Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/output_checker.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 import re |
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2 from logging import getLogger |
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3 |
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4 from galaxy.tool_util.parser.stdio import StdioErrorLevel |
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5 from galaxy.util import unicodify |
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6 from galaxy.util.bunch import Bunch |
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7 |
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8 log = getLogger(__name__) |
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9 |
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10 DETECTED_JOB_STATE = Bunch( |
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11 OK='ok', |
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12 OUT_OF_MEMORY_ERROR='oom_error', |
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13 GENERIC_ERROR='generic_error', |
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14 ) |
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15 |
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16 ERROR_PEEK_SIZE = 2000 |
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17 |
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18 |
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19 def check_output_regex(job_id_tag, regex, stream, stream_name, job_messages, max_error_level): |
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20 """ |
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21 check a single regex against a stream |
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22 |
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23 regex the regex to check |
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24 stream the stream to search in |
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25 job_messages a list where the descriptions of the detected regexes can be appended |
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26 max_error_level the maximum error level that has been detected so far |
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27 returns the max of the error_level of the regex and the given max_error_level |
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28 """ |
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29 regex_match = re.search(regex.match, stream, re.IGNORECASE) |
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30 if regex_match: |
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31 reason = __regex_err_msg(regex_match, stream_name, regex) |
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32 job_messages.append(reason) |
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33 return max(max_error_level, regex.error_level) |
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34 return max_error_level |
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35 |
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36 |
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37 def check_output(stdio_regexes, stdio_exit_codes, stdout, stderr, tool_exit_code, job_id_tag): |
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38 """ |
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39 Check the output of a tool - given the stdout, stderr, and the tool's |
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40 exit code, return DETECTED_JOB_STATE.OK if the tool exited succesfully or |
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41 error type otherwise. No exceptions should be thrown. If this code encounters |
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42 an exception, it returns OK so that the workflow can continue; |
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43 otherwise, a bug in this code could halt workflow progress. |
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44 |
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45 Note that, if the tool did not define any exit code handling or |
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46 any stdio/stderr handling, then it reverts back to previous behavior: |
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47 if stderr contains anything, then False is returned. |
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48 """ |
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49 # By default, the tool succeeded. This covers the case where the code |
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50 # has a bug but the tool was ok, and it lets a workflow continue. |
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51 state = DETECTED_JOB_STATE.OK |
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52 |
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53 stdout = unicodify(stdout, strip_null=True) |
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54 stderr = unicodify(stderr, strip_null=True) |
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55 |
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56 # messages (descriptions of the detected exit_code and regexes) |
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57 # to be prepended to the stdout/stderr after all exit code and regex tests |
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58 # are done (otherwise added messages are searched again). |
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59 # messages are added it the order of detection |
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60 |
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61 # If job is failed, track why. |
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62 job_messages = [] |
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63 |
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64 try: |
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65 # Check exit codes and match regular expressions against stdout and |
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66 # stderr if this tool was configured to do so. |
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67 # If there is a regular expression for scanning stdout/stderr, |
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68 # then we assume that the tool writer overwrote the default |
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69 # behavior of just setting an error if there is *anything* on |
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70 # stderr. |
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71 if len(stdio_regexes) > 0 or len(stdio_exit_codes) > 0: |
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72 # Check the exit code ranges in the order in which |
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73 # they were specified. Each exit_code is a StdioExitCode |
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74 # that includes an applicable range. If the exit code was in |
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75 # that range, then apply the error level and add a message. |
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76 # If we've reached a fatal error rule, then stop. |
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77 max_error_level = StdioErrorLevel.NO_ERROR |
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78 if tool_exit_code is not None: |
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79 for stdio_exit_code in stdio_exit_codes: |
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80 if (tool_exit_code >= stdio_exit_code.range_start and |
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81 tool_exit_code <= stdio_exit_code.range_end): |
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82 # Tack on a generic description of the code |
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83 # plus a specific code description. For example, |
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84 # this might prepend "Job 42: Warning (Out of Memory)\n". |
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85 code_desc = stdio_exit_code.desc |
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86 if None is code_desc: |
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87 code_desc = "" |
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88 desc = "%s: Exit code %d (%s)" % ( |
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89 StdioErrorLevel.desc(stdio_exit_code.error_level), |
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90 tool_exit_code, |
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91 code_desc) |
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92 reason = { |
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93 'type': 'exit_code', |
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94 'desc': desc, |
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95 'exit_code': tool_exit_code, |
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96 'code_desc': code_desc, |
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97 'error_level': stdio_exit_code.error_level, |
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98 } |
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99 job_messages.append(reason) |
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100 max_error_level = max(max_error_level, |
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101 stdio_exit_code.error_level) |
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102 if max_error_level >= StdioErrorLevel.MAX: |
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103 break |
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104 |
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105 if max_error_level < StdioErrorLevel.FATAL_OOM: |
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106 # We'll examine every regex. Each regex specifies whether |
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107 # it is to be run on stdout, stderr, or both. (It is |
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108 # possible for neither stdout nor stderr to be scanned, |
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109 # but those regexes won't be used.) We record the highest |
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110 # error level, which are currently "warning" and "fatal". |
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111 # If fatal, then we set the job's state to ERROR. |
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112 # If warning, then we still set the job's state to OK |
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113 # but include a message. We'll do this if we haven't seen |
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114 # a fatal error yet |
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115 for regex in stdio_regexes: |
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116 # If ( this regex should be matched against stdout ) |
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117 # - Run the regex's match pattern against stdout |
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118 # - If it matched, then determine the error level. |
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119 # o If it was fatal, then we're done - break. |
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120 if regex.stderr_match: |
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121 max_error_level = check_output_regex(job_id_tag, regex, stderr, 'stderr', job_messages, max_error_level) |
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122 if max_error_level >= StdioErrorLevel.MAX: |
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123 break |
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124 |
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125 if regex.stdout_match: |
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126 max_error_level = check_output_regex(job_id_tag, regex, stdout, 'stdout', job_messages, max_error_level) |
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127 if max_error_level >= StdioErrorLevel.MAX: |
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128 break |
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129 |
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130 # If we encountered a fatal error, then we'll need to set the |
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131 # job state accordingly. Otherwise the job is ok: |
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132 if max_error_level == StdioErrorLevel.FATAL_OOM: |
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133 state = DETECTED_JOB_STATE.OUT_OF_MEMORY_ERROR |
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134 elif max_error_level >= StdioErrorLevel.FATAL: |
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135 reason = '' |
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136 if job_messages: |
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137 reason = f" Reasons are {job_messages}" |
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138 log.info(f"Job error detected, failing job.{reason}") |
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139 state = DETECTED_JOB_STATE.GENERIC_ERROR |
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140 |
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141 # When there are no regular expressions and no exit codes to check, |
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142 # default to the previous behavior: when there's anything on stderr |
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143 # the job has an error, and the job is ok otherwise. |
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144 else: |
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145 # TODO: Add in the tool and job id: |
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146 # log.debug( "Tool did not define exit code or stdio handling; " |
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147 # + "checking stderr for success" ) |
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148 if stderr: |
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149 state = DETECTED_JOB_STATE.GENERIC_ERROR |
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150 peek = stderr[0:ERROR_PEEK_SIZE] if stderr else "" |
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151 log.info(f"Job failed because of contents in the standard error stream: [{peek}]") |
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152 except Exception: |
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153 log.exception("Job state check encountered unexpected exception; assuming execution successful") |
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154 |
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155 return state, stdout, stderr, job_messages |
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156 |
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157 |
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158 def __regex_err_msg(match, stream, regex): |
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159 """ |
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160 Return a message about the match on tool output using the given |
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161 ToolStdioRegex regex object. The regex_match is a MatchObject |
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162 that will contain the string matched on. |
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163 """ |
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164 # Get the description for the error level: |
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165 desc = StdioErrorLevel.desc(regex.error_level) + ": " |
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166 mstart = match.start() |
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167 mend = match.end() |
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168 if mend - mstart > 256: |
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169 match_str = match.string[mstart : mstart + 256] + "..." |
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170 else: |
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171 match_str = match.string[mstart: mend] |
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172 |
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173 # If there's a description for the regular expression, then use it. |
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174 # Otherwise, we'll take the first 256 characters of the match. |
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175 if regex.desc is not None: |
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176 desc += regex.desc |
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177 else: |
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178 desc += "Matched on %s" % match_str |
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179 return { |
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180 "type": "regex", |
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181 "stream": stream, |
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182 "desc": desc, |
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183 "code_desc": regex.desc, |
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184 "match": match_str, |
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185 "error_level": regex.error_level, |
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186 } |