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