Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/tool_util/lint.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 """This modules contains the functions that drive the tool linting framework."""
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2 from __future__ import print_function
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3
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4 import inspect
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5
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6 from galaxy.tool_util.parser import get_tool_source
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7 from galaxy.util import submodules
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8 from galaxy.util.getargspec import getfullargspec
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9
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10
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11 LEVEL_ALL = "all"
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12 LEVEL_WARN = "warn"
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13 LEVEL_ERROR = "error"
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14
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15
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16 def lint_tool_source(tool_source, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=[], skip_types=[], name=None):
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17 lint_context = LintContext(level=level, skip_types=skip_types, object_name=name)
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18 lint_tool_source_with(lint_context, tool_source, extra_modules)
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19
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20 return not lint_context.failed(fail_level)
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21
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22
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23 def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=[], skip_types=[], name=None):
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24 lint_context = LintContext(level=level, skip_types=skip_types, object_name=name)
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25 lint_xml_with(lint_context, tool_xml, extra_modules)
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26
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27 return not lint_context.failed(fail_level)
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29
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30 def lint_tool_source_with(lint_context, tool_source, extra_modules=[]):
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31 import galaxy.tool_util.linters
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32 tool_xml = getattr(tool_source, "xml_tree", None)
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33 linter_modules = submodules.import_submodules(galaxy.tool_util.linters, ordered=True)
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34 linter_modules.extend(extra_modules)
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35 for module in linter_modules:
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36 tool_type = tool_source.parse_tool_type() or "default"
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37 lint_tool_types = getattr(module, "lint_tool_types", ["default"])
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38 if not ("*" in lint_tool_types or tool_type in lint_tool_types):
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39 continue
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40
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41 for (name, value) in inspect.getmembers(module):
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42 if callable(value) and name.startswith("lint_"):
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43 # Look at the first argument to the linter to decide
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44 # if we should lint the XML description or the abstract
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45 # tool parser object.
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46 first_arg = getfullargspec(value).args[0]
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47 if first_arg == "tool_xml":
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48 if tool_xml is None:
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49 # XML linter and non-XML tool, skip for now
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50 continue
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51 else:
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52 lint_context.lint(name, value, tool_xml)
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53 else:
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54 lint_context.lint(name, value, tool_source)
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55
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56
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57 def lint_xml_with(lint_context, tool_xml, extra_modules=[]):
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58 tool_source = get_tool_source(xml_tree=tool_xml)
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59 return lint_tool_source_with(lint_context, tool_source, extra_modules=extra_modules)
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60
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61
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62 # TODO: Nothing inherently tool-y about LintContext and in fact
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63 # it is reused for repositories in planemo. Therefore, it should probably
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64 # be moved to galaxy.util.lint.
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65 class LintContext(object):
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66
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67 def __init__(self, level, skip_types=[], object_name=None):
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68 self.skip_types = skip_types
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69 self.level = level
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70 self.object_name = object_name
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71 self.found_errors = False
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72 self.found_warns = False
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73
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74 def lint(self, name, lint_func, lint_target):
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75 name = name.replace("tsts", "tests")[len("lint_"):]
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76 if name in self.skip_types:
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77 return
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78 self.printed_linter_info = False
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79 self.valid_messages = []
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80 self.info_messages = []
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81 self.warn_messages = []
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82 self.error_messages = []
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83 lint_func(lint_target, self)
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84 # TODO: colorful emoji if in click CLI.
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85 if self.error_messages:
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86 status = "FAIL"
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87 elif self.warn_messages:
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88 status = "WARNING"
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89 else:
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90 status = "CHECK"
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91
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92 def print_linter_info():
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93 if self.printed_linter_info:
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94 return
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95 self.printed_linter_info = True
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96 print("Applying linter %s... %s" % (name, status))
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97
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98 for message in self.error_messages:
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99 self.found_errors = True
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100 print_linter_info()
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101 print(".. ERROR: %s" % message)
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102
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103 if self.level != LEVEL_ERROR:
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104 for message in self.warn_messages:
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105 self.found_warns = True
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106 print_linter_info()
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107 print(".. WARNING: %s" % message)
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108
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109 if self.level == LEVEL_ALL:
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110 for message in self.info_messages:
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111 print_linter_info()
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112 print(".. INFO: %s" % message)
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113 for message in self.valid_messages:
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114 print_linter_info()
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115 print(".. CHECK: %s" % message)
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116
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117 def __handle_message(self, message_list, message, *args):
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118 if args:
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119 message = message % args
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120 message_list.append(message)
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121
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122 def valid(self, message, *args):
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123 self.__handle_message(self.valid_messages, message, *args)
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124
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125 def info(self, message, *args):
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126 self.__handle_message(self.info_messages, message, *args)
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127
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128 def error(self, message, *args):
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129 self.__handle_message(self.error_messages, message, *args)
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130
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131 def warn(self, message, *args):
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132 self.__handle_message(self.warn_messages, message, *args)
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133
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134 def failed(self, fail_level):
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135 found_warns = self.found_warns
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136 found_errors = self.found_errors
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137 if fail_level == LEVEL_WARN:
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138 lint_fail = (found_warns or found_errors)
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139 else:
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140 lint_fail = found_errors
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141 return lint_fail