Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/parser/stdio.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 class StdioErrorLevel: |
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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: |
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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: |
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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 |