Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/__init__.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 logging |
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2 import os |
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3 |
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4 from bioblend.config import ( |
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5 BioBlendConfigLocations, |
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6 Config, |
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7 ) |
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8 |
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9 # Current version of the library |
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10 __version__ = '0.15.0' |
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11 |
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12 # default chunk size (in bytes) for reading remote data |
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13 try: |
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14 import resource |
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15 CHUNK_SIZE = resource.getpagesize() |
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16 except Exception: |
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17 CHUNK_SIZE = 4096 |
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18 |
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19 |
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20 config = Config() |
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21 |
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22 |
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23 def get_version(): |
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24 """ |
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25 Returns a string with the current version of the library (e.g., "0.2.0") |
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26 """ |
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27 return __version__ |
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28 |
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29 |
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30 def init_logging(): |
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31 """ |
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32 Initialize BioBlend's logging from a configuration file. |
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33 """ |
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34 for config_file in BioBlendConfigLocations: |
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35 try: |
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36 logging.config.fileConfig(os.path.expanduser(config_file)) |
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37 except Exception: |
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38 pass |
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39 |
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40 |
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41 class NullHandler(logging.Handler): |
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42 def emit(self, record): |
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43 pass |
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44 |
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45 |
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46 # By default, do not force any logging by the library. If you want to see the |
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47 # log messages in your scripts, add the following to the top of your script: |
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48 # import logging |
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49 # logging.basicConfig(filename="bioblend.log", level=logging.DEBUG) |
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50 default_format_string = "%(asctime)s %(name)s [%(levelname)s]: %(message)s" |
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51 log = logging.getLogger('bioblend') |
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52 log.addHandler(NullHandler()) |
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53 init_logging() |
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54 |
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55 # Convenience functions to set logging to a particular file or stream |
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56 # To enable either of these, simply add the following at the top of a |
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57 # bioblend module: |
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58 # import bioblend |
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59 # bioblend.set_stream_logger(__name__) |
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60 |
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61 |
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62 def set_file_logger(name, filepath, level=logging.INFO, format_string=None): |
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63 global log |
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64 if not format_string: |
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65 format_string = default_format_string |
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66 logger = logging.getLogger(name) |
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67 logger.setLevel(level) |
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68 fh = logging.FileHandler(filepath) |
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69 fh.setLevel(level) |
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70 formatter = logging.Formatter(format_string) |
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71 fh.setFormatter(formatter) |
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72 logger.addHandler(fh) |
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73 log = logger |
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74 |
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75 |
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76 def set_stream_logger(name, level=logging.DEBUG, format_string=None): |
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77 global log |
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78 if not format_string: |
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79 format_string = default_format_string |
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80 logger = logging.getLogger(name) |
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81 logger.setLevel(level) |
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82 fh = logging.StreamHandler() |
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83 fh.setLevel(level) |
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84 formatter = logging.Formatter(format_string) |
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85 fh.setFormatter(formatter) |
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86 logger.addHandler(fh) |
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87 log = logger |
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88 |
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89 |
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90 class ConnectionError(Exception): |
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91 """ |
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92 An exception class that is raised when unexpected HTTP responses come back. |
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93 |
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94 Should make it easier to debug when strange HTTP things happen such as a |
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95 proxy server getting in the way of the request etc. |
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96 @see: body attribute to see the content of the http response |
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97 """ |
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98 def __init__(self, message, body=None, status_code=None): |
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99 super().__init__(message) |
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100 self.body = body |
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101 self.status_code = status_code |
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102 |
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103 def __str__(self): |
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104 return "{}: {}".format(self.args[0], self.body) |