Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/lint.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """Utilities to help linting various targets."""
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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
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6 import requests
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7 from galaxy.tool_util.lint import LintContext
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8 from six.moves.urllib.request import urlopen
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9
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10 import planemo.linters.biocontainer_registered
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11 import planemo.linters.conda_requirements
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12 import planemo.linters.doi
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13 import planemo.linters.urls
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14 import planemo.linters.xsd
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15 from planemo.io import error
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16 from planemo.shed import find_urls_for_xml
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17 from planemo.xml import validation
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18
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19
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20 def build_lint_args(ctx, **kwds):
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21 """Handle common report, error, and skip linting arguments."""
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22 report_level = kwds.get("report_level", "all")
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23 fail_level = kwds.get("fail_level", "warn")
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24 skip = kwds.get("skip", None)
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25 if skip is None:
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26 skip = ctx.global_config.get("lint_skip", "")
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27 if isinstance(skip, list):
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28 skip = ",".join(skip)
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29
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30 skip_types = [s.strip() for s in skip.split(",")]
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31 lint_args = dict(
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32 level=report_level,
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33 fail_level=fail_level,
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34 extra_modules=_lint_extra_modules(**kwds),
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35 skip_types=skip_types,
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36 )
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37 return lint_args
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38
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39
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40 # TODO: Move this back to tool_lint.
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41 def _lint_extra_modules(**kwds):
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42 linters = []
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43 if kwds.get("xsd", True):
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44 linters.append(planemo.linters.xsd)
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45
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46 if kwds.get("doi", False):
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47 linters.append(planemo.linters.doi)
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48
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49 if kwds.get("urls", False):
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50 linters.append(planemo.linters.urls)
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51
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52 if kwds.get("conda_requirements", False):
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53 linters.append(planemo.linters.conda_requirements)
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54
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55 if kwds.get("biocontainer", False):
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56 linters.append(planemo.linters.biocontainer_registered)
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57
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58 return linters
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59
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60
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61 def setup_lint(ctx, **kwds):
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62 """Setup lint_args and lint_ctx to begin linting a target."""
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63 lint_args = build_lint_args(ctx, **kwds)
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64 lint_ctx = LintContext(lint_args["level"])
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65 return lint_args, lint_ctx
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66
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67
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68 def handle_lint_complete(lint_ctx, lint_args, failed=False):
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69 """Complete linting of a target and decide exit code."""
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70 if not failed:
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71 failed = lint_ctx.failed(lint_args["fail_level"])
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72 if failed:
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73 error("Failed linting")
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74 return 1 if failed else 0
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75
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76
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77 def lint_dois(tool_xml, lint_ctx):
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78 """Find referenced DOIs and check they have valid with https://doi.org."""
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79 dois = find_dois_for_xml(tool_xml)
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80 for publication in dois:
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81 is_doi(publication, lint_ctx)
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82
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83
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84 def find_dois_for_xml(tool_xml):
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85 dois = []
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86 for element in tool_xml.getroot().findall("citations"):
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87 for citation in list(element):
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88 if citation.tag == 'citation' and citation.attrib.get('type', '') == 'doi':
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89 dois.append(citation.text)
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90 return dois
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91
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92
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93 def is_doi(publication_id, lint_ctx):
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94 """Check if dx.doi knows about the ``publication_id``."""
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95 base_url = "https://doi.org"
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96 if publication_id is None:
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97 lint_ctx.error('Empty DOI citation')
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98 return
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99 publication_id = publication_id.strip()
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100 doiless_publication_id = publication_id.split("doi:", 1)[-1]
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101 if not doiless_publication_id:
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102 lint_ctx.error('Empty DOI citation')
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103 return
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104 url = "%s/%s" % (base_url, doiless_publication_id)
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105 r = requests.get(url)
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106 if r.status_code == 200:
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107 if publication_id != doiless_publication_id:
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108 lint_ctx.error("%s is valid, but Galaxy expects DOI without 'doi:' prefix" % publication_id)
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109 else:
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110 lint_ctx.info("%s is a valid DOI" % publication_id)
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111 elif r.status_code == 404:
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112 lint_ctx.error("%s is not a valid DOI" % publication_id)
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113 else:
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114 lint_ctx.warn("dx.doi returned unexpected status code %d" % r.status_code)
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115
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116
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117 def lint_xsd(lint_ctx, schema_path, path):
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118 """Lint XML at specified path with supplied schema."""
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119 name = lint_ctx.object_name or os.path.basename(path)
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120 validator = validation.get_validator(require=True)
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121 validation_result = validator.validate(schema_path, path)
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122 if not validation_result.passed:
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123 msg = "Invalid XML found in file: %s. Errors [%s]"
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124 msg = msg % (name, validation_result.output)
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125 lint_ctx.error(msg)
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126 else:
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127 lint_ctx.info("File validates against XML schema.")
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128
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129
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130 def lint_urls(root, lint_ctx):
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131 """Find referenced URLs and verify they are valid."""
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132 urls, docs = find_urls_for_xml(root)
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133
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134 # This is from Google Chome on macOS, current at time of writing:
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135 BROWSER_USER_AGENT = "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/62.0.3202.75 Safari/537.36"
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136
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137 def validate_url(url, lint_ctx, user_agent=None):
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138 is_valid = True
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139 if url.startswith('http://') or url.startswith('https://'):
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140 if user_agent:
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141 headers = {"User-Agent": user_agent, 'Accept': '*/*'}
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142 else:
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143 headers = None
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144 r = None
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145 try:
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146 r = requests.get(url, headers=headers, stream=True)
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147 r.raise_for_status()
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148 next(r.iter_content(1000))
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149 except Exception as e:
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150 if r and r.status_code == 429:
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151 # too many requests
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152 pass
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153 else:
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154 is_valid = False
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155 lint_ctx.error("Error '%s' accessing %s" % (e, url))
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156 else:
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157 try:
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158 with urlopen(url) as handle:
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159 handle.read(100)
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160 except Exception as e:
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161 is_valid = False
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162 lint_ctx.error("Error '%s' accessing %s" % (e, url))
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163 if is_valid:
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164 lint_ctx.info("URL OK %s" % url)
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165
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166 for url in urls:
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167 validate_url(url, lint_ctx)
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168 for url in docs:
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169 validate_url(url, lint_ctx, BROWSER_USER_AGENT)
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170
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171
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172 __all__ = (
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173 "build_lint_args",
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174 "handle_lint_complete",
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175 "lint_dois",
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176 "lint_urls",
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177 "lint_xsd",
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178 )