Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/bioblend/__init__.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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import logging import os from bioblend.config import BioBlendConfigLocations, Config # Current version of the library __version__ = '0.13.0' # default chunk size (in bytes) for reading remote data try: import resource CHUNK_SIZE = resource.getpagesize() except Exception: CHUNK_SIZE = 4096 config = Config() def get_version(): """ Returns a string with the current version of the library (e.g., "0.2.0") """ return __version__ def init_logging(): """ Initialize BioBlend's logging from a configuration file. """ for config_file in BioBlendConfigLocations: try: logging.config.fileConfig(os.path.expanduser(config_file)) except Exception: pass class NullHandler(logging.Handler): def emit(self, record): pass # By default, do not force any logging by the library. If you want to see the # log messages in your scripts, add the following to the top of your script: # import logging # logging.basicConfig(filename="bioblend.log", level=logging.DEBUG) default_format_string = "%(asctime)s %(name)s [%(levelname)s]: %(message)s" log = logging.getLogger('bioblend') log.addHandler(NullHandler()) init_logging() # Convenience functions to set logging to a particular file or stream # To enable either of these, simply add the following at the top of a # bioblend module: # import bioblend # bioblend.set_stream_logger(__name__) def set_file_logger(name, filepath, level=logging.INFO, format_string=None): global log if not format_string: format_string = default_format_string logger = logging.getLogger(name) logger.setLevel(level) fh = logging.FileHandler(filepath) fh.setLevel(level) formatter = logging.Formatter(format_string) fh.setFormatter(formatter) logger.addHandler(fh) log = logger def set_stream_logger(name, level=logging.DEBUG, format_string=None): global log if not format_string: format_string = default_format_string logger = logging.getLogger(name) logger.setLevel(level) fh = logging.StreamHandler() fh.setLevel(level) formatter = logging.Formatter(format_string) fh.setFormatter(formatter) logger.addHandler(fh) log = logger class ConnectionError(Exception): """ An exception class that is raised when unexpected HTTP responses come back. Should make it easier to debug when strange HTTP things happen such as a proxy server getting in the way of the request etc. @see: body attribute to see the content of the http response """ def __init__(self, message, body=None, status_code=None): super(ConnectionError, self).__init__(message) self.body = body self.status_code = status_code def __str__(self): return "{0}: {1}".format(self.args[0], self.body)