2.1.1.1. wc_utils.config package¶

2.1.1.1.1. Submodules¶

2.1.1.1.2. wc_utils.config.core module¶

Read configuration settings from files, environment variables, and function arguments

Author: Jonathan Karr <karr@mssm.edu>
Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Date: 2016-10-25
Copyright: 2016-2018, Karr Lab
License: MIT

class wc_utils.config.core.AltResourceName(file_in_package)[source]¶

Bases: object

Get pathname of resource file; a substitute for pkg_resources.resource_filename

Finds paths to resource files in a package that cannot be imported by the standard Python import system.

Usage:

`pkg_resources.resource_filename(package, *path_components_of_resource_in_package)
`AltResourceName(any_file_in_package).resource_filename(*path_components_of_resource_in_package)

package_root[source]¶

root directory of a package

Type: str

static get_package_root(file_in_package)[source]¶

Obtain root directory of a package by following __init__.py files up the file hierarchy

Parameters: file_in_package (str) – pathname of a file in a package
Returns: pathname of root of package
Return type: str
Raises: ValueError – if file_in_package is not the pathname of a file in a package

resource_filename(*args)[source]¶

Get pathname of resource file; replaces pkg_resources.resource_filename

Parameters: args (list) – pathname components of resource file
Returns: pathname of resource file
Return type: str

class wc_utils.config.core.ConfigManager(paths=None)[source]¶

Bases: object

Obtain configuration information from ini files, environment variables, and/or function arguments.

Load configuration information from an ini format file, environment variables, and/or function arguments. Validate the configuration against a configuration schema. Return the configuration as a nested dictionary.

Optionally, configuration values can be templates for substitution with string.Template.

paths[source]¶

paths to configuration files and schema

Type: ConfigPaths

get_config(extra=None, context=None)[source]¶

Setup configuration from config file(s), environment variables, and/or function arguments.

Setup configuration from default values specified in paths.default.
If paths.user is set, find the first file in it that exists, and override the default configuration with the values specified in the file.
Override configuration with values from environment variables. Environment variables can be set with the following syntax:
```
CONFIG.level1.level2...=val
```
Override configuration with additional configuration in extra.
Substitute context into templates
Validate configuration against the schema specified in paths.schema.

Parameters

extra (dict, optional) – additional configuration to override
context (dict, optional) – context for template substitution

Returns

nested dictionary with the configuration settings loaded from the configuration source(s).

Return type

configobj.ConfigObj

Raises

InvalidConfigError – if configuration doesn’t validate against schema
ValueError – if no configuration is found

validate(config, value_sources)[source]¶

Validate configuration

Parameters

config (ConfigObj) – configuration

Raises

InvalidConfigError – if configuration doesn’t validate against schema
ValueError – if no configuration is found

class wc_utils.config.core.ConfigPaths(default=None, schema=None, user=None)[source]¶

Bases: object

Paths to configuration files and schema

default[source]¶

the default config filename

Type: str

schema[source]¶

the config schema filename

Type: str

user[source]¶

an iterable of other config files

Type: list

deepcopy()[source]¶

Returns a deep copy of the object

Returns: deep copy of the object
Return type: ConfigPaths

exception wc_utils.config.core.ExtraValuesError(sources, config)[source]¶

Bases: Exception

Represents an error due to extra configuration that is not part of the schema

sources[source]¶

list of sources of configuration values

Type: list of str

config[source]¶

configuration

Type: configobj.ConfigObj

msg[source]¶

string representation of message

Type: str

__str__()[source]¶

Get string representation of error

Returns: string representation of error
Return type: str

exception wc_utils.config.core.InvalidConfigError(sources, config, result)[source]¶

Bases: Exception

Represents an error due to reading an invalid configuration that doesn’t adhere to the schema

sources[source]¶

list of sources of configuration values

Type: list of str

config[source]¶

configuration

Type: configobj.ConfigObj

result[source]¶

dictionary of configuration errors

Type: dict

msg[source]¶

string representation of message

Type: str

__str__()[source]¶

Get string representation of error

Returns: string representation of error
Return type: str

wc_utils.config.core.any_checker(value)[source]¶

Convert value to its built-in data type if possible

Convert a string value to its built-in data type (integer, float, boolean, str or list of these) if possible

Parameters: value (object) – a value to be converted
Returns: the converted value
Return type: type
Raises: VdtTypeError – if the value cannot be converted

wc_utils.config.core.get_config(extra=None)[source]¶

Get configuration

Parameters: extra (dict, optional) – additional configuration to override
Returns: nested dictionary with the configuration settings loaded from the configuration source(s).
Return type: configobj.ConfigObj

2.1.1.1. wc_utils.config package¶

2.1.1.1.1. Submodules¶

2.1.1.1.2. wc_utils.config.core module¶

2.1.1.1.3. Module contents¶