Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/bioblend/__init__.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 os
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3
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4 from bioblend.config import BioBlendConfigLocations, Config
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5
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6 # Current version of the library
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7 __version__ = '0.13.0'
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8
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9 # default chunk size (in bytes) for reading remote data
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10 try:
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11 import resource
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12 CHUNK_SIZE = resource.getpagesize()
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13 except Exception:
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14 CHUNK_SIZE = 4096
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16
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17 config = Config()
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18
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19
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20 def get_version():
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21 """
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22 Returns a string with the current version of the library (e.g., "0.2.0")
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23 """
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24 return __version__
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25
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26
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27 def init_logging():
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28 """
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29 Initialize BioBlend's logging from a configuration file.
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30 """
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31 for config_file in BioBlendConfigLocations:
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32 try:
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33 logging.config.fileConfig(os.path.expanduser(config_file))
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34 except Exception:
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35 pass
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36
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37
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38 class NullHandler(logging.Handler):
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39 def emit(self, record):
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40 pass
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42
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43 # By default, do not force any logging by the library. If you want to see the
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44 # log messages in your scripts, add the following to the top of your script:
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45 # import logging
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46 # logging.basicConfig(filename="bioblend.log", level=logging.DEBUG)
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47 default_format_string = "%(asctime)s %(name)s [%(levelname)s]: %(message)s"
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48 log = logging.getLogger('bioblend')
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49 log.addHandler(NullHandler())
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50 init_logging()
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51
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52 # Convenience functions to set logging to a particular file or stream
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53 # To enable either of these, simply add the following at the top of a
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54 # bioblend module:
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55 # import bioblend
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56 # bioblend.set_stream_logger(__name__)
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57
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58
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59 def set_file_logger(name, filepath, level=logging.INFO, format_string=None):
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60 global log
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61 if not format_string:
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62 format_string = default_format_string
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63 logger = logging.getLogger(name)
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64 logger.setLevel(level)
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65 fh = logging.FileHandler(filepath)
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66 fh.setLevel(level)
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67 formatter = logging.Formatter(format_string)
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68 fh.setFormatter(formatter)
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69 logger.addHandler(fh)
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70 log = logger
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71
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72
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73 def set_stream_logger(name, level=logging.DEBUG, format_string=None):
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74 global log
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75 if not format_string:
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76 format_string = default_format_string
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77 logger = logging.getLogger(name)
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78 logger.setLevel(level)
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79 fh = logging.StreamHandler()
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80 fh.setLevel(level)
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81 formatter = logging.Formatter(format_string)
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82 fh.setFormatter(formatter)
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83 logger.addHandler(fh)
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84 log = logger
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85
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86
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87 class ConnectionError(Exception):
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88 """
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89 An exception class that is raised when unexpected HTTP responses come back.
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90
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91 Should make it easier to debug when strange HTTP things happen such as a
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92 proxy server getting in the way of the request etc.
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93 @see: body attribute to see the content of the http response
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94 """
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95 def __init__(self, message, body=None, status_code=None):
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96 super(ConnectionError, self).__init__(message)
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97 self.body = body
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98 self.status_code = status_code
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99
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100 def __str__(self):
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101 return "{0}: {1}".format(self.args[0], self.body)