annotate toolfactory/rgToolFactory2.py @ 142:b36f12eb99dc draft

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author fubar
date Sat, 17 Apr 2021 12:29:31 +0000
parents 6b414af9ca11
children 4de39d209c5b
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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 json
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20 import logging
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21 import os
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22 import re
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23 import shlex
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24 import shutil
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25 import subprocess
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26 import sys
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27 import tarfile
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28 import tempfile
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29 import time
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30
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31 from bioblend import ConnectionError
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32 from bioblend import toolshed
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33
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34 import galaxyxml.tool as gxt
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35 import galaxyxml.tool.parameters as gxtp
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36
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37 import lxml
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38
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39 import yaml
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40
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41 myversion = "V2.2 February 2021"
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42 verbose = True
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43 debug = True
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44 toolFactoryURL = "https://github.com/fubar2/toolfactory"
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45 foo = len(lxml.__version__)
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46 FAKEEXE = "~~~REMOVE~~~ME~~~"
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47 # need this until a PR/version bump to fix galaxyxml prepending the exe even
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48 # with override.
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49
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50
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51 def timenow():
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52 """return current time as a string"""
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53 return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
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54
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55
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56 cheetah_escape_table = {"$": "\\$", "#": "\\#"}
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57
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58
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59 def cheetah_escape(text):
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60 """Produce entities within text."""
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61 return "".join([cheetah_escape_table.get(c, c) for c in text])
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62
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63
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64 def parse_citations(citations_text):
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65 """"""
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66 citations = [c for c in citations_text.split("**ENTRY**") if c.strip()]
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67 citation_tuples = []
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68 for citation in citations:
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69 if citation.startswith("doi"):
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70 citation_tuples.append(("doi", citation[len("doi") :].strip()))
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71 else:
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72 citation_tuples.append(("bibtex", citation[len("bibtex") :].strip()))
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73 return citation_tuples
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74
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75
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76 class ScriptRunner:
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77 """Wrapper for an arbitrary script
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78 uses galaxyxml
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79
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80 """
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81
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82 def __init__(self, args=None): # noqa
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83 """
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84 prepare command line cl for running the tool here
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85 and prepare elements needed for galaxyxml tool generation
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86 """
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87 self.ourcwd = os.getcwd()
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88 self.collections = []
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89 if len(args.collection) > 0:
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90 try:
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91 self.collections = [
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92 json.loads(x) for x in args.collection if len(x.strip()) > 1
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93 ]
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94 except Exception:
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95 print(
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96 f"--collections parameter {str(args.collection)} is malformed - should be a dictionary"
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97 )
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98 try:
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99 self.infiles = [
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100 json.loads(x) for x in args.input_files if len(x.strip()) > 1
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101 ]
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102 except Exception:
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103 print(
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104 f"--input_files parameter {str(args.input_files)} is malformed - should be a dictionary"
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105 )
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106 try:
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107 self.outfiles = [
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108 json.loads(x) for x in args.output_files if len(x.strip()) > 1
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109 ]
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110 except Exception:
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111 print(
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112 f"--output_files parameter {args.output_files} is malformed - should be a dictionary"
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113 )
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114 try:
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115 self.addpar = [
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116 json.loads(x) for x in args.additional_parameters if len(x.strip()) > 1
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117 ]
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118 except Exception:
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119 print(
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120 f"--additional_parameters {args.additional_parameters} is malformed - should be a dictionary"
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121 )
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122 try:
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123 self.selpar = [
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124 json.loads(x) for x in args.selecttext_parameters if len(x.strip()) > 1
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125 ]
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126 except Exception:
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127 print(
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128 f"--selecttext_parameters {args.selecttext_parameters} is malformed - should be a dictionary"
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129 )
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130 self.args = args
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131 self.cleanuppar()
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132 self.lastclredirect = None
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133 self.lastxclredirect = None
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134 self.cl = []
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135 self.xmlcl = []
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136 self.is_positional = self.args.parampass == "positional"
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137 if self.args.sysexe:
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138 if ' ' in self.args.sysexe:
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139 self.executeme = self.args.sysexe.split(' ')
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140 else:
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141 self.executeme = [self.args.sysexe, ]
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142 else:
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143 if self.args.packages:
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144 self.executeme = [self.args.packages.split(",")[0].split(":")[0].strip(), ]
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145 else:
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146 self.executeme = None
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147 aCL = self.cl.append
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148 aXCL = self.xmlcl.append
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149 assert args.parampass in [
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150 "0",
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151 "argparse",
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152 "positional",
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153 ], 'args.parampass must be "0","positional" or "argparse"'
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154 self.tool_name = re.sub("[^a-zA-Z0-9_]+", "", args.tool_name)
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155 self.tool_id = self.tool_name
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156 self.newtool = gxt.Tool(
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157 self.tool_name,
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158 self.tool_id,
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159 self.args.tool_version,
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160 self.args.tool_desc,
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161 FAKEEXE,
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162 )
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163 self.newtarpath = "%s_toolshed.gz" % self.tool_name
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164 self.tooloutdir = "./tfout"
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165 self.repdir = "./TF_run_report_tempdir"
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166 self.testdir = os.path.join(self.tooloutdir, "test-data")
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167 if not os.path.exists(self.tooloutdir):
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168 os.mkdir(self.tooloutdir)
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169 if not os.path.exists(self.testdir):
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170 os.mkdir(self.testdir)
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171 if not os.path.exists(self.repdir):
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172 os.mkdir(self.repdir)
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173 self.tinputs = gxtp.Inputs()
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174 self.toutputs = gxtp.Outputs()
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175 self.testparam = []
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176 if self.args.script_path:
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177 self.prepScript()
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178 if self.args.command_override:
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179 scos = open(self.args.command_override, "r").readlines()
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180 self.command_override = [x.rstrip() for x in scos]
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181 else:
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182 self.command_override = None
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183 if self.args.test_override:
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184 stos = open(self.args.test_override, "r").readlines()
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185 self.test_override = [x.rstrip() for x in stos]
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186 else:
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187 self.test_override = None
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188 if self.args.script_path:
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189 for ex in self.executeme:
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190 aCL(ex)
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191 aXCL(ex)
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192 aCL(self.sfile)
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193 aXCL("$runme")
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194 else:
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195 for ex in self.executeme:
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196 aCL(ex)
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197 aXCL(ex)
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198
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199 self.elog = os.path.join(self.repdir, "%s_error_log.txt" % self.tool_name)
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200 self.tlog = os.path.join(self.repdir, "%s_runner_log.txt" % self.tool_name)
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201 if self.args.parampass == "0":
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202 self.clsimple()
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203 else:
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204 if self.args.parampass == "positional":
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205 self.prepclpos()
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206 self.clpositional()
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207 else:
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208 self.prepargp()
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209 self.clargparse()
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210 if self.args.cl_suffix: # DIY CL end
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211 clp = shlex.split(self.args.cl_suffix)
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212 for c in clp:
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213 aCL(c)
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214 aXCL(c)
126
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215
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216 def clsimple(self):
131
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217 """no parameters or repeats - uses < and > for i/o"""
126
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218 aCL = self.cl.append
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219 aXCL = self.xmlcl.append
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220 if len(self.infiles) > 0:
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221 aCL("<")
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222 aCL(self.infiles[0]["infilename"])
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diff changeset
223 aXCL("<")
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diff changeset
224 aXCL("$%s" % self.infiles[0]["infilename"])
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diff changeset
225 if len(self.outfiles) > 0:
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parents: 124
diff changeset
226 aCL(">")
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diff changeset
227 aCL(self.outfiles[0]["name"])
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228 aXCL(">")
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diff changeset
229 aXCL("$%s" % self.outfiles[0]["name"])
121
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230
126
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231 def prepargp(self):
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232 clsuffix = []
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233 xclsuffix = []
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234 for i, p in enumerate(self.infiles):
135
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235 nam = p["infilename"]
126
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diff changeset
236 if p["origCL"].strip().upper() == "STDIN":
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237 appendme = [
135
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238 nam,
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parents: 134
diff changeset
239 nam,
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parents: 134
diff changeset
240 "< %s" % nam,
126
def0f754ee1b Uploaded
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parents: 124
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241 ]
def0f754ee1b Uploaded
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parents: 124
diff changeset
242 xappendme = [
135
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243 nam,
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parents: 134
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244 nam,
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parents: 134
diff changeset
245 "< $%s" % nam,
126
def0f754ee1b Uploaded
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parents: 124
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246 ]
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parents: 124
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247 else:
135
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248 rep = p["repeat"] == "1"
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249 over = ""
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250 if rep:
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251 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
126
def0f754ee1b Uploaded
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252 appendme = [p["CL"], p["CL"], ""]
135
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diff changeset
253 xappendme = [p["CL"], "$%s" % p["CL"], over]
126
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254 clsuffix.append(appendme)
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255 xclsuffix.append(xappendme)
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parents: 124
diff changeset
256 for i, p in enumerate(self.outfiles):
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parents: 124
diff changeset
257 if p["origCL"].strip().upper() == "STDOUT":
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parents: 124
diff changeset
258 self.lastclredirect = [">", p["name"]]
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259 self.lastxclredirect = [">", "$%s" % p["name"]]
121
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260 else:
126
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261 clsuffix.append([p["name"], p["name"], ""])
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262 xclsuffix.append([p["name"], "$%s" % p["name"], ""])
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parents: 124
diff changeset
263 for p in self.addpar:
131
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264 nam = p["name"]
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265 rep = p["repeat"] == "1"
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parents: 130
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266 if rep:
135
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267 over = f'#for $rep in $R_{nam}:\n--{nam} "$rep.{nam}"\n#end for'
131
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parents: 130
diff changeset
268 else:
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diff changeset
269 over = p["override"]
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parents: 130
diff changeset
270 clsuffix.append([p["CL"], nam, over])
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parents: 130
diff changeset
271 xclsuffix.append([p["CL"], nam, over])
126
def0f754ee1b Uploaded
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parents: 124
diff changeset
272 for p in self.selpar:
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parents: 124
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273 clsuffix.append([p["CL"], p["name"], p["override"]])
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parents: 124
diff changeset
274 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
def0f754ee1b Uploaded
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parents: 124
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275 self.xclsuffix = xclsuffix
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parents: 124
diff changeset
276 self.clsuffix = clsuffix
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parents: 124
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277
def0f754ee1b Uploaded
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parents: 124
diff changeset
278 def prepclpos(self):
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parents: 124
diff changeset
279 clsuffix = []
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parents: 124
diff changeset
280 xclsuffix = []
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parents: 124
diff changeset
281 for i, p in enumerate(self.infiles):
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parents: 124
diff changeset
282 if p["origCL"].strip().upper() == "STDIN":
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parents: 124
diff changeset
283 appendme = [
def0f754ee1b Uploaded
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parents: 124
diff changeset
284 "999",
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parents: 124
diff changeset
285 p["infilename"],
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parents: 124
diff changeset
286 "< $%s" % p["infilename"],
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parents: 124
diff changeset
287 ]
def0f754ee1b Uploaded
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parents: 124
diff changeset
288 xappendme = [
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parents: 124
diff changeset
289 "999",
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parents: 124
diff changeset
290 p["infilename"],
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parents: 124
diff changeset
291 "< $%s" % p["infilename"],
def0f754ee1b Uploaded
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parents: 124
diff changeset
292 ]
def0f754ee1b Uploaded
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parents: 124
diff changeset
293 else:
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parents: 124
diff changeset
294 appendme = [p["CL"], p["infilename"], ""]
def0f754ee1b Uploaded
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parents: 124
diff changeset
295 xappendme = [p["CL"], "$%s" % p["infilename"], ""]
def0f754ee1b Uploaded
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parents: 124
diff changeset
296 clsuffix.append(appendme)
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parents: 124
diff changeset
297 xclsuffix.append(xappendme)
def0f754ee1b Uploaded
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parents: 124
diff changeset
298 for i, p in enumerate(self.outfiles):
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parents: 124
diff changeset
299 if p["origCL"].strip().upper() == "STDOUT":
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parents: 124
diff changeset
300 self.lastclredirect = [">", p["name"]]
def0f754ee1b Uploaded
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parents: 124
diff changeset
301 self.lastxclredirect = [">", "$%s" % p["name"]]
def0f754ee1b Uploaded
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parents: 124
diff changeset
302 else:
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parents: 124
diff changeset
303 clsuffix.append([p["CL"], p["name"], ""])
def0f754ee1b Uploaded
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parents: 124
diff changeset
304 xclsuffix.append([p["CL"], "$%s" % p["name"], ""])
def0f754ee1b Uploaded
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parents: 124
diff changeset
305 for p in self.addpar:
131
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fubar
parents: 130
diff changeset
306 nam = p["name"]
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fubar
parents: 130
diff changeset
307 rep = p["repeat"] == "1" # repeats make NO sense
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fubar
parents: 130
diff changeset
308 if rep:
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fubar
parents: 130
diff changeset
309 print(f'### warning. Repeats for {nam} ignored - not permitted in positional parameter command lines!')
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fubar
parents: 130
diff changeset
310 over = p["override"]
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fubar
parents: 130
diff changeset
311 clsuffix.append([p["CL"], nam, over])
133
b843d75a5107 Uploaded
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parents: 132
diff changeset
312 xclsuffix.append([p["CL"], '"$%s"' % nam, over])
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
313 for p in self.selpar:
133
b843d75a5107 Uploaded
fubar
parents: 132
diff changeset
314 clsuffix.append([p["CL"], p["name"], p["override"]])
134
1f353bee783f Uploaded
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parents: 133
diff changeset
315 xclsuffix.append([p["CL"], '"$%s"' % p["name"], p["override"]])
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
316 clsuffix.sort()
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
317 xclsuffix.sort()
def0f754ee1b Uploaded
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parents: 124
diff changeset
318 self.xclsuffix = xclsuffix
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
319 self.clsuffix = clsuffix
121
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fubar
parents:
diff changeset
320
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fubar
parents:
diff changeset
321 def prepScript(self):
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fubar
parents:
diff changeset
322 rx = open(self.args.script_path, "r").readlines()
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fubar
parents:
diff changeset
323 rx = [x.rstrip() for x in rx]
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fubar
parents:
diff changeset
324 rxcheck = [x.strip() for x in rx if x.strip() > ""]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
325 assert len(rxcheck) > 0, "Supplied script is empty. Cannot run"
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fubar
parents:
diff changeset
326 self.script = "\n".join(rx)
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fubar
parents:
diff changeset
327 fhandle, self.sfile = tempfile.mkstemp(
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
328 prefix=self.tool_name, suffix="_%s" % (self.executeme[0])
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
329 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
330 tscript = open(self.sfile, "w")
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fubar
parents:
diff changeset
331 tscript.write(self.script)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
332 tscript.close()
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fubar
parents:
diff changeset
333 self.escapedScript = [cheetah_escape(x) for x in rx]
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fubar
parents:
diff changeset
334 self.spacedScript = [f" {x}" for x in rx if x.strip() > ""]
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
335 art = "%s.%s" % (self.tool_name, self.executeme[0])
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
336 artifact = open(art, "wb")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
337 artifact.write(bytes("\n".join(self.escapedScript), "utf8"))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
338 artifact.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
339
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
340 def cleanuppar(self):
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fubar
parents:
diff changeset
341 """ positional parameters are complicated by their numeric ordinal"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
342 if self.args.parampass == "positional":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
343 for i, p in enumerate(self.infiles):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
344 assert (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
345 p["CL"].isdigit() or p["CL"].strip().upper() == "STDIN"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
346 ), "Positional parameters must be ordinal integers - got %s for %s" % (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
347 p["CL"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
348 p["label"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
349 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
350 for i, p in enumerate(self.outfiles):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
351 assert (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
352 p["CL"].isdigit() or p["CL"].strip().upper() == "STDOUT"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
353 ), "Positional parameters must be ordinal integers - got %s for %s" % (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
354 p["CL"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
355 p["name"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
356 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
357 for i, p in enumerate(self.addpar):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
358 assert p[
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
359 "CL"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
360 ].isdigit(), "Positional parameters must be ordinal integers - got %s for %s" % (
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
361 p["CL"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
362 p["name"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
363 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
364 for i, p in enumerate(self.infiles):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
365 infp = copy.copy(p)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
366 infp["origCL"] = infp["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
367 if self.args.parampass in ["positional", "0"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
368 infp["infilename"] = infp["label"].replace(" ", "_")
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
369 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
370 infp["infilename"] = infp["CL"]
121
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fubar
parents:
diff changeset
371 self.infiles[i] = infp
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fubar
parents:
diff changeset
372 for i, p in enumerate(self.outfiles):
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
373 p["origCL"] = p["CL"] # keep copy
121
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fubar
parents:
diff changeset
374 self.outfiles[i] = p
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fubar
parents:
diff changeset
375 for i, p in enumerate(self.addpar):
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
376 p["origCL"] = p["CL"]
121
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fubar
parents:
diff changeset
377 self.addpar[i] = p
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
378
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
379 def clpositional(self):
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fubar
parents:
diff changeset
380 # inputs in order then params
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fubar
parents:
diff changeset
381 aCL = self.cl.append
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
382 for (k, v, koverride) in self.clsuffix:
121
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fubar
parents:
diff changeset
383 if " " in v:
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fubar
parents:
diff changeset
384 aCL("%s" % v)
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fubar
parents:
diff changeset
385 else:
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fubar
parents:
diff changeset
386 aCL(v)
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fubar
parents:
diff changeset
387 aXCL = self.xmlcl.append
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
388 for (k, v, koverride) in self.xclsuffix:
121
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fubar
parents:
diff changeset
389 aXCL(v)
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fubar
parents:
diff changeset
390 if self.lastxclredirect:
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fubar
parents:
diff changeset
391 aXCL(self.lastxclredirect[0])
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fubar
parents:
diff changeset
392 aXCL(self.lastxclredirect[1])
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fubar
parents:
diff changeset
393
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
394 def clargparse(self):
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fubar
parents:
diff changeset
395 """argparse style"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
396 aCL = self.cl.append
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fubar
parents:
diff changeset
397 aXCL = self.xmlcl.append
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fubar
parents:
diff changeset
398 # inputs then params in argparse named form
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fubar
parents:
diff changeset
399
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
400 for (k, v, koverride) in self.xclsuffix:
121
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fubar
parents:
diff changeset
401 if koverride > "":
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fubar
parents:
diff changeset
402 k = koverride
131
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fubar
parents: 130
diff changeset
403 aXCL(k)
121
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fubar
parents:
diff changeset
404 else:
131
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fubar
parents: 130
diff changeset
405 if len(k.strip()) == 1:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
406 k = "-%s" % k
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
407 else:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
408 k = "--%s" % k
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
409 aXCL(k)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
410 aXCL(v)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
411 for (k, v, koverride) in self.clsuffix:
121
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fubar
parents:
diff changeset
412 if koverride > "":
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fubar
parents:
diff changeset
413 k = koverride
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fubar
parents:
diff changeset
414 elif len(k.strip()) == 1:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
415 k = "-%s" % k
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fubar
parents:
diff changeset
416 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
417 k = "--%s" % k
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fubar
parents:
diff changeset
418 aCL(k)
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fubar
parents:
diff changeset
419 aCL(v)
129
c35ff02652bf Uploaded
fubar
parents: 127
diff changeset
420 if self.lastxclredirect:
c35ff02652bf Uploaded
fubar
parents: 127
diff changeset
421 aXCL(self.lastxclredirect[0])
c35ff02652bf Uploaded
fubar
parents: 127
diff changeset
422 aXCL(self.lastxclredirect[1])
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
423
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
424 def getNdash(self, newname):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
425 if self.is_positional:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
426 ndash = 0
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
427 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
428 ndash = 2
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
429 if len(newname) < 2:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
430 ndash = 1
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
431 return ndash
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
432
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
433 def doXMLparam(self):
135
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
434 """Add all needed elements to tool""" # noqa
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
435 for p in self.outfiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
436 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
437 newfmt = p["format"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
438 newcl = p["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
439 test = p["test"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
440 oldcl = p["origCL"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
441 test = test.strip()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
442 ndash = self.getNdash(newcl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
443 aparm = gxtp.OutputData(
124
f267ed4a3026 Uploaded
fubar
parents: 122
diff changeset
444 name=newname, format=newfmt, num_dashes=ndash, label=newname
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
445 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
446 aparm.positional = self.is_positional
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
447 if self.is_positional:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
448 if oldcl.upper() == "STDOUT":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
449 aparm.positional = 9999999
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
450 aparm.command_line_override = "> $%s" % newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
451 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
452 aparm.positional = int(oldcl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
453 aparm.command_line_override = "$%s" % newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
454 self.toutputs.append(aparm)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
455 ld = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
456 if test.strip() > "":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
457 if test.startswith("diff"):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
458 c = "diff"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
459 ld = 0
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
460 if test.split(":")[1].isdigit:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
461 ld = int(test.split(":")[1])
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
462 tp = gxtp.TestOutput(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
463 name=newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
464 value="%s_sample" % newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
465 compare=c,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
466 lines_diff=ld,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
467 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
468 elif test.startswith("sim_size"):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
469 c = "sim_size"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
470 tn = test.split(":")[1].strip()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
471 if tn > "":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
472 if "." in tn:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
473 delta = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
474 delta_frac = min(1.0, float(tn))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
475 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
476 delta = int(tn)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
477 delta_frac = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
478 tp = gxtp.TestOutput(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
479 name=newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
480 value="%s_sample" % newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
481 compare=c,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
482 delta=delta,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
483 delta_frac=delta_frac,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
484 )
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
485 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
486 c = test
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
487 tp = gxtp.TestOutput(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
488 name=newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
489 value="%s_sample" % newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
490 compare=c,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
491 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
492 self.testparam.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
493 for p in self.infiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
494 newname = p["infilename"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
495 newfmt = p["format"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
496 ndash = self.getNdash(newname)
135
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
497 reps = p.get("repeat", "0") == "1"
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
498 if not len(p["label"]) > 0:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
499 alab = p["CL"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
500 else:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
501 alab = p["label"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
502 aninput = gxtp.DataParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
503 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
504 optional=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
505 label=alab,
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
506 help=p["help"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
507 format=newfmt,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
508 multiple=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
509 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
510 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
511 aninput.positional = self.is_positional
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
512 if self.is_positional:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
513 if p["origCL"].upper() == "STDIN":
127
98c8a76b3638 Uploaded
fubar
parents: 126
diff changeset
514 aninput.positional = 9999998
98c8a76b3638 Uploaded
fubar
parents: 126
diff changeset
515 aninput.command_line_override = "> $%s" % newname
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
516 else:
127
98c8a76b3638 Uploaded
fubar
parents: 126
diff changeset
517 aninput.positional = int(p["origCL"])
98c8a76b3638 Uploaded
fubar
parents: 126
diff changeset
518 aninput.command_line_override = "$%s" % newname
131
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
519 if reps:
133
b843d75a5107 Uploaded
fubar
parents: 132
diff changeset
520 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {alab} as needed")
131
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
521 repe.append(aninput)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
522 self.tinputs.append(repe)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
523 tparm = gxtp.TestRepeat(name=f"R_{newname}")
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
524 tparm2 = gxtp.TestParam(newname, value="%s_sample" % newname)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
525 tparm.append(tparm2)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
526 self.testparam.append(tparm)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
527 else:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
528 self.tinputs.append(aninput)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
529 tparm = gxtp.TestParam(newname, value="%s_sample" % newname)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
530 self.testparam.append(tparm)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
531 for p in self.addpar:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
532 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
533 newval = p["value"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
534 newlabel = p["label"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
535 newhelp = p["help"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
536 newtype = p["type"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
537 newcl = p["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
538 oldcl = p["origCL"]
131
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
539 reps = p["repeat"] == "1"
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
540 if not len(newlabel) > 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
541 newlabel = newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
542 ndash = self.getNdash(newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
543 if newtype == "text":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
544 aparm = gxtp.TextParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
545 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
546 label=newlabel,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
547 help=newhelp,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
548 value=newval,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
549 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
550 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
551 elif newtype == "integer":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
552 aparm = gxtp.IntegerParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
553 newname,
130
e8e8071c9d0c Uploaded
fubar
parents: 129
diff changeset
554 label=newlabel,
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
555 help=newhelp,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
556 value=newval,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
557 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
558 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
559 elif newtype == "float":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
560 aparm = gxtp.FloatParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
561 newname,
130
e8e8071c9d0c Uploaded
fubar
parents: 129
diff changeset
562 label=newlabel,
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
563 help=newhelp,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
564 value=newval,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
565 num_dashes=ndash,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
566 )
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
567 elif newtype == "boolean":
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
568 aparm = gxtp.BooleanParam(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
569 newname,
130
e8e8071c9d0c Uploaded
fubar
parents: 129
diff changeset
570 label=newlabel,
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
571 help=newhelp,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
572 value=newval,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
573 num_dashes=ndash,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
574 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
575 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
576 raise ValueError(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
577 'Unrecognised parameter type "%s" for\
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
578 additional parameter %s in makeXML'
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
579 % (newtype, newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
580 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
581 aparm.positional = self.is_positional
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
582 if self.is_positional:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
583 aparm.positional = int(oldcl)
131
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
584 if reps:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
585 repe = gxtp.Repeat(name=f"R_{newname}", title=f"Add as many {newlabel} as needed")
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
586 repe.append(aparm)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
587 self.tinputs.append(repe)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
588 tparm = gxtp.TestRepeat(name=f"R_{newname}")
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
589 tparm2 = gxtp.TestParam(newname, value=newval)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
590 tparm.append(tparm2)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
591 self.testparam.append(tparm)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
592 else:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
593 self.tinputs.append(aparm)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
594 tparm = gxtp.TestParam(newname, value=newval)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
595 self.testparam.append(tparm)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
596 for p in self.selpar:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
597 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
598 newval = p["value"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
599 newlabel = p["label"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
600 newhelp = p["help"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
601 newtype = p["type"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
602 newcl = p["CL"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
603 if not len(newlabel) > 0:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
604 newlabel = newname
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
605 ndash = self.getNdash(newname)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
606 if newtype == "selecttext":
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
607 newtext = p["texts"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
608 aparm = gxtp.SelectParam(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
609 newname,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
610 label=newlabel,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
611 help=newhelp,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
612 num_dashes=ndash,
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
613 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
614 for i in range(len(newval)):
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
615 anopt = gxtp.SelectOption(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
616 value=newval[i],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
617 text=newtext[i],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
618 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
619 aparm.append(anopt)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
620 aparm.positional = self.is_positional
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
621 if self.is_positional:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
622 aparm.positional = int(newcl)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
623 self.tinputs.append(aparm)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
624 tparm = gxtp.TestParam(newname, value=newval)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
625 self.testparam.append(tparm)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
626 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
627 raise ValueError(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
628 'Unrecognised parameter type "%s" for\
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
629 selecttext parameter %s in makeXML'
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
630 % (newtype, newname)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
631 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
632 for p in self.collections:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
633 newkind = p["kind"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
634 newname = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
635 newlabel = p["label"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
636 newdisc = p["discover"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
637 collect = gxtp.OutputCollection(newname, label=newlabel, type=newkind)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
638 disc = gxtp.DiscoverDatasets(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
639 pattern=newdisc, directory=f"{newname}", visible="false"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
640 )
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
641 collect.append(disc)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
642 self.toutputs.append(collect)
131
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
643 try:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
644 tparm = gxtp.TestOutputCollection(newname) # broken until PR merged.
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
645 self.testparam.append(tparm)
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
646 except Exception:
72d190989c68 Uploaded
fubar
parents: 130
diff changeset
647 print("#### WARNING: Galaxyxml version does not have the PR merged yet - tests for collections must be over-ridden until then!")
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
648
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
649 def doNoXMLparam(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
650 """filter style package - stdin to stdout"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
651 if len(self.infiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
652 alab = self.infiles[0]["label"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
653 if len(alab) == 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
654 alab = self.infiles[0]["infilename"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
655 max1s = (
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
656 "Maximum one input if parampass is 0 but multiple input files supplied - %s"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
657 % str(self.infiles)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
658 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
659 assert len(self.infiles) == 1, max1s
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
660 newname = self.infiles[0]["infilename"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
661 aninput = gxtp.DataParam(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
662 newname,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
663 optional=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
664 label=alab,
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
665 help=self.infiles[0]["help"],
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
666 format=self.infiles[0]["format"],
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
667 multiple=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
668 num_dashes=0,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
669 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
670 aninput.command_line_override = "< $%s" % newname
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
671 aninput.positional = True
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
672 self.tinputs.append(aninput)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
673 tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
674 self.testparam.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
675 if len(self.outfiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
676 newname = self.outfiles[0]["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
677 newfmt = self.outfiles[0]["format"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
678 anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
679 anout.command_line_override = "> $%s" % newname
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
680 anout.positional = self.is_positional
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
681 self.toutputs.append(anout)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
682 tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
683 self.testparam.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
684
135
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
685 def makeXML(self): # noqa
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
686 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
687 Create a Galaxy xml tool wrapper for the new script
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
688 Uses galaxyhtml
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
689 Hmmm. How to get the command line into correct order...
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
690 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
691 if self.command_override:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
692 self.newtool.command_override = self.command_override # config file
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
693 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
694 self.newtool.command_override = self.xmlcl
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
695 cite = gxtp.Citations()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
696 acite = gxtp.Citation(type="doi", value="10.1093/bioinformatics/bts573")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
697 cite.append(acite)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
698 self.newtool.citations = cite
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
699 safertext = ""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
700 if self.args.help_text:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
701 helptext = open(self.args.help_text, "r").readlines()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
702 safertext = "\n".join([cheetah_escape(x) for x in helptext])
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
703 if len(safertext.strip()) == 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
704 safertext = (
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
705 "Ask the tool author (%s) to rebuild with help text please\n"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
706 % (self.args.user_email)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
707 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
708 if self.args.script_path:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
709 if len(safertext) > 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
710 safertext = safertext + "\n\n------\n" # transition allowed!
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
711 scr = [x for x in self.spacedScript if x.strip() > ""]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
712 scr.insert(0, "\n\nScript::\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
713 if len(scr) > 300:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
714 scr = (
122
c763ae9237ca Uploaded
fubar
parents: 121
diff changeset
715 scr[:100]
c763ae9237ca Uploaded
fubar
parents: 121
diff changeset
716 + [" >300 lines - stuff deleted", " ......"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
717 + scr[-100:]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
718 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
719 scr.append("\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
720 safertext = safertext + "\n".join(scr)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
721 self.newtool.help = safertext
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
722 self.newtool.version_command = f'echo "{self.args.tool_version}"'
135
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
723 std = gxtp.Stdios()
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
724 std1 = gxtp.Stdio()
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
725 std.append(std1)
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
726 self.newtool.stdios = std
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
727 requirements = gxtp.Requirements()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
728 if self.args.packages:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
729 for d in self.args.packages.split(","):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
730 ver = ""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
731 d = d.replace("==", ":")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
732 d = d.replace("=", ":")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
733 if ":" in d:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
734 packg, ver = d.split(":")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
735 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
736 packg = d
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
737 requirements.append(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
738 gxtp.Requirement("package", packg.strip(), ver.strip())
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
739 )
135
7805fdac70ed Uploaded
fubar
parents: 134
diff changeset
740 self.newtool.requirements = requirements
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
741 if self.args.parampass == "0":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
742 self.doNoXMLparam()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
743 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
744 self.doXMLparam()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
745 self.newtool.outputs = self.toutputs
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
746 self.newtool.inputs = self.tinputs
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
747 if self.args.script_path:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
748 configfiles = gxtp.Configfiles()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
749 configfiles.append(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
750 gxtp.Configfile(name="runme", text="\n".join(self.escapedScript))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
751 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
752 self.newtool.configfiles = configfiles
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
753 tests = gxtp.Tests()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
754 test_a = gxtp.Test()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
755 for tp in self.testparam:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
756 test_a.append(tp)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
757 tests.append(test_a)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
758 self.newtool.tests = tests
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
759 self.newtool.add_comment(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
760 "Created by %s at %s using the Galaxy Tool Factory."
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
761 % (self.args.user_email, timenow())
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
762 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
763 self.newtool.add_comment("Source in git at: %s" % (toolFactoryURL))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
764 exml0 = self.newtool.export()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
765 exml = exml0.replace(FAKEEXE, "") # temporary work around until PR accepted
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
766 if (
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
767 self.test_override
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
768 ): # cannot do this inside galaxyxml as it expects lxml objects for tests
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
769 part1 = exml.split("<tests>")[0]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
770 part2 = exml.split("</tests>")[1]
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
771 fixed = "%s\n%s\n%s" % (part1, "\n".join(self.test_override), part2)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
772 exml = fixed
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
773 # exml = exml.replace('range="1:"', 'range="1000:"')
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
774 xf = open("%s.xml" % self.tool_name, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
775 xf.write(exml)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
776 xf.write("\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
777 xf.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
778 # ready for the tarball
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
779
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
780 def run(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
781 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
782 generate test outputs by running a command line
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
783 won't work if command or test override in play - planemo is the
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
784 easiest way to generate test outputs for that case so is
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
785 automagically selected
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
786 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
787 scl = " ".join(self.cl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
788 err = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
789 if self.args.parampass != "0":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
790 if os.path.exists(self.elog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
791 ste = open(self.elog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
792 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
793 ste = open(self.elog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
794 if self.lastclredirect:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
795 sto = open(self.lastclredirect[1], "wb") # is name of an output file
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
796 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
797 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
798 sto = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
799 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
800 sto = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
801 sto.write(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
802 "## Executing Toolfactory generated command line = %s\n" % scl
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
803 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
804 sto.flush()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
805 subp = subprocess.run(
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
806 self.cl, shell=False, stdout=sto, stderr=ste
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
807 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
808 sto.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
809 ste.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
810 retval = subp.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
811 else: # work around special case - stdin and write to stdout
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
812 if len(self.infiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
813 sti = open(self.infiles[0]["name"], "rb")
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
814 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
815 sti = sys.stdin
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
816 if len(self.outfiles) > 0:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
817 sto = open(self.outfiles[0]["name"], "wb")
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
818 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
819 sto = sys.stdout
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
820 subp = subprocess.run(
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
821 self.cl, shell=False, stdout=sto, stdin=sti
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
822 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
823 sto.write("## Executing Toolfactory generated command line = %s\n" % scl)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
824 retval = subp.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
825 sto.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
826 sti.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
827 if os.path.isfile(self.tlog) and os.stat(self.tlog).st_size == 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
828 os.unlink(self.tlog)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
829 if os.path.isfile(self.elog) and os.stat(self.elog).st_size == 0:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
830 os.unlink(self.elog)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
831 if retval != 0 and err: # problem
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
832 sys.stderr.write(err)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
833 logging.debug("run done")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
834 return retval
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
835
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
836 def shedLoad(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
837 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
838 use bioblend to create new repository
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
839 or update existing
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
840
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
841 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
842 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
843 sto = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
844 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
845 sto = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
846
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
847 ts = toolshed.ToolShedInstance(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
848 url=self.args.toolshed_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
849 key=self.args.toolshed_api_key,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
850 verify=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
851 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
852 repos = ts.repositories.get_repositories()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
853 rnames = [x.get("name", "?") for x in repos]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
854 rids = [x.get("id", "?") for x in repos]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
855 tfcat = "ToolFactory generated tools"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
856 if self.tool_name not in rnames:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
857 tscat = ts.categories.get_categories()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
858 cnames = [x.get("name", "?").strip() for x in tscat]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
859 cids = [x.get("id", "?") for x in tscat]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
860 catID = None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
861 if tfcat.strip() in cnames:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
862 ci = cnames.index(tfcat)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
863 catID = cids[ci]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
864 res = ts.repositories.create_repository(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
865 name=self.args.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
866 synopsis="Synopsis:%s" % self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
867 description=self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
868 type="unrestricted",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
869 remote_repository_url=self.args.toolshed_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
870 homepage_url=None,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
871 category_ids=catID,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
872 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
873 tid = res.get("id", None)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
874 sto.write(f"#create_repository {self.args.tool_name} tid={tid} res={res}\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
875 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
876 i = rnames.index(self.tool_name)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
877 tid = rids[i]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
878 try:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
879 res = ts.repositories.update_repository(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
880 id=tid, tar_ball_path=self.newtarpath, commit_message=None
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
881 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
882 sto.write(f"#update res id {id} ={res}\n")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
883 except ConnectionError:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
884 sto.write(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
885 "####### Is the toolshed running and the API key correct? Bioblend shed upload failed\n"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
886 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
887 sto.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
888
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
889 def eph_galaxy_load(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
890 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
891 use ephemeris to load the new tool from the local toolshed after planemo uploads it
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
892 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
893 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
894 tout = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
895 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
896 tout = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
897 cll = [
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
898 "shed-tools",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
899 "install",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
900 "-g",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
901 self.args.galaxy_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
902 "--latest",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
903 "-a",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
904 self.args.galaxy_api_key,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
905 "--name",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
906 self.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
907 "--owner",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
908 "fubar",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
909 "--toolshed",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
910 self.args.toolshed_url,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
911 "--section_label",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
912 "ToolFactory",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
913 ]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
914 tout.write("running\n%s\n" % " ".join(cll))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
915 subp = subprocess.run(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
916 cll,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
917 cwd=self.ourcwd,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
918 shell=False,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
919 stderr=tout,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
920 stdout=tout,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
921 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
922 tout.write(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
923 "installed %s - got retcode %d\n" % (self.tool_name, subp.returncode)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
924 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
925 tout.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
926 return subp.returncode
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
927
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
928 def writeShedyml(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
929 """for planemo"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
930 yuser = self.args.user_email.split("@")[0]
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
931 yfname = os.path.join(self.tooloutdir, ".shed.yml")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
932 yamlf = open(yfname, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
933 odict = {
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
934 "name": self.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
935 "owner": yuser,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
936 "type": "unrestricted",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
937 "description": self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
938 "synopsis": self.args.tool_desc,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
939 "category": "TF Generated Tools",
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
940 }
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
941 yaml.dump(odict, yamlf, allow_unicode=True)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
942 yamlf.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
943
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
944 def makeTool(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
945 """write xmls and input samples into place"""
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
946 if self.args.parampass == 0:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
947 self.doNoXMLparam()
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
948 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
949 self.makeXML()
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
950 if self.args.script_path:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
951 stname = os.path.join(self.tooloutdir, self.sfile)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
952 if not os.path.exists(stname):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
953 shutil.copyfile(self.sfile, stname)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
954 xreal = "%s.xml" % self.tool_name
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
955 xout = os.path.join(self.tooloutdir, xreal)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
956 shutil.copyfile(xreal, xout)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
957 for p in self.infiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
958 pth = p["name"]
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
959 dest = os.path.join(self.testdir, "%s_sample" % p["infilename"])
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
960 shutil.copyfile(pth, dest)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
961 dest = os.path.join(self.repdir, "%s_sample" % p["infilename"])
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
962 shutil.copyfile(pth, dest)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
963
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
964 def makeToolTar(self, report_fail=False):
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
965 """move outputs into test-data and prepare the tarball"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
966 excludeme = "_planemo_test_report.html"
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
967
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
968 def exclude_function(tarinfo):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
969 filename = tarinfo.name
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
970 return None if filename.endswith(excludeme) else tarinfo
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
971
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
972 if os.path.exists(self.tlog):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
973 tout = open(self.tlog, "a")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
974 else:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
975 tout = open(self.tlog, "w")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
976 for p in self.outfiles:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
977 oname = p["name"]
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
978 tdest = os.path.join(self.testdir, "%s_sample" % oname)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
979 src = os.path.join(self.testdir, oname)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
980 if not os.path.isfile(tdest):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
981 if os.path.isfile(src):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
982 shutil.copyfile(src, tdest)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
983 dest = os.path.join(self.repdir, "%s.sample" % (oname))
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
984 shutil.copyfile(src, dest)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
985 else:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
986 if report_fail:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
987 tout.write(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
988 "###Tool may have failed - output file %s not found in testdir after planemo run %s."
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
989 % (tdest, self.testdir)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
990 )
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
991 tf = tarfile.open(self.newtarpath, "w:gz")
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
992 tf.add(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
993 name=self.tooloutdir,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
994 arcname=self.tool_name,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
995 filter=exclude_function,
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
996 )
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
997 tf.close()
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
998 shutil.copyfile(self.newtarpath, self.args.new_tool)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
999
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1000 def moveRunOutputs(self):
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1001 """need to move planemo or run outputs into toolfactory collection"""
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1002 with os.scandir(self.tooloutdir) as outs:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1003 for entry in outs:
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1004 if not entry.is_file():
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1005 continue
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1006 if "." in entry.name:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1007 _, ext = os.path.splitext(entry.name)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1008 if ext in [".tgz", ".json"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1009 continue
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1010 if ext in [".yml", ".xml", ".yaml"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1011 newname = f"{entry.name.replace('.','_')}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1012 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1013 newname = entry.name
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1014 else:
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1015 newname = f"{entry.name}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1016 dest = os.path.join(self.repdir, newname)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1017 src = os.path.join(self.tooloutdir, entry.name)
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1018 shutil.copyfile(src, dest)
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1019 if self.args.include_tests:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1020 with os.scandir(self.testdir) as outs:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1021 for entry in outs:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1022 if (not entry.is_file()) or entry.name.endswith(
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1023 "_planemo_test_report.html"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1024 ):
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1025 continue
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1026 if "." in entry.name:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1027 _, ext = os.path.splitext(entry.name)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1028 if ext in [".tgz", ".json"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1029 continue
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1030 if ext in [".yml", ".xml", ".yaml"]:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1031 newname = f"{entry.name.replace('.','_')}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1032 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1033 newname = entry.name
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1034 else:
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1035 newname = f"{entry.name}.txt"
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1036 dest = os.path.join(self.repdir, newname)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1037 src = os.path.join(self.testdir, entry.name)
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1038 shutil.copyfile(src, dest)
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1039
126
def0f754ee1b Uploaded
fubar
parents: 124
diff changeset
1040 def planemo_test_once(self):
121
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1041 """planemo is a requirement so is available for testing but needs a
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1042 different call if in the biocontainer - see above
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1043 and for generating test outputs if command or test overrides are
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1044 supplied test outputs are sent to repdir for display
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1045 """
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1046 xreal = "%s.xml" % self.tool_name
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1047 tool_test_path = os.path.join(
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1048 self.repdir, f"{self.tool_name}_planemo_test_report.html"
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diff changeset
1049 )
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1050 if os.path.exists(self.tlog):
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parents:
diff changeset
1051 tout = open(self.tlog, "a")
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1052 else:
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diff changeset
1053 tout = open(self.tlog, "w")
126
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diff changeset
1054 cll = [
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1055 "planemo",
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1056 "test",
139
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diff changeset
1057 "--galaxy_python_version",
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1058 self.args.python_version,
126
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diff changeset
1059 "--conda_auto_init",
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diff changeset
1060 "--test_data",
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1061 os.path.abspath(self.testdir),
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diff changeset
1062 "--test_output",
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1063 os.path.abspath(tool_test_path),
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1064 "--galaxy_root",
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1065 self.args.galaxy_root,
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diff changeset
1066 "--update_test_data",
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1067 os.path.abspath(xreal),
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diff changeset
1068 ]
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diff changeset
1069 p = subprocess.run(
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diff changeset
1070 cll,
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1071 shell=False,
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1072 cwd=self.tooloutdir,
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1073 stderr=tout,
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diff changeset
1074 stdout=tout,
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1075 )
121
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1076 tout.close()
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diff changeset
1077 return p.returncode
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diff changeset
1078
137
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diff changeset
1079 def set_planemo_galaxy_root(self, galaxyroot='/galaxy-central', config_path=".planemo.yml"):
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1080 # bug in planemo - bogus '--dev-wheels' passed to run_tests.sh as at april 2021 - need a fiddled copy so it is ignored until fixed
138
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diff changeset
1081 CONFIG_TEMPLATE = """## Planemo Global Configuration File.
137
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1082 ## Everything in this file is completely optional - these values can all be
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1083 ## configured via command line options for the corresponding commands.
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1084
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1085 ## Specify a default galaxy_root for test and server commands here.
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1086 galaxy_root: %s
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1087 ## Username used with toolshed(s).
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1088 #shed_username: "<TODO>"
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diff changeset
1089 sheds:
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diff changeset
1090 # For each tool shed you wish to target, uncomment key or both email and
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diff changeset
1091 # password.
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diff changeset
1092 toolshed:
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diff changeset
1093 #key: "<TODO>"
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diff changeset
1094 #email: "<TODO>"
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diff changeset
1095 #password: "<TODO>"
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diff changeset
1096 testtoolshed:
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diff changeset
1097 #key: "<TODO>"
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diff changeset
1098 #email: "<TODO>"
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diff changeset
1099 #password: "<TODO>"
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diff changeset
1100 local:
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diff changeset
1101 #key: "<TODO>"
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diff changeset
1102 #email: "<TODO>"
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1103 #password: "<TODO>"
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1104 """
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1105 if not os.path.exists(config_path):
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diff changeset
1106 with open(config_path, "w") as f:
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diff changeset
1107 f.write(CONFIG_TEMPLATE % galaxyroot)
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1108
121
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1109
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1110 def main():
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parents:
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1111 """
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parents:
diff changeset
1112 This is a Galaxy wrapper.
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parents:
diff changeset
1113 It expects to be called by a special purpose tool.xml
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parents:
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1114
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parents:
diff changeset
1115 """
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parents:
diff changeset
1116 parser = argparse.ArgumentParser()
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parents:
diff changeset
1117 a = parser.add_argument
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parents:
diff changeset
1118 a("--script_path", default=None)
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parents:
diff changeset
1119 a("--history_test", default=None)
129
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diff changeset
1120 a("--cl_suffix", default=None)
121
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parents:
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1121 a("--sysexe", default=None)
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parents:
diff changeset
1122 a("--packages", default=None)
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parents:
diff changeset
1123 a("--tool_name", default="newtool")
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parents:
diff changeset
1124 a("--tool_dir", default=None)
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parents:
diff changeset
1125 a("--input_files", default=[], action="append")
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parents:
diff changeset
1126 a("--output_files", default=[], action="append")
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parents:
diff changeset
1127 a("--user_email", default="Unknown")
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parents:
diff changeset
1128 a("--bad_user", default=None)
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parents:
diff changeset
1129 a("--make_Tool", default="runonly")
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parents:
diff changeset
1130 a("--help_text", default=None)
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parents:
diff changeset
1131 a("--tool_desc", default=None)
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parents:
diff changeset
1132 a("--tool_version", default=None)
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parents:
diff changeset
1133 a("--citations", default=None)
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parents:
diff changeset
1134 a("--command_override", default=None)
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parents:
diff changeset
1135 a("--test_override", default=None)
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parents:
diff changeset
1136 a("--additional_parameters", action="append", default=[])
126
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diff changeset
1137 a("--selecttext_parameters", action="append", default=[])
121
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parents:
diff changeset
1138 a("--edit_additional_parameters", action="store_true", default=False)
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parents:
diff changeset
1139 a("--parampass", default="positional")
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parents:
diff changeset
1140 a("--tfout", default="./tfout")
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parents:
diff changeset
1141 a("--new_tool", default="new_tool")
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parents:
diff changeset
1142 a("--galaxy_url", default="http://localhost:8080")
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parents:
diff changeset
1143 a("--toolshed_url", default="http://localhost:9009")
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parents:
diff changeset
1144 # make sure this is identical to tool_sheds_conf.xml
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parents:
diff changeset
1145 # localhost != 127.0.0.1 so validation fails
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parents:
diff changeset
1146 a("--toolshed_api_key", default="fakekey")
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parents:
diff changeset
1147 a("--galaxy_api_key", default="fakekey")
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parents:
diff changeset
1148 a("--galaxy_root", default="/galaxy-central")
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diff changeset
1149 a("--galaxy_venv", default="/galaxy_venv")
126
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diff changeset
1150 a("--collection", action="append", default=[])
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diff changeset
1151 a("--include_tests", default=False, action="store_true")
139
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diff changeset
1152 a("--python_version", default="3.9")
121
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diff changeset
1153 args = parser.parse_args()
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parents:
diff changeset
1154 assert not args.bad_user, (
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parents:
diff changeset
1155 'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy \
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fubar
parents:
diff changeset
1156 admin adds %s to "admin_users" in the galaxy.yml Galaxy configuration file'
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parents:
diff changeset
1157 % (args.bad_user, args.bad_user)
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parents:
diff changeset
1158 )
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parents:
diff changeset
1159 assert args.tool_name, "## Tool Factory expects a tool name - eg --tool_name=DESeq"
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parents:
diff changeset
1160 assert (
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parents:
diff changeset
1161 args.sysexe or args.packages
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parents:
diff changeset
1162 ), "## Tool Factory wrapper expects an interpreter \
2050b2475ae5 Uploaded
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parents:
diff changeset
1163 or an executable package in --sysexe or --packages"
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parents:
diff changeset
1164 r = ScriptRunner(args)
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parents:
diff changeset
1165 r.writeShedyml()
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parents:
diff changeset
1166 r.makeTool()
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parents:
diff changeset
1167 if args.make_Tool == "generate":
126
def0f754ee1b Uploaded
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diff changeset
1168 r.run()
121
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parents:
diff changeset
1169 r.moveRunOutputs()
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parents:
diff changeset
1170 r.makeToolTar()
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diff changeset
1171 else:
126
def0f754ee1b Uploaded
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parents: 124
diff changeset
1172 r.planemo_test_once()
121
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parents:
diff changeset
1173 r.moveRunOutputs()
126
def0f754ee1b Uploaded
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parents: 124
diff changeset
1174 r.makeToolTar(report_fail=True)
121
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parents:
diff changeset
1175 if args.make_Tool == "gentestinstall":
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parents:
diff changeset
1176 r.shedLoad()
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parents:
diff changeset
1177 r.eph_galaxy_load()
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fubar
parents:
diff changeset
1178
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parents:
diff changeset
1179
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parents:
diff changeset
1180 if __name__ == "__main__":
2050b2475ae5 Uploaded
fubar
parents:
diff changeset
1181 main()