annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/stdio.py @ 1:56ad4e20f292 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400 (2020-07-31)
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1 class StdioErrorLevel(object):
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2 """
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3 These determine stdio-based error levels from matching on regular expressions
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4 and exit codes. They are meant to be used comparatively, such as showing
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5 that warning < fatal. This is really meant to just be an enum.
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6 """
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7 NO_ERROR = 0
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8 LOG = 1
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9 QC = 1.1
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10 WARNING = 2
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11 FATAL = 3
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12 FATAL_OOM = 4
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13 MAX = 4
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14 descs = {
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15 NO_ERROR: 'No error',
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16 LOG: 'Log',
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17 QC: 'QC',
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18 WARNING: 'Warning',
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19 FATAL: 'Fatal error',
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20 FATAL_OOM: 'Out of memory error',
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21 }
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22
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23 @staticmethod
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24 def desc(error_level):
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25 err_msg = "Unknown error"
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26 if error_level > 0 and error_level <= StdioErrorLevel.MAX:
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27 err_msg = StdioErrorLevel.descs[error_level]
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28 return err_msg
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29
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30
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31 class ToolStdioExitCode(object):
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32 """
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33 This is a container for the <stdio> element's <exit_code> subelement.
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34 The exit_code element has a range of exit codes and the error level.
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35 """
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36
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37 def __init__(self, as_dict=None):
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38 as_dict = as_dict or {}
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39 self.range_start = as_dict.get("range_start", float("-inf"))
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40 self.range_end = as_dict.get("range_end", float("inf"))
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41 self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL)
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42 self.desc = as_dict.get("desc", "")
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43
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44 def to_dict(self):
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45 return {
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46 "class": "ToolStdioExitCode",
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47 "range_start": self.range_start,
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48 "range_end": self.range_end,
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49 "error_level": self.error_level,
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50 "desc": self.desc,
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51 }
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52
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53
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54 class ToolStdioRegex(object):
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55 """
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56 This is a container for the <stdio> element's regex subelement.
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57 The regex subelement has a "match" attribute, a "sources"
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58 attribute that contains "output" and/or "error", and a "level"
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59 attribute that contains "warning" or "fatal".
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60 """
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61
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62 def __init__(self, as_dict=None):
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63 as_dict = as_dict or {}
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64 self.match = as_dict.get("match", "")
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65 self.stdout_match = as_dict.get("stdout_match", False)
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66 self.stderr_match = as_dict.get("stderr_match", False)
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67 self.error_level = as_dict.get("error_level", StdioErrorLevel.FATAL)
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68 self.desc = as_dict.get("desc", "")
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69
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70 def to_dict(self):
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71 return {
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72 "class": "ToolStdioRegex",
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73 "match": self.match,
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74 "stdout_match": self.stdout_match,
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75 "stderr_match": self.stderr_match,
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76 "error_level": self.error_level,
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77 "desc": self.desc,
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78 }
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79
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80
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81 def error_on_exit_code(out_of_memory_exit_code=None):
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82 exit_codes = []
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83
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84 if out_of_memory_exit_code:
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85 exit_code_oom = ToolStdioExitCode()
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86 exit_code_oom.range_start = int(out_of_memory_exit_code)
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87 exit_code_oom.range_end = int(out_of_memory_exit_code)
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88 _set_oom(exit_code_oom)
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89 exit_codes.append(exit_code_oom)
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90
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91 exit_code_lower = ToolStdioExitCode()
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92 exit_code_lower.range_start = float("-inf")
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93 exit_code_lower.range_end = -1
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94 _set_fatal(exit_code_lower)
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95 exit_codes.append(exit_code_lower)
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96 exit_code_high = ToolStdioExitCode()
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97 exit_code_high.range_start = 1
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98 exit_code_high.range_end = float("inf")
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99 _set_fatal(exit_code_high)
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100 exit_codes.append(exit_code_high)
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101 return exit_codes, []
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102
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103
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104 def aggressive_error_checks():
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105 exit_codes, _ = error_on_exit_code()
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106 # these regexes are processed as case insensitive by default
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107 regexes = [
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108 _oom_regex("MemoryError"),
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109 _oom_regex("std::bad_alloc"),
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110 _oom_regex("java.lang.OutOfMemoryError"),
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111 _oom_regex("Out of memory"),
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112 _error_regex("exception:"),
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113 _error_regex("error:")
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114 ]
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115 return exit_codes, regexes
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116
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117
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118 def _oom_regex(match):
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119 regex = ToolStdioRegex()
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120 _set_oom(regex)
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121 regex.match = match
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122 regex.stdout_match = True
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123 regex.stderr_match = True
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124 return regex
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125
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126
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127 def _error_regex(match):
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128 regex = ToolStdioRegex()
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129 _set_fatal(regex)
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130 regex.match = match
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131 regex.stdout_match = True
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132 regex.stderr_match = True
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133 return regex
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134
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135
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136 def _set_oom(obj):
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137 obj.error_level = StdioErrorLevel.FATAL_OOM
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138
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139
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140 def _set_fatal(obj):
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141 obj.error_level = StdioErrorLevel.FATAL