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