Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/ephemeris_log.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 import logging
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2 import tempfile
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3
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4
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5 class ProgressConsoleHandler(logging.StreamHandler):
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6 """
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7 A handler class which allows the cursor to stay on
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8 one line for selected messages
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9 """
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10 on_same_line = False
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11
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12 def emit(self, record):
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13 try:
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14 msg = self.format(record)
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15 stream = self.stream
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16 same_line = hasattr(record, 'same_line')
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17 if self.on_same_line and not same_line:
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18 stream.write('\r\n')
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19 stream.write(msg)
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20 if same_line:
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21 stream.write('.')
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22 self.on_same_line = True
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23 else:
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24 stream.write('\r\n')
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25 self.on_same_line = False
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26 self.flush()
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27 except (KeyboardInterrupt, SystemExit):
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28 raise
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29 except Exception:
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30 self.handleError(record)
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31
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32
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33 def disable_external_library_logging():
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34 # Omit (most of the) logging by external libraries
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35 logging.getLogger('bioblend').setLevel(logging.ERROR)
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36 logging.getLogger('requests').setLevel(logging.ERROR)
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37 try:
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38 logging.captureWarnings(True) # Capture HTTPS warngings from urllib3
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39 except AttributeError:
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40 pass
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42
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43 def setup_global_logger(name, log_file=None):
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44 formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s')
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45 progress = ProgressConsoleHandler()
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46 console = logging.StreamHandler()
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47 console.setFormatter(formatter)
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48
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49 logger = logging.getLogger(name)
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50 logger.setLevel(logging.DEBUG)
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51 logger.addHandler(progress)
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52
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53 if not log_file:
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54 # delete = false is chosen here because it is always nice to have a log file
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55 # ready if you need to debug. Not having the "if only I had set a log file"
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56 # moment after the fact.
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57 temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False)
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58 log_file = temp.name
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59 file_handler = logging.FileHandler(log_file)
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60 logger.addHandler(file_handler)
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61 logger.info("Storing log file in: {0}".format(log_file))
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62 return logger