--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo/lib/python3.7/site-packages/galaxy/util/heartbeat.py	Fri Jul 31 00:32:28 2020 -0400
@@ -0,0 +1,193 @@
+import os
+import sys
+import threading
+import time
+import traceback
+
+from six import iteritems
+
+
+def get_current_thread_object_dict():
+    """
+    Get a dictionary of all 'Thread' objects created via the threading
+    module keyed by thread_id. Note that not all interpreter threads
+    have a thread objects, only the main thread and any created via the
+    'threading' module. Threads created via the low level 'thread' module
+    will not be in the returned dictionary.
+
+    HACK: This mucks with the internals of the threading module since that
+          module does not expose any way to match 'Thread' objects with
+          intepreter thread identifiers (though it should).
+    """
+    rval = dict()
+    # Acquire the lock and then union the contents of 'active' and 'limbo'
+    # threads into the return value.
+    threading._active_limbo_lock.acquire()
+    rval.update(threading._active)
+    rval.update(threading._limbo)
+    threading._active_limbo_lock.release()
+    return rval
+
+
+class Heartbeat(threading.Thread):
+    """
+    Thread that periodically dumps the state of all threads to a file
+    """
+
+    def __init__(self, config, name="Heartbeat Thread", period=20, fname="heartbeat.log"):
+        threading.Thread.__init__(self, name=name)
+        self.config = config
+        self.should_stop = False
+        self.period = period
+        self.fname = fname
+        self.file = None
+        self.fname_nonsleeping = None
+        self.file_nonsleeping = None
+        self.pid = None
+        self.nonsleeping_heartbeats = {}
+        # Event to wait on when sleeping, allows us to interrupt for shutdown
+        self.wait_event = threading.Event()
+
+    def run(self):
+        self.pid = os.getpid()
+        self.fname = self.fname.format(
+            server_name=self.config.server_name,
+            pid=self.pid
+        )
+        fname, ext = os.path.splitext(self.fname)
+        self.fname_nonsleeping = fname + '.nonsleeping' + ext
+        wait = self.period
+        if self.period <= 0:
+            wait = 60
+        while not self.should_stop:
+            if self.period > 0:
+                self.dump()
+            self.wait_event.wait(wait)
+
+    def open_logs(self):
+        if self.file is None or self.file.closed:
+            self.file = open(self.fname, "a")
+            self.file_nonsleeping = open(self.fname_nonsleeping, "a")
+            self.file.write("Heartbeat for pid %d thread started at %s\n\n" % (self.pid, time.asctime()))
+            self.file_nonsleeping.write("Non-Sleeping-threads for pid %d thread started at %s\n\n" % (self.pid, time.asctime()))
+
+    def close_logs(self):
+        if self.file is not None and not self.file.closed:
+            self.file.write("Heartbeat for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()))
+            self.file_nonsleeping.write("Non-Sleeping-threads for pid %d thread stopped at %s\n\n" % (self.pid, time.asctime()))
+            self.file.close()
+            self.file_nonsleeping.close()
+
+    def dump(self):
+        self.open_logs()
+        try:
+            # Print separator with timestamp
+            self.file.write("Traceback dump for all threads at %s:\n\n" % time.asctime())
+            # Print the thread states
+            threads = get_current_thread_object_dict()
+            for thread_id, frame in iteritems(sys._current_frames()):
+                if thread_id in threads:
+                    object = repr(threads[thread_id])
+                else:
+                    object = "<No Thread object>"
+                self.file.write("Thread %s, %s:\n\n" % (thread_id, object))
+                traceback.print_stack(frame, file=self.file)
+                self.file.write("\n")
+            self.file.write("End dump\n\n")
+            self.file.flush()
+            self.print_nonsleeping(threads)
+        except Exception:
+            self.file.write("Caught exception attempting to dump thread states:")
+            traceback.print_exc(None, self.file)
+            self.file.write("\n")
+
+    def shutdown(self):
+        self.should_stop = True
+        self.wait_event.set()
+        self.close_logs()
+        self.join()
+
+    def thread_is_sleeping(self, last_stack_frame):
+        """
+        Returns True if the given stack-frame represents a known
+        sleeper function (at least in python 2.5)
+        """
+        _filename = last_stack_frame[0]
+        # _line = last_stack_frame[1]
+        _funcname = last_stack_frame[2]
+        _text = last_stack_frame[3]
+        # Ugly hack to tell if a thread is supposedly sleeping or not
+        # These are the most common sleeping functions I've found.
+        # Is there a better way? (python interpreter internals?)
+        # Tested only with python 2.5
+        if _funcname == "wait" and _text == "waiter.acquire()":
+            return True
+        if _funcname == "wait" and _text == "_sleep(delay)":
+            return True
+        if _funcname == "accept" and _text[-14:] == "_sock.accept()":
+            return True
+        if _funcname in ("monitor", "__monitor", "app_loop", "check") \
+                and _text.startswith("time.sleep(") and _text.endswith(")"):
+            return True
+        if _funcname == "drain_events" and _text == "sleep(polling_interval)":
+            return True
+        # Ugly hack: always skip the heartbeat thread
+        # TODO: get the current thread-id in python
+        #   skip heartbeat thread by thread-id, not by filename
+        if _filename.find("/lib/galaxy/util/heartbeat.py") != -1:
+            return True
+        # By default, assume the thread is not sleeping
+        return False
+
+    def get_interesting_stack_frame(self, stack_frames):
+        """
+        Scans a given backtrace stack frames, returns a single
+        quadraple of [filename, line, function-name, text] of
+        the single, deepest, most interesting frame.
+
+        Interesting being::
+
+          inside the galaxy source code ("/lib/galaxy"),
+          prefreably not an egg.
+        """
+        for _filename, _line, _funcname, _text in reversed(stack_frames):
+            idx = _filename.find("/lib/galaxy/")
+            if idx != -1:
+                relative_filename = _filename[idx:]
+                return (relative_filename, _line, _funcname, _text)
+        # no "/lib/galaxy" code found, return the innermost frame
+        return stack_frames[-1]
+
+    def print_nonsleeping(self, threads_object_dict):
+        self.file_nonsleeping.write("Non-Sleeping threads at %s:\n\n" % time.asctime())
+        all_threads_are_sleeping = True
+        threads = get_current_thread_object_dict()
+        for thread_id, frame in iteritems(sys._current_frames()):
+            if thread_id in threads:
+                object = repr(threads[thread_id])
+            else:
+                object = "<No Thread object>"
+            tb = traceback.extract_stack(frame)
+            if self.thread_is_sleeping(tb[-1]):
+                if thread_id in self.nonsleeping_heartbeats:
+                    del self.nonsleeping_heartbeats[thread_id]
+                continue
+
+            # Count non-sleeping thread heartbeats
+            if thread_id in self.nonsleeping_heartbeats:
+                self.nonsleeping_heartbeats[thread_id] += 1
+            else:
+                self.nonsleeping_heartbeats[thread_id] = 1
+
+            good_frame = self.get_interesting_stack_frame(tb)
+            self.file_nonsleeping.write("Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n  File %s:%d\n    Function \"%s\"\n      %s\n" %
+                (thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3]))
+            all_threads_are_sleeping = False
+
+        if all_threads_are_sleeping:
+            self.file_nonsleeping.write("All threads are sleeping.\n")
+        self.file_nonsleeping.write("\n")
+        self.file_nonsleeping.flush()
+
+    def dump_signal_handler(self, signum, frame):
+        self.dump()