Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/shed_lint.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 """Logic related to linting shed repositories."""
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2 from __future__ import absolute_import
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3
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4 import os
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5 import xml.etree.ElementTree as ET
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6
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7 import yaml
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8 from galaxy.tool_util.lint import lint_tool_source_with
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9 from galaxy.tool_util.linters.help import rst_invalid
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10 from galaxy.util import unicodify
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11
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12 from planemo.io import info
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13 from planemo.lint import (
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14 handle_lint_complete,
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15 lint_urls,
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16 lint_xsd,
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17 setup_lint,
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18 )
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19 from planemo.shed import (
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20 CURRENT_CATEGORIES,
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21 REPO_TYPE_SUITE,
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22 REPO_TYPE_TOOL_DEP,
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23 REPO_TYPE_UNRESTRICTED,
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24 validate_repo_name,
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25 validate_repo_owner,
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26 )
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27 from planemo.shed2tap import base
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28 from planemo.tool_lint import (
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29 handle_tool_load_error,
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30 )
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31 from planemo.tools import yield_tool_sources
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32 from planemo.xml import XSDS_PATH
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33
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34
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35 TOOL_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "tool_dependencies.xsd")
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36 REPO_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "repository_dependencies.xsd")
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37
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38
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39 VALID_REPOSITORY_TYPES = [
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40 REPO_TYPE_UNRESTRICTED,
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41 REPO_TYPE_TOOL_DEP,
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42 REPO_TYPE_SUITE,
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43 ]
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44
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45 SHED_METADATA = [
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46 "description",
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47 "long_description",
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48 "remote_repository_url",
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49 "homepage_url",
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50 "categories",
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51 ]
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52
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53
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54 def lint_repository(ctx, realized_repository, **kwds):
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55 """Lint a realized shed repository.
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56
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57 See :mod:`planemo.shed` for details on constructing a realized
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58 repository data structure.
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59 """
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60 failed = False
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61 path = realized_repository.real_path
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62 info("Linting repository %s" % path)
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63 lint_args, lint_ctx = setup_lint(ctx, **kwds)
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64 lint_ctx.lint(
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65 "lint_expansion",
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66 lint_expansion,
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67 realized_repository,
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68 )
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69 lint_ctx.lint(
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70 "lint_expected_files",
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71 lint_expected_files,
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72 realized_repository,
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73 )
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74 lint_ctx.lint(
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75 "lint_tool_dependencies_xsd",
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76 lint_tool_dependencies_xsd,
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77 realized_repository,
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78 )
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79 lint_ctx.lint(
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80 "lint_tool_dependencies_sha256sum",
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81 lint_tool_dependencies_sha256sum,
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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_tool_dependencies_actions",
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86 lint_tool_dependencies_actions,
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87 realized_repository,
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88 )
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89 lint_ctx.lint(
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90 "lint_repository_dependencies",
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91 lint_repository_dependencies,
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92 realized_repository,
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93 )
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94 lint_ctx.lint(
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95 "lint_shed_yaml",
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96 lint_shed_yaml,
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97 realized_repository,
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98 )
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99 lint_ctx.lint(
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100 "lint_readme",
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101 lint_readme,
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102 realized_repository,
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103 )
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104 if kwds["urls"]:
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105 lint_ctx.lint(
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106 "lint_urls",
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107 lint_tool_dependencies_urls,
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108 realized_repository,
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109 )
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110 if kwds["tools"]:
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111 tools_failed = lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args)
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112 failed = failed or tools_failed
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113 if kwds["ensure_metadata"]:
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114 lint_ctx.lint(
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115 "lint_shed_metadata",
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116 lint_shed_metadata,
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117 realized_repository,
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118 )
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119 return handle_lint_complete(lint_ctx, lint_args, failed=failed)
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120
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121
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122 def lint_repository_tools(ctx, realized_repository, lint_ctx, lint_args):
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123 path = realized_repository.path
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124 for (tool_path, tool_source) in yield_tool_sources(ctx, path,
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125 recursive=True):
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126 original_path = tool_path.replace(path, realized_repository.real_path)
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127 info("+Linting tool %s" % original_path)
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128 if handle_tool_load_error(tool_path, tool_source):
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129 return True
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parents:
diff changeset
130 lint_tool_source_with(
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parents:
diff changeset
131 lint_ctx,
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diff changeset
132 tool_source,
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diff changeset
133 extra_modules=lint_args["extra_modules"]
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parents:
diff changeset
134 )
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diff changeset
135
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diff changeset
136
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parents:
diff changeset
137 def lint_expansion(realized_repository, lint_ctx):
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parents:
diff changeset
138 missing = realized_repository.missing
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parents:
diff changeset
139 if missing:
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diff changeset
140 msg = "Failed to expand inclusions %s" % missing
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diff changeset
141 lint_ctx.warn(msg)
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parents:
diff changeset
142 else:
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diff changeset
143 lint_ctx.info("Included files all found.")
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144
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145
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diff changeset
146 def lint_shed_metadata(realized_repository, lint_ctx):
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147 found_all = True
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diff changeset
148 for key in SHED_METADATA:
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diff changeset
149 if key not in realized_repository.config:
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diff changeset
150 found_all = False
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diff changeset
151 lint_ctx.warn(
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parents:
diff changeset
152 "Missing shed metadata field [%s] for repository" % key
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diff changeset
153 )
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diff changeset
154 if found_all:
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parents:
diff changeset
155 lint_ctx.info(
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156 "Found all shed metadata fields required for automated repository "
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157 "creation and/or updates."
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diff changeset
158 )
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159
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160
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161 def lint_readme(realized_repository, lint_ctx):
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162 path = realized_repository.real_path
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163 readme_rst = os.path.join(path, "README.rst")
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164 readme = os.path.join(path, "README")
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165 readme_txt = os.path.join(path, "README.txt")
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166
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167 readme_found = False
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168 for readme in [readme_rst, readme, readme_txt]:
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parents:
diff changeset
169 if os.path.exists(readme):
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170 readme_found = readme
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171
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172 readme_md = os.path.join(path, "README.md")
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parents:
diff changeset
173 if not readme_found and os.path.exists(readme_md):
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parents:
diff changeset
174 lint_ctx.warn("Tool Shed doesn't render markdown, "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
175 "README.md is invalid readme.")
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diff changeset
176 return
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parents:
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177
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parents:
diff changeset
178 if not readme_found:
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diff changeset
179 # TODO: filter on TYPE and make this a warning if
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diff changeset
180 # unrestricted repository - need to update iuc standards
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diff changeset
181 # first though.
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182 lint_ctx.info("No README found skipping.")
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diff changeset
183 return
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parents:
diff changeset
184
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parents:
diff changeset
185 if readme_found.endswith(".rst"):
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parents:
diff changeset
186 with open(readme_found, "r") as fh:
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187 readme_text = fh.read()
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parents:
diff changeset
188 invalid_rst = rst_invalid(readme_text)
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parents:
diff changeset
189 if invalid_rst:
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diff changeset
190 template = "Invalid restructured text found in README [%s]."
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parents:
diff changeset
191 msg = template % invalid_rst
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diff changeset
192 lint_ctx.warn(msg)
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diff changeset
193 return
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parents:
diff changeset
194 lint_ctx.info("README found containing valid reStructuredText.")
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diff changeset
195 else:
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diff changeset
196 lint_ctx.info("README found containing plain text.")
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parents:
diff changeset
197
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diff changeset
198
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diff changeset
199 def lint_tool_dependencies_urls(realized_repository, lint_ctx):
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200 path = realized_repository.real_path
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diff changeset
201 tool_dependencies = os.path.join(path, "tool_dependencies.xml")
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parents:
diff changeset
202 if not os.path.exists(tool_dependencies):
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parents:
diff changeset
203 lint_ctx.info("No tool_dependencies.xml, skipping.")
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parents:
diff changeset
204 return
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parents:
diff changeset
205
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parents:
diff changeset
206 root = ET.parse(tool_dependencies).getroot()
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diff changeset
207 lint_urls(root, lint_ctx)
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parents:
diff changeset
208
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diff changeset
209
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parents:
diff changeset
210 def lint_tool_dependencies_sha256sum(realized_repository, lint_ctx):
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parents:
diff changeset
211 tool_dependencies = os.path.join(realized_repository.real_path, "tool_dependencies.xml")
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parents:
diff changeset
212 if not os.path.exists(tool_dependencies):
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parents:
diff changeset
213 lint_ctx.info("No tool_dependencies.xml, skipping.")
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parents:
diff changeset
214 return
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shellac
parents:
diff changeset
215
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parents:
diff changeset
216 root = ET.parse(tool_dependencies).getroot()
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shellac
parents:
diff changeset
217
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parents:
diff changeset
218 count = 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
219 for action in root.findall(".//action"):
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parents:
diff changeset
220 assert action.tag == "action"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
221 if action.attrib.get('type', '') not in ['download_by_url', 'download_file']:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
222 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
223 url = action.text.strip()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
224 checksum = action.attrib.get('sha256sum', '')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
225 if not checksum:
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parents:
diff changeset
226 lint_ctx.warn("Missing checksum for %s" % url)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
227 elif len(checksum) != 64 or not set("0123456789abcdef").issuperset(checksum.lower()):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
228 lint_ctx.error("Invalid checksum %r for %s" % (checksum, url))
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parents:
diff changeset
229 else:
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parents:
diff changeset
230 # TODO - See planned --verify option to check it matches
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parents:
diff changeset
231 # lint_ctx.info("SHA256 checkum listed for %s" % url)
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parents:
diff changeset
232 count += 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
233 if count:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
234 lint_ctx.info("Found %i download action(s) with SHA256 checksums" % count)
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shellac
parents:
diff changeset
235
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
236
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
237 def lint_tool_dependencies_xsd(realized_repository, lint_ctx):
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parents:
diff changeset
238 path = realized_repository.real_path
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parents:
diff changeset
239 tool_dependencies = os.path.join(path, "tool_dependencies.xml")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
240 if not os.path.exists(tool_dependencies):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
241 lint_ctx.info("No tool_dependencies.xml, skipping.")
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shellac
parents:
diff changeset
242 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
243 lint_xsd(lint_ctx, TOOL_DEPENDENCIES_XSD, tool_dependencies)
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shellac
parents:
diff changeset
244
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
245
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
246 def lint_tool_dependencies_actions(realized_repository, lint_ctx):
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parents:
diff changeset
247 path = realized_repository.real_path
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shellac
parents:
diff changeset
248 tool_dependencies = os.path.join(path, "tool_dependencies.xml")
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shellac
parents:
diff changeset
249 if not os.path.exists(tool_dependencies):
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shellac
parents:
diff changeset
250 lint_ctx.info("No tool_dependencies.xml, skipping.")
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shellac
parents:
diff changeset
251 return
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
252 try:
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parents:
diff changeset
253 base.Dependencies(tool_dependencies)
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parents:
diff changeset
254 lint_ctx.info("Parsed tool dependencies.")
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parents:
diff changeset
255 except Exception as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
256 import sys
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257 import traceback
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258 exc_type, exc_value, exc_traceback = sys.exc_info()
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259 traceback.print_tb(exc_traceback, limit=1, file=sys.stdout)
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260 traceback.print_exc()
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261 template = "Problem parsing tool_dependenies.xml [%s]"
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262 msg = template % unicodify(e)
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263 lint_ctx.warn(msg)
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264 return
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265
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266
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267 def lint_expected_files(realized_repository, lint_ctx):
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268 if realized_repository.is_package:
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269 if not os.path.exists(realized_repository.tool_dependencies_path):
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270 lint_ctx.warn("Package repository does not contain a "
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271 "tool_dependencies.xml file.")
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272
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273 if realized_repository.is_suite:
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274 if not os.path.exists(realized_repository.repo_dependencies_path):
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275 lint_ctx.warn("Suite repository does not contain a "
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276 "repository_dependencies.xml file.")
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277
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278
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279 def lint_repository_dependencies(realized_repository, lint_ctx):
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280 path = realized_repository.real_path
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281 repo_dependencies = os.path.join(path, "repository_dependencies.xml")
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282 if not os.path.exists(repo_dependencies):
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283 lint_ctx.info("No repository_dependencies.xml, skipping.")
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284 return
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285 lint_xsd(lint_ctx, REPO_DEPENDENCIES_XSD, repo_dependencies)
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286
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287
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288 def lint_shed_yaml(realized_repository, lint_ctx):
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289 path = realized_repository.real_path
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290 shed_yaml = os.path.join(path, ".shed.yml")
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291 if not os.path.exists(shed_yaml):
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292 lint_ctx.info("No .shed.yml file found, skipping.")
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293 return
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294 try:
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295 with open(shed_yaml, "r") as fh:
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296 yaml.safe_load(fh)
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297 except Exception as e:
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298 lint_ctx.warn("Failed to parse .shed.yml file [%s]" % unicodify(e))
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299 return
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300 lint_ctx.info(".shed.yml found and appears to be valid YAML.")
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301 _lint_shed_contents(lint_ctx, realized_repository)
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302
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303
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304 def _lint_shed_contents(lint_ctx, realized_repository):
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305 config = realized_repository.config
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306
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307 def _lint_if_present(key, func, *args):
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308 value = config.get(key, None)
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309 if value is not None:
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310 msg = func(value, *args)
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311 if msg:
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312 lint_ctx.warn(msg)
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313
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314 _lint_if_present("owner", validate_repo_owner)
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315 _lint_if_present("name", validate_repo_name)
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316 _lint_if_present("type", _validate_repo_type, config["name"])
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317 _lint_if_present("categories", _validate_categories, realized_repository)
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318
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319
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320 def _validate_repo_type(repo_type, name):
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321 if repo_type not in VALID_REPOSITORY_TYPES:
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322 return "Invalid repository type specified [%s]" % repo_type
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323
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324 is_dep = repo_type == "tool_dependency_definition"
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325 is_suite = repo_type == "repository_suite_definition"
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326 if is_dep and not name.startswith("package_"):
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327 return ("Tool dependency definition repositories should have names "
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328 "starting with package_")
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329 if is_suite and not name.startswith("suite_"):
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330 return ("Repository suite definition repositories should have names "
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331 "starting with suite_")
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332 if name.startswith("package_") or name.startswith("suite_"):
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333 if repo_type == "unrestricted":
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334 return ("Repository name indicated specialized repository type "
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335 "but repository is listed as unrestricted.")
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336
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337
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338 def _validate_categories(categories, realized_repository):
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339 msg = None
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340 if len(categories) == 0:
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341 msg = "Repository should specify one or more categories."
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342 else:
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343 for category in categories:
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344 unknown_categories = []
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345 if category not in CURRENT_CATEGORIES:
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346 unknown_categories.append(category)
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347 if unknown_categories:
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348 msg = "Categories [%s] unknown." % unknown_categories
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349 if realized_repository.is_package:
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diff changeset
350 if "Tool Dependency Packages" not in categories:
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351 msg = ("Packages should be placed and should only be placed "
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352 "in the category 'Tool Dependency Packages'.")
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353
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diff changeset
354 return msg
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355
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356
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357 __all__ = (
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358 "lint_repository",
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359 )