Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/lint.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """This modules contains the functions that drive the tool linting framework.""" |
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2 |
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3 import inspect |
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4 |
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5 from galaxy.tool_util.parser import get_tool_source |
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6 from galaxy.util import submodules |
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7 from galaxy.util.getargspec import getfullargspec |
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8 |
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9 |
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10 LEVEL_ALL = "all" |
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11 LEVEL_WARN = "warn" |
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12 LEVEL_ERROR = "error" |
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13 |
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14 |
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15 def lint_tool_source(tool_source, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=None, skip_types=None, name=None): |
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16 extra_modules = extra_modules or [] |
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17 skip_types = skip_types or [] |
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18 lint_context = LintContext(level=level, skip_types=skip_types, object_name=name) |
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19 lint_tool_source_with(lint_context, tool_source, extra_modules) |
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20 |
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21 return not lint_context.failed(fail_level) |
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22 |
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23 |
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24 def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=None, skip_types=None, name=None): |
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25 extra_modules = extra_modules or [] |
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26 skip_types = skip_types or [] |
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27 lint_context = LintContext(level=level, skip_types=skip_types, object_name=name) |
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28 lint_xml_with(lint_context, tool_xml, extra_modules) |
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29 |
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30 return not lint_context.failed(fail_level) |
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31 |
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32 |
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33 def lint_tool_source_with(lint_context, tool_source, extra_modules=None): |
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34 extra_modules = extra_modules or [] |
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35 import galaxy.tool_util.linters |
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36 tool_xml = getattr(tool_source, "xml_tree", None) |
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37 linter_modules = submodules.import_submodules(galaxy.tool_util.linters, ordered=True) |
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38 linter_modules.extend(extra_modules) |
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39 for module in linter_modules: |
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40 tool_type = tool_source.parse_tool_type() or "default" |
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41 lint_tool_types = getattr(module, "lint_tool_types", ["default"]) |
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42 if not ("*" in lint_tool_types or tool_type in lint_tool_types): |
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43 continue |
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44 |
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45 for (name, value) in inspect.getmembers(module): |
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46 if callable(value) and name.startswith("lint_"): |
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47 # Look at the first argument to the linter to decide |
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48 # if we should lint the XML description or the abstract |
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49 # tool parser object. |
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50 first_arg = getfullargspec(value).args[0] |
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51 if first_arg == "tool_xml": |
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52 if tool_xml is None: |
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53 # XML linter and non-XML tool, skip for now |
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54 continue |
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55 else: |
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56 lint_context.lint(name, value, tool_xml) |
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57 else: |
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58 lint_context.lint(name, value, tool_source) |
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59 |
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60 |
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61 def lint_xml_with(lint_context, tool_xml, extra_modules=None): |
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62 extra_modules = extra_modules or [] |
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63 tool_source = get_tool_source(xml_tree=tool_xml) |
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64 return lint_tool_source_with(lint_context, tool_source, extra_modules=extra_modules) |
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65 |
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66 |
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67 # TODO: Nothing inherently tool-y about LintContext and in fact |
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68 # it is reused for repositories in planemo. Therefore, it should probably |
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69 # be moved to galaxy.util.lint. |
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70 class LintContext: |
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71 |
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72 def __init__(self, level, skip_types=None, object_name=None): |
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73 self.skip_types = skip_types or [] |
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74 self.level = level |
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75 self.object_name = object_name |
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76 self.found_errors = False |
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77 self.found_warns = False |
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78 |
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79 def lint(self, name, lint_func, lint_target): |
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80 name = name.replace("tsts", "tests")[len("lint_"):] |
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81 if name in self.skip_types: |
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82 return |
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83 self.printed_linter_info = False |
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84 self.valid_messages = [] |
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85 self.info_messages = [] |
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86 self.warn_messages = [] |
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87 self.error_messages = [] |
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88 lint_func(lint_target, self) |
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89 # TODO: colorful emoji if in click CLI. |
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90 if self.error_messages: |
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91 status = "FAIL" |
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92 elif self.warn_messages: |
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93 status = "WARNING" |
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94 else: |
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95 status = "CHECK" |
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96 |
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97 def print_linter_info(): |
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98 if self.printed_linter_info: |
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99 return |
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100 self.printed_linter_info = True |
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101 print(f"Applying linter {name}... {status}") |
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102 |
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103 for message in self.error_messages: |
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104 self.found_errors = True |
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105 print_linter_info() |
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106 print(".. ERROR: %s" % message) |
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107 |
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108 if self.level != LEVEL_ERROR: |
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109 for message in self.warn_messages: |
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110 self.found_warns = True |
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111 print_linter_info() |
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112 print(".. WARNING: %s" % message) |
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113 |
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114 if self.level == LEVEL_ALL: |
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115 for message in self.info_messages: |
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116 print_linter_info() |
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117 print(".. INFO: %s" % message) |
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118 for message in self.valid_messages: |
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119 print_linter_info() |
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120 print(".. CHECK: %s" % message) |
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121 |
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122 def __handle_message(self, message_list, message, *args): |
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123 if args: |
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124 message = message % args |
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125 message_list.append(message) |
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126 |
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127 def valid(self, message, *args): |
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128 self.__handle_message(self.valid_messages, message, *args) |
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129 |
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130 def info(self, message, *args): |
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131 self.__handle_message(self.info_messages, message, *args) |
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132 |
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133 def error(self, message, *args): |
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134 self.__handle_message(self.error_messages, message, *args) |
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135 |
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136 def warn(self, message, *args): |
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137 self.__handle_message(self.warn_messages, message, *args) |
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138 |
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139 def failed(self, fail_level): |
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140 found_warns = self.found_warns |
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141 found_errors = self.found_errors |
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142 if fail_level == LEVEL_WARN: |
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143 lint_fail = (found_warns or found_errors) |
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144 else: |
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145 lint_fail = found_errors |
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146 return lint_fail |