diff --git a/.gitignore b/.gitignore
index d123a62472dd92ae9d213c1dfd577e91fdad3b40..b59df5c30a75add3fb5155c1e392d91c87ae7149 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
/dist
/mutalyzer.egg-info
/static
+/mutalyzer.conf
diff --git a/extras/config.example b/extras/config.example
index 62bf3ce30edb865a31f1a21c174f5c0fc99497ae..251ca14333ac6cf18b68d62ccb632fc47947aa1c 100644
--- a/extras/config.example
+++ b/extras/config.example
@@ -1,7 +1,9 @@
#
# Mutalyzer config file.
#
-# Copy this file to /etc/mutalyzer/config and modify to suit your preferences.
+# Specify the location of this file in the MUTALYZER_SETTINGS environment
+# variable.
+
#
# These settings are used by the Retriever module.
diff --git a/extras/config.user.example b/extras/config.user.example
index fe0887d72c6b17bc0c0e00f51a435ef9cb46ed29..fd3f1428a8ee37d248bed33a19316948cb342a1d 100644
--- a/extras/config.user.example
+++ b/extras/config.user.example
@@ -1,8 +1,8 @@
#
# Mutalyzer config file.
#
-# Copy this file to ~/.config/mutalyzer/config to overwrite definitions from
-# /etc/mutalyzer.config.
+# Specify the location of this file in the MUTALYZER_SETTINGS environment
+# variable.
# Use this email address for retrieval of records at the NCBI.
email = "mutalyzer@humgen.nl"
diff --git a/mutalyzer/config.py b/mutalyzer/config.py
index 0627927cacee381a91033a666f8f8ba17c477779..dc8b5a83ebf14e62110050b9cad3af6806657eef 100644
--- a/mutalyzer/config.py
+++ b/mutalyzer/config.py
@@ -1,5 +1,5 @@
"""
-Module for reading the configuration values from configuration files.
+Module for reading the configuration values from a configuration file.
All communication with this module should be done by using the get function
which returns a configuration value, given a name.
@@ -7,28 +7,19 @@ which returns a configuration value, given a name.
Reading the configuration file is implemented lazily and as such done upon the
first call to the get function.
-Configuration values are read from two locations, in this order:
-1) /etc/mutalyzer/config
-2) $XDG_CONFIG_HOME/mutalyzer/config
-
-If both files exist, values defined in the second overwrite values defined in
-the first.
+Configuration is read from the file specified by the `MUTALYZER_SETTINGS`
+environment variable, or `mutalyzer.conf` in the current directory if it is
+not set.
"""
import os
+
from configobj import ConfigObj
from mutalyzer.util import singleton
-SYSTEM_CONFIGURATION = '/etc/mutalyzer/config'
-USER_CONFIGURATION = os.path.join(
- os.environ.get('XDG_CONFIG_HOME', None) or \
- os.path.join(os.path.expanduser('~'), '.config'),
- 'mutalyzer', 'config')
-
-
class ConfigurationError(Exception):
"""
Raised when a configuration file cannot be read.
@@ -40,14 +31,10 @@ def get(name):
"""
Get a configuration value by name.
- @arg name: Name for the configuration value.
- @type name: string
+ :arg name: Name for the configuration value.
+ :type name: string
- @raise ConfigurationError: If configuration value could not be read.
- Reasons are:
- - Configuration file could not be parsed.
- - Not all variables are present in configuration file.
- - Given configuration value name does not exist.
+ :raise ConfigurationError: If configuration value could not be read.
"""
return _Config().get(name)
@@ -60,51 +47,19 @@ class _Config():
Please note the limitations from the use of the @singleton decorator as
described in its docstring.
"""
- def __init__(self, filename=None):
+ def __init__(self):
"""
Initialise the class with variables read from the configuration
- file. In principle, this is the only place in the code where a
- hard coded constant is used (the name and path to the configuration
- file).
-
- Configuration values are read from two locations, in this order:
- 1) /etc/mutalyzer/config
- 2) $XDG_CONFIG_HOME/mutalyzer/config
-
- If both files exist, values defined in the second overwrite values
- defined in the first.
-
- An exception to this system is when the optional {filename} argument
- is set. In that case, the locations listed above are ignored and the
- configuration is read from {filename}.
-
- @kwarg filename: Optional filename to read configuration from. If
- present, this overrides automatic detection of configuration file
- location.
- @type filename: string
-
- @raise ConfigurationError: If configuration could not be read.
- Reasons are:
- - Supplied argument {filename} could not be opened.
- - Configuration file could not be parsed.
- - Not all variables are present in configuration file.
+ file.
+
+ Configuration values are read from the file specified by the
+ `MUTALYZER_SETTINGS` environment variable, or `mutalyzer.conf` in the
+ current directory if it is not set.
+
+ :raises ConfigurationError: If configuration could not be read.
"""
- config = None
-
- if filename:
- config = self._load_config(filename)
- else:
- if os.path.isfile(SYSTEM_CONFIGURATION):
- config = self._load_config(SYSTEM_CONFIGURATION)
- if os.path.isfile(USER_CONFIGURATION):
- user_config = self._load_config(USER_CONFIGURATION)
- if config:
- config.merge(user_config)
- else:
- config = user_config
-
- if not config:
- raise ConfigurationError('Could not locate configuration.')
+ filename = os.environ.get('MUTALYZER_SETTINGS', 'mutalyzer.conf')
+ config = self._load_config(filename)
# We define default values for many configuration settings (except for
# some that are mandatory for the user to define, i.e. those in the
@@ -191,35 +146,31 @@ class _Config():
except KeyError as e:
raise ConfigurationError('Missing configuration value: %s' % e)
- #__init__
def get(self, name):
"""
Get a configuration value by name.
- @arg name: Name for the configuration value.
- @type name: string
+ :arg name: Name for the configuration value.
+ :type name: string
- @raise ConfigurationError: If given configuration value name does not
- exist.
+ :raises ConfigurationError: If given configuration value name does not
+ exist.
"""
try:
return self._values[name]
except KeyError:
raise ConfigurationError('No such configuration value: %s' % name)
- #get
def _load_config(self, filename):
"""
- Create a ConfigObj from the configuration in {filename}.
+ Create a `ConfigObj` from the configuration in `filename`.
"""
try:
return ConfigObj(filename)
except IOError:
- raise ConfigurationError('Could not open configuration file: %s' \
+ raise ConfigurationError('Could not open configuration file: %s'
% filename)
except SyntaxError:
- raise ConfigurationError('Could not parse configuration file: %s' \
+ raise ConfigurationError('Could not parse configuration file: %s'
% filename)
- #_load_config
-#_Config