Source code for bioblend

import logging
import os

from bioblend.config import BioBlendConfigLocations, Config

# Current version of the library
__version__ = '0.11.0'

# default chunk size (in bytes) for reading remote data
try:
    import resource
    CHUNK_SIZE = resource.getpagesize()
except Exception:
    CHUNK_SIZE = 4096


config = Config()


[docs]def get_version(): """ Returns a string with the current version of the library (e.g., "0.2.0") """ return __version__
[docs]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
[docs]class NullHandler(logging.Handler):
[docs] 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__)
[docs]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
[docs]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
[docs]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)