Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/heartbeat.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 import os
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2 import sys
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3 import threading
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4 import time
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5 import traceback
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6
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7 from six import iteritems
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8
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9
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10 def get_current_thread_object_dict():
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11 """
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12 Get a dictionary of all 'Thread' objects created via the threading
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13 module keyed by thread_id. Note that not all interpreter threads
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14 have a thread objects, only the main thread and any created via the
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15 'threading' module. Threads created via the low level 'thread' module
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16 will not be in the returned dictionary.
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17
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18 HACK: This mucks with the internals of the threading module since that
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19 module does not expose any way to match 'Thread' objects with
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20 intepreter thread identifiers (though it should).
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21 """
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22 rval = dict()
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23 # Acquire the lock and then union the contents of 'active' and 'limbo'
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24 # threads into the return value.
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25 threading._active_limbo_lock.acquire()
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26 rval.update(threading._active)
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27 rval.update(threading._limbo)
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28 threading._active_limbo_lock.release()
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29 return rval
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30
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31
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32 class Heartbeat(threading.Thread):
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33 """
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34 Thread that periodically dumps the state of all threads to a file
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35 """
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36
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37 def __init__(self, config, name="Heartbeat Thread", period=20, fname="heartbeat.log"):
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38 threading.Thread.__init__(self, name=name)
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39 self.config = config
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40 self.should_stop = False
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41 self.period = period
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42 self.fname = fname
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43 self.file = None
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44 self.fname_nonsleeping = None
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45 self.file_nonsleeping = None
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46 self.pid = None
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47 self.nonsleeping_heartbeats = {}
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48 # Event to wait on when sleeping, allows us to interrupt for shutdown
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49 self.wait_event = threading.Event()
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50
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51 def run(self):
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52 self.pid = os.getpid()
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53 self.fname = self.fname.format(
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54 server_name=self.config.server_name,
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55 pid=self.pid
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56 )
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57 fname, ext = os.path.splitext(self.fname)
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58 self.fname_nonsleeping = fname + '.nonsleeping' + ext
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59 wait = self.period
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60 if self.period <= 0:
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61 wait = 60
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62 while not self.should_stop:
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63 if self.period > 0:
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64 self.dump()
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65 self.wait_event.wait(wait)
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66
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67 def open_logs(self):
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68 if self.file is None or self.file.closed:
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69 self.file = open(self.fname, "a")
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70 self.file_nonsleeping = open(self.fname_nonsleeping, "a")
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71 self.file.write("Heartbeat for pid %d thread started at %s\n\n" % (self.pid, time.asctime()))
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72 self.file_nonsleeping.write("Non-Sleeping-threads for pid %d thread started at %s\n\n" % (self.pid, time.asctime()))
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73
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74 def close_logs(self):
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75 if self.file is not None and not self.file.closed:
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76 self.file.write("Heartbeat for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()))
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77 self.file_nonsleeping.write("Non-Sleeping-threads for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()))
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78 self.file.close()
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79 self.file_nonsleeping.close()
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80
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81 def dump(self):
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82 self.open_logs()
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83 try:
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84 # Print separator with timestamp
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85 self.file.write("Traceback dump for all threads at %s:\n\n" % time.asctime())
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86 # Print the thread states
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87 threads = get_current_thread_object_dict()
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88 for thread_id, frame in iteritems(sys._current_frames()):
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89 if thread_id in threads:
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90 object = repr(threads[thread_id])
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91 else:
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92 object = "<No Thread object>"
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93 self.file.write("Thread %s, %s:\n\n" % (thread_id, object))
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94 traceback.print_stack(frame, file=self.file)
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95 self.file.write("\n")
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96 self.file.write("End dump\n\n")
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97 self.file.flush()
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98 self.print_nonsleeping(threads)
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99 except Exception:
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100 self.file.write("Caught exception attempting to dump thread states:")
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101 traceback.print_exc(None, self.file)
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102 self.file.write("\n")
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103
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104 def shutdown(self):
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105 self.should_stop = True
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106 self.wait_event.set()
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107 self.close_logs()
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108 self.join()
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109
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110 def thread_is_sleeping(self, last_stack_frame):
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111 """
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112 Returns True if the given stack-frame represents a known
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113 sleeper function (at least in python 2.5)
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114 """
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115 _filename = last_stack_frame[0]
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116 # _line = last_stack_frame[1]
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117 _funcname = last_stack_frame[2]
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118 _text = last_stack_frame[3]
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119 # Ugly hack to tell if a thread is supposedly sleeping or not
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120 # These are the most common sleeping functions I've found.
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121 # Is there a better way? (python interpreter internals?)
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122 # Tested only with python 2.5
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123 if _funcname == "wait" and _text == "waiter.acquire()":
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124 return True
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125 if _funcname == "wait" and _text == "_sleep(delay)":
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126 return True
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127 if _funcname == "accept" and _text[-14:] == "_sock.accept()":
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128 return True
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129 if _funcname in ("monitor", "__monitor", "app_loop", "check") \
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130 and _text.startswith("time.sleep(") and _text.endswith(")"):
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131 return True
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132 if _funcname == "drain_events" and _text == "sleep(polling_interval)":
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133 return True
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134 # Ugly hack: always skip the heartbeat thread
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135 # TODO: get the current thread-id in python
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136 # skip heartbeat thread by thread-id, not by filename
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137 if _filename.find("/lib/galaxy/util/heartbeat.py") != -1:
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138 return True
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139 # By default, assume the thread is not sleeping
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140 return False
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141
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142 def get_interesting_stack_frame(self, stack_frames):
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143 """
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144 Scans a given backtrace stack frames, returns a single
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145 quadraple of [filename, line, function-name, text] of
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146 the single, deepest, most interesting frame.
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147
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148 Interesting being::
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149
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150 inside the galaxy source code ("/lib/galaxy"),
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151 prefreably not an egg.
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152 """
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153 for _filename, _line, _funcname, _text in reversed(stack_frames):
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154 idx = _filename.find("/lib/galaxy/")
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155 if idx != -1:
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156 relative_filename = _filename[idx:]
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157 return (relative_filename, _line, _funcname, _text)
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158 # no "/lib/galaxy" code found, return the innermost frame
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159 return stack_frames[-1]
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160
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161 def print_nonsleeping(self, threads_object_dict):
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162 self.file_nonsleeping.write("Non-Sleeping threads at %s:\n\n" % time.asctime())
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163 all_threads_are_sleeping = True
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164 threads = get_current_thread_object_dict()
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165 for thread_id, frame in iteritems(sys._current_frames()):
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166 if thread_id in threads:
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167 object = repr(threads[thread_id])
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168 else:
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169 object = "<No Thread object>"
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170 tb = traceback.extract_stack(frame)
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171 if self.thread_is_sleeping(tb[-1]):
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172 if thread_id in self.nonsleeping_heartbeats:
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173 del self.nonsleeping_heartbeats[thread_id]
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174 continue
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175
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176 # Count non-sleeping thread heartbeats
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177 if thread_id in self.nonsleeping_heartbeats:
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178 self.nonsleeping_heartbeats[thread_id] += 1
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179 else:
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180 self.nonsleeping_heartbeats[thread_id] = 1
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181
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182 good_frame = self.get_interesting_stack_frame(tb)
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183 self.file_nonsleeping.write("Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function \"%s\"\n %s\n" %
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184 (thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3]))
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185 all_threads_are_sleeping = False
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186
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187 if all_threads_are_sleeping:
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188 self.file_nonsleeping.write("All threads are sleeping.\n")
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189 self.file_nonsleeping.write("\n")
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190 self.file_nonsleeping.flush()
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191
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192 def dump_signal_handler(self, signum, frame):
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193 self.dump()