
848 id=tid, tar_ball_path=self.newtarpath, commit_message=None
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
849 )
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
850 sto.write(f"#update res id {id} ={res}\n")
100
c749364c2283 Uploaded
fubar
parents: 99
diff changeset
851 except ConnectionError:
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
852 sto.write(
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
853 "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
854 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
855 sto.close()
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
856
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
857 def eph_galaxy_load(self):
113
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
858 """
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
859 use ephemeris to load the new tool from the local toolshed after planemo uploads it
6873c211b250 Uploaded
fubar
parents: 112
diff changeset
860 """
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
861 if os.path.exists(self.tlog):
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
862 tout = open(self.tlog, "a")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
863 else:
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
864 tout = open(self.tlog, "w")
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
865 cll = [
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
866 "shed-tools",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
867 "install",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
868 "-g",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
869 self.args.galaxy_url,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
870 "--latest",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
871 "-a",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
872 self.args.galaxy_api_key,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
873 "--name",
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
874 self.tool_name,
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
875 "--owner",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
876 "fubar",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
877 "--toolshed",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
878 self.args.toolshed_url,
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
879 "--section_label",
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
880 "ToolFactory",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
881 ]
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
882 tout.write("running\n%s\n" % " ".join(cll))
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
883 subp = subprocess.run(
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
884 cll, env=self.ourenv, cwd=self.ourcwd, shell=False, stderr=tout, stdout=tout
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
885 )
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
886 tout.write(
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
887 "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
888 )
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
889 tout.close()
98
67628c7dc9f3 Uploaded
fubar
parents: 97
diff changeset
890 return subp.returncode
63
b3254219d4fb Uploaded
fubar
parents: 62
diff changeset
891
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
892
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
893
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
894 def writeShedyml(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
895 """for planemo"""
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
896 yuser = self.args.user_email.split("@")[0]
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
897 yfname = os.path.join(self.tooloutdir, ".shed.yml")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
898 yamlf = open(yfname, "w")
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
899 odict = {
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
900 "name": self.tool_name,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
901 "owner": yuser,
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
902 "type": "unrestricted",
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
903 "description": self.args.tool_desc,
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
904 "synopsis": self.args.tool_desc,
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
905 "category": "TF Generated Tools",
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
906 }
48
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
907 yaml.dump(odict, yamlf, allow_unicode=True)
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
908 yamlf.close()
5a7a5b06bce0 Uploaded
fubar
parents:
diff changeset
909
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
910 def makeTool(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
911 """write xmls and input samples into place"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
912 self.makeXML()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
913 if self.args.script_path:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
914 stname = os.path.join(self.tooloutdir, "%s" % (self.sfile))
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
915 if not os.path.exists(stname):
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
916 shutil.copyfile(self.sfile, stname)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
917 xreal = "%s.xml" % self.tool_name
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
918 xout = os.path.join(self.tooloutdir, xreal)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
919 shutil.copyfile(xreal, xout)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
920 for p in self.infiles:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
921 pth = p[IPATHPOS]
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
922 dest = os.path.join(self.testdir, "%s_sample" % p[ICLPOS])
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
923 shutil.copyfile(pth, dest)
49
35a912ce0c83 Can now make the bwa example from planemo :)
fubar
parents: 48
diff changeset
924
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
925 def makeToolTar(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
926 """move outputs into test-data and prepare the tarball"""
101
557d5f06f213 Uploaded
fubar
parents: 100
diff changeset
927 excludeme = "_planemo_test_report.html"
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
928
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
929 def exclude_function(tarinfo):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
930 filename = tarinfo.name
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
931 return None if filename.endswith(excludeme) else tarinfo
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
932
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
933 for p in self.outfiles:
96
d54976fc996a Uploaded
fubar
parents: 95
diff changeset
934 oname = p[ONAMEPOS]
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
935 tdest = os.path.join(self.testdir, "%s_sample" % oname)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
936 if not os.path.isfile(tdest):
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
937 src = os.path.join(self.testdir, oname)
99
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
938 if os.path.isfile(src):
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
939 shutil.copyfile(src, tdest)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
940 dest = os.path.join(self.repdir, "%s.sample" % (oname))
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
941 shutil.copyfile(src, dest)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
942 else:
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
943 print(
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
944 "### problem - output file %s not found in testdir %s"
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
945 % (tdest, self.testdir)
d4d88d393285 Uploaded
fubar
parents: 98
diff changeset
946 )
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
947 tf = tarfile.open(self.newtarpath, "w:gz")
66
bc1977b1f7b5 Uploaded
fubar
parents: 65
diff changeset
948 tf.add(name=self.tooloutdir, arcname=self.tool_name, filter=exclude_function)
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
949 tf.close()
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
950 shutil.copyfile(self.newtarpath, self.args.new_tool)
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
951
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
952 def moveRunOutputs(self):
75
25dd9364a32a Uploaded
fubar
parents: 74
diff changeset
953 """need to move planemo or run outputs into toolfactory collection"""
50
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
954 with os.scandir(self.tooloutdir) as outs:
bf432f4486c7 Uploaded
fubar
parents: 49
diff changeset
955 for entry in outs:
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
956 if not entry.is_file():
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
957 continue
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
958 if "." in entry.name:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
959 nayme, ext = os.path.splitext(entry.name)
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
960 if ext in [".yml", ".xml", ".json", ".yaml"]:
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
961 ext = f"{ext}.txt"
80
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
962 else:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
963 ext = ".txt"
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
964 ofn = "%s%s" % (entry.name.replace(".", "_"), ext)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
965 dest = os.path.join(self.repdir, ofn)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
966 src = os.path.join(self.tooloutdir, entry.name)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
967 shutil.copyfile(src, dest)
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
968 with os.scandir(self.testdir) as outs:
f423a77bc669 Uploaded
fubar
parents: 78
diff changeset
969 for entry in outs:
106
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
970 if (
6de08f44e551 Uploaded
fubar
parents: 105
diff changeset
971 (not entry.is_file())
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972 or entry.name.endswith("_sample")
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973 or entry.name.endswith("_planemo_test_report.html")
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974 ):
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975 continue
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976 if "." in entry.name:
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977 nayme, ext = os.path.splitext(entry.name)
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978 else:
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979 ext = ".txt"
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980 newname = f"{entry.name}{ext}"
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981 dest = os.path.join(self.repdir, newname)
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982 src = os.path.join(self.testdir, entry.name)
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983 shutil.copyfile(src, dest)
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984
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985
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986 def main():
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987 """
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988 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
49
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989 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath"
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990 --tool_name "foo" --interpreter "Rscript"
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991 </command>
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992 """
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993 parser = argparse.ArgumentParser()
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994 a = parser.add_argument
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995 a("--script_path", default=None)
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996 a("--history_test", default=None)
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997 a("--cl_prefix", default=None)
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998 a("--sysexe", default=None)
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999 a("--packages", default=None)
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1000 a("--tool_name", default="newtool")
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1001 a("--tool_dir", default=None)
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1002 a("--input_files", default=[], action="append")
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1003 a("--output_files", default=[], action="append")
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1004 a("--user_email", default="Unknown")
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1005 a("--bad_user", default=None)
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1006 a("--make_Tool", default="runonly")
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1007 a("--help_text", default=None)
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1008 a("--tool_desc", default=None)
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1009 a("--tool_version", default=None)
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1010 a("--citations", default=None)
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1011 a("--command_override", default=None)
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1012 a("--test_override", default=None)
48
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1013 a("--additional_parameters", action="append", default=[])
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1014 a("--edit_additional_parameters", action="store_true", default=False)
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1015 a("--parampass", default="positional")
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1016 a("--tfout", default="./tfout")
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1017 a("--new_tool", default="new_tool")
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1018 a("--galaxy_url", default="http://localhost:8080")
106
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1019 a("--toolshed_url", default="http://localhost:9009")
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1020 # make sure this is identical to tool_sheds_conf.xml localhost != 127.0.0.1 so validation fails
63
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1021 a("--toolshed_api_key", default="fakekey")
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1022 a("--galaxy_api_key", default="fakekey")
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1023 a("--galaxy_root", default="/galaxy-central")
101
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1024 a("--galaxy_venv", default="/galaxy_venv")
48
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1025 args = parser.parse_args()
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1026 assert not args.bad_user, (
113
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1027 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
48
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1028 % (args.bad_user, args.bad_user)
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1029 )
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1030 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
48
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1031 assert (
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1032 args.sysexe or args.packages
48
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1033 ), "## Tool Factory wrapper expects an interpreter or an executable package"
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1034 args.input_files = [x.replace('"', "").replace("'", "") for x in args.input_files]
48
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1035 # remove quotes we need to deal with spaces in CL params
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1036 for i, x in enumerate(args.additional_parameters):
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1037 args.additional_parameters[i] = args.additional_parameters[i].replace('"', "")
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1038 r = ScriptRunner(args)
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1039 r.writeShedyml()
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1040 r.makeTool()
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1041 if args.make_Tool == "generate":
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1042 retcode = r.run() # for testing toolfactory itself
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1043 r.moveRunOutputs()
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1044 r.makeToolTar()
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1045 else:
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1046 r.planemo_biodocker_test() # test to make outputs and then test
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1047 r.moveRunOutputs()
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1048 r.makeToolTar()
101
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1049 if args.make_Tool == "gentestinstall":
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1050 r.shedLoad()
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1051 r.eph_galaxy_load()
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1052
48
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1053
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1054 if __name__ == "__main__":
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1055 main()