1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
import contextlib
import logging
import logging.config
import os
from typing import (
Optional,
Union,
)
from bioblend.config import (
BioBlendConfigLocations,
Config,
)
# Current version of the library
__version__ = "1.2.0"
# 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() -> str:
"""
Returns a string with the current version of the library (e.g., "0.2.0")
"""
return __version__
def init_logging() -> None:
"""
Initialize BioBlend's logging from a configuration file.
"""
for config_file in BioBlendConfigLocations:
with contextlib.suppress(Exception):
logging.config.fileConfig(os.path.expanduser(config_file))
class NullHandler(logging.Handler):
def emit(self, record: logging.LogRecord) -> None:
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: str, filepath: str, level: Union[int, str] = logging.INFO, format_string: Optional[str] = None
) -> 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: str, level: Union[int, str] = logging.DEBUG, format_string: Optional[str] = None) -> 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: str, body: Optional[Union[bytes, str]] = None, status_code: Optional[int] = None
) -> None:
super().__init__(message)
self.body = body
self.status_code = status_code
def __str__(self) -> str:
return f"{self.args[0]}: {self.body!s}"
class TimeoutException(Exception):
pass
|
