Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/shed_lint.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 import os
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2 import yaml
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3 from galaxy.tools.lint import LintContext
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4 from galaxy.tools.linters.help import rst_invalid
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5 from planemo.lint import lint_xsd
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6 from planemo.shed import (
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7 REPO_TYPE_UNRESTRICTED,
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8 REPO_TYPE_TOOL_DEP,
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9 REPO_TYPE_SUITE,
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10 CURRENT_CATEGORIES,
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11 validate_repo_owner,
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12 validate_repo_name,
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13 )
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14 from planemo.tool_lint import (
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15 build_lint_args,
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16 yield_tool_xmls,
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17 handle_tool_load_error,
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18 )
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19 from planemo.shed2tap import base
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20 from planemo.xml import XSDS_PATH
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21
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22
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23 from planemo.io import info
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24 from planemo.io import error
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25
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26 from galaxy.tools.lint import lint_xml_with
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27
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28 TOOL_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "tool_dependencies.xsd")
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29 REPO_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "repository_dependencies.xsd")
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30
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31
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32 VALID_REPOSITORY_TYPES = [
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33 REPO_TYPE_UNRESTRICTED,
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34 REPO_TYPE_TOOL_DEP,
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35 REPO_TYPE_SUITE,
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36 ]
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37
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38 SHED_METADATA = [
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39 "description",
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40 "long_description",
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41 "remote_repository_url",
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42 "homepage_url",
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43 "categories",
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44 ]
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45
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46
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47 def lint_repository(ctx, realized_repository, **kwds):
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48 # TODO: this really needs to start working with realized path.
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49 failed = False
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50 path = realized_repository.real_path
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51 info("Linting repository %s" % path)
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52 lint_args = build_lint_args(ctx, **kwds)
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53 lint_ctx = LintContext(lint_args["level"])
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54 lint_ctx.lint(
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55 "lint_expansion",
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56 lint_expansion,
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57 realized_repository,
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58 )
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59 lint_ctx.lint(
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60 "lint_expected_files",
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61 lint_expected_files,
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62 realized_repository,
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63 )
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64 lint_ctx.lint(
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65 "lint_tool_dependencies_xsd",
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66 lint_tool_dependencies_xsd,
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67 path,
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68 )
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69 lint_ctx.lint(
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70 "lint_tool_dependencies_actions",
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71 lint_tool_dependencies_actions,
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72 path,
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73 )
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74 lint_ctx.lint(
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75 "lint_repository_dependencies",
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76 lint_repository_dependencies,
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77 path,
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78 )
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79 lint_ctx.lint(
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80 "lint_shed_yaml",
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81 lint_shed_yaml,
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82 realized_repository,
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83 )
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84 lint_ctx.lint(
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85 "lint_readme",
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86 lint_readme,
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87 path,
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88 )
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89 if kwds["tools"]:
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90 for (tool_path, tool_xml) in yield_tool_xmls(ctx, path,
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91 recursive=True):
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92 info("+Linting tool %s" % tool_path)
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93 if handle_tool_load_error(tool_path, tool_xml):
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94 failed = True
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95 continue
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96 lint_xml_with(
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97 lint_ctx,
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98 tool_xml,
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99 extra_modules=lint_args["extra_modules"]
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100 )
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101 if kwds["ensure_metadata"]:
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102 lint_ctx.lint(
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103 "lint_shed_metadata",
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104 lint_shed_metadata,
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105 realized_repository,
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106 )
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107 if not failed:
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108 failed = lint_ctx.failed(lint_args["fail_level"])
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109 if failed:
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110 error("Failed linting")
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111 return 1 if failed else 0
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112
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113
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114 def lint_expansion(realized_repository, lint_ctx):
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115 missing = realized_repository.missing
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116 if missing:
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117 msg = "Failed to expand inclusions %s" % missing
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118 lint_ctx.warn(msg)
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119 else:
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120 lint_ctx.info("Included files all found.")
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121
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122
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123 def lint_shed_metadata(realized_repository, lint_ctx):
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124 found_all = True
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125 for key in SHED_METADATA:
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126 if key not in realized_repository.config:
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127 found_all = False
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128 lint_ctx.warn(
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129 "Missing shed metadata field [%s] for repository" % key
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130 )
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131 if found_all:
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132 lint_ctx.info(
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133 "Found all shed metadata fields required for automated repository "
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134 "creation and/or updates."
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135 )
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136
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137
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138 def lint_readme(path, lint_ctx):
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139 readme_rst = os.path.join(path, "README.rst")
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140 readme = os.path.join(path, "README")
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141 readme_txt = os.path.join(path, "README.txt")
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142
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143 readme_found = False
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144 for readme in [readme_rst, readme, readme_txt]:
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145 if os.path.exists(readme):
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146 readme_found = readme
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147
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148 readme_md = os.path.join(path, "README.md")
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149 if not readme_found and os.path.exists(readme_md):
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150 lint_ctx.warn("Tool Shed doesn't render markdown, "
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151 "README.md is invalid readme.")
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152 return
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153
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154 if not readme_found:
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155 # TODO: filter on TYPE and make this a warning if
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156 # unrestricted repository - need to update iuc standards
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157 # first though.
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158 lint_ctx.info("No README found skipping.")
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159 return
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160
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161 if readme_found.endswith(".rst"):
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162 readme_text = open(readme_found, "r").read()
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163 invalid_rst = rst_invalid(readme_text)
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164 if invalid_rst:
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165 template = "Invalid restructured text found in README [%s]."
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166 msg = template % invalid_rst
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167 lint_ctx.warn(msg)
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168 return
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169 lint_ctx.info("README found containing valid reStructuredText.")
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170 else:
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171 lint_ctx.info("README found containing plain text.")
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172
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173
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174 def lint_tool_dependencies_xsd(path, lint_ctx):
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175 tool_dependencies = os.path.join(path, "tool_dependencies.xml")
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176 if not os.path.exists(tool_dependencies):
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177 lint_ctx.info("No tool_dependencies.xml, skipping.")
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178 return
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179 lint_xsd(lint_ctx, TOOL_DEPENDENCIES_XSD, tool_dependencies)
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180
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181
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182 def lint_tool_dependencies_actions(path, lint_ctx):
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183 tool_dependencies = os.path.join(path, "tool_dependencies.xml")
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184 if not os.path.exists(tool_dependencies):
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185 lint_ctx.info("No tool_dependencies.xml, skipping.")
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186 return
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187 try:
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188 base.Dependencies(tool_dependencies)
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189 lint_ctx.info("Parsed tool dependencies.")
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190 except Exception as e:
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191 import sys
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192 import traceback
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193 exc_type, exc_value, exc_traceback = sys.exc_info()
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194 traceback.print_tb(exc_traceback, limit=1, file=sys.stdout)
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195 traceback.print_exc()
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196 template = "Problem parsing tool_dependenies.xml [%s]"
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197 msg = template % str(e)
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198 lint_ctx.warn(msg)
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199 return
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200
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201
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202 def lint_expected_files(realized_repository, lint_ctx):
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203 if realized_repository.is_package:
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204 if not os.path.exists(realized_repository.tool_dependencies_path):
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205 lint_ctx.warn("Package repository does not contain a "
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206 "tool_dependencies.xml file.")
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207
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208 if realized_repository.is_suite:
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209 if not os.path.exists(realized_repository.repo_dependencies_path):
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210 lint_ctx.warn("Suite repository does not contain a "
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211 "repository_dependencies.xml file.")
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212
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213
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214 def lint_repository_dependencies(path, lint_ctx):
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215 repo_dependencies = os.path.join(path, "repository_dependencies.xml")
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216 if not os.path.exists(repo_dependencies):
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217 lint_ctx.info("No repository_dependencies.xml, skipping.")
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218 return
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219 lint_xsd(lint_ctx, REPO_DEPENDENCIES_XSD, repo_dependencies)
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220
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221
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222 def lint_shed_yaml(realized_repository, lint_ctx):
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223 path = realized_repository.real_path
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224 shed_yaml = os.path.join(path, ".shed.yml")
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225 if not os.path.exists(shed_yaml):
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226 lint_ctx.info("No .shed.yml file found, skipping.")
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227 return
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228 try:
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229 yaml.load(open(shed_yaml, "r"))
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230 except Exception as e:
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231 lint_ctx.warn("Failed to parse .shed.yml file [%s]" % str(e))
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232 return
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233 lint_ctx.info(".shed.yml found and appears to be valid YAML.")
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234 _lint_shed_contents(lint_ctx, realized_repository)
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235
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236
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237 def _lint_shed_contents(lint_ctx, realized_repository):
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238 config = realized_repository.config
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239
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240 def _lint_if_present(key, func, *args):
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241 value = config.get(key, None)
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242 if value is not None:
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243 msg = func(value, *args)
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244 if msg:
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245 lint_ctx.warn(msg)
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246
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247 _lint_if_present("owner", validate_repo_owner)
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248 _lint_if_present("name", validate_repo_name)
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249 _lint_if_present("type", _validate_repo_type, config["name"])
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250 _lint_if_present("categories", _validate_categories, realized_repository)
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251
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252
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253 def _validate_repo_type(repo_type, name):
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254 if repo_type not in VALID_REPOSITORY_TYPES:
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255 return "Invalid repository type specified [%s]" % repo_type
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256
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257 is_dep = repo_type == "tool_dependency_definition"
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258 is_suite = repo_type == "repository_suite_definition"
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259 if is_dep and not name.startswith("package_"):
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260 return ("Tool dependency definition repositories should have names "
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261 "starting with package_")
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262 if is_suite and not name.startswith("suite_"):
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263 return ("Repository suite definition repositories should have names "
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264 "starting with suite_")
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265 if name.startswith("package_") or name.startswith("suite_"):
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266 if repo_type == "unrestricted":
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267 return ("Repository name indicated specialized repository type "
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268 "but repository is listed as unrestricted.")
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269
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270
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271 def _validate_categories(categories, realized_repository):
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272 msg = None
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273 if len(categories) == 0:
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274 msg = "Repository should specify one or more categories."
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275 else:
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276 for category in categories:
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277 unknown_categories = []
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278 if category not in CURRENT_CATEGORIES:
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279 unknown_categories.append(category)
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280 if unknown_categories:
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281 msg = "Categories [%s] unknown." % unknown_categories
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282 if realized_repository.is_package:
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283 if "Tool Dependency Packages" not in categories:
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284 msg = ("Packages should be placed and should only be placed "
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285 "in the category 'Tool Dependency Packages'.")
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286
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287 return msg