Welcome to BioMAJ Manager’s documentation!¶

Contents:

decorators API reference¶

Global decorators for BioMAJ Manager

biomajmanager.decorators.bank_required(func)[source]¶

Decorator function that checks a bank name is set

Parameters:	func (Function) – Decorated function
Returns:	Result of function called
Return type:	func
Raises:	SystemExit – If no bank set

biomajmanager.decorators.deprecated(func)[source]¶

This is a decorator which can be used to mark functions as deprecated.

It will result in a warning being emitted when the functionis used.

Parameters:	func (Function) – Decorated function
Returns:	Result of functio called
Return type:	func

biomajmanager.decorators.user_granted(func)[source]¶

Decorator function that checks a user has enough right to perform action

Parameters:	func (Function) – Decorated function
Returns:	Result of function called
Return type:	func
Raises:	SystemExit – If no owner found either in bank nor in config file

links API reference¶

manager API reference¶

Manager.SAVE_BANK_LINE_PATTERN: Print pattern (str), %-20s\t%-30s\t%-20s\t%-20s\t%-20s\n

Manager.simulate: Simulate mode (bool), False

Manager.verbose: Verbose mode (bool), False

news API reference¶

News.MAX_NEWS: Maximum number of news returned while reading news directory (int), 5

plugins API reference¶

Plugins mechanism to load user defined method

class biomajmanager.plugins.BMPlugin[source]¶

Base plugin class for BioMAJ manager

get_config()[source]¶

Get the BioMAJ manager config as object

Returns:	configparser instance
Return type:	:class:’configparser`

get_manager()[source]¶

Get the BioMAJ manager instance

Returns:	Manager
Return type:	`biomaj.manager.Manager`

get_name()[source]¶: Get the name of the plugin. Based on the class name

set_config(config)[source]¶: Set BioMAJ manager config object

set_manager(manager)[source]¶: Set BioMAJ manager config object

class biomajmanager.plugins.Plugins(manager=None, name=None)[source]¶

Plugin class for BioMAJ Manager

__init__(manager=None, name=None)[source]¶

Create the plugin object

Parameters:	manager (`biomajmanager.manager.Manager`) – Manager instance name (String) – Name of the plugin to load. [DEFAULT: load all plugins]
Raises:	SystemExit – If ‘manager’ arg is not given SystemExit – If ‘PLUGINS’ section not found in `manager.properties` SystemExit – If ‘plugins.dir’ not set in `manager.properties` SystemExit – If ‘plugins.list’ not set in `manager.properties` SystemExit – If ‘plugins.dir’ does not exist

__weakref__¶: list of weak references to the object (if defined)

utils API reference¶

Utils.DATE_FMT: date format pattern (str), %Y-%m-%d %H:%M:%S

Utils.show_warn: show warnings mesasge (bool), True

Utils.show_debug: show debug message (bool), True

Utils.show_verbose: show verbose message (bool), True

Utils.timer_start: Start timer value (float), 0.0

Utils.timer_stop: Stop timer value (float), 0.0

Utilities class for BioMAJ Manager

class biomajmanager.utils.Utils[source]¶

Utility class

__weakref__¶: list of weak references to the object (if defined)

static _print(msg, to=<open file '<stdout>', mode 'w'>)[source]¶

Redefined print function to support python 2 and 3

Parameters:	msg (str) – Message to print to (file) – File handle
Returns:	Message to print
Return type:	str

static clean_symlinks(path=None, delete=False)[source]¶

Search for broken symlinks.

Given a path, it search for all symlinks ‘path’ directory and remove broken symlinks. If delete is True, remove broken symlink(s), otherwise lists broken symlinks.

Parameters:	path (str) – Path to search symlinks from delete (bool) – Wether to delete or not broken symlink(s)
Returns:	Number of cleaned/deleted link(s)
Return type:	int
Raises:	SystemExit – If path not found, or not given SystemExit – If remove of symlink(s) failed

static elapsed_time()[source]¶

Get the elapsed time between start and stop timer.

Stop timer call is not required. If not set, it is automatically called as soon as the method is called

Returns:	Elapsed time
Return type:	float
Raises:	SystemExit – If Utils.timer_start is not defined

static error(msg)[source]¶

Prints error message on STDERR and exits with exit code 1

Parameters:	msg (str) – Message to print
Returns:	Error message
Return type:	str
Raises:	SystemExit –

static get_broken_links(path=None)[source]¶

Search for broken symlinks from a particular path.

If path is not given or None, then it search from the production directory.

Parameters:	path (str) – Path to search broken links from
Returns:	Number of found broekn links
Return type:	int
Raises:	SystemExit – If path does not exist

static get_deepest_dir(path=None, full=False)[source]¶

Return only one deepest dir from the path

Parameters:	path (str) – Path full (bool) – Returns complete path or not
Returns:	Directory name
Return type:	str

static get_deepest_dirs(path=None, full=False)[source]¶

Get the last directories from a path

Parameters:	path (str) – Path to start from full (bool) – Get the full path otherwise the directory only
Returns:	List of directories
Return type:	list
Raises:	SystemExit – If ‘path’ not given or does not exist

static get_files(path=None)[source]¶

Return the list of file(s) found for a given path

Parameters:	path (str) – Path to search from
Returns:	List of file(s) found
Return type:	list
Raises:	SystemExit – If path does not exist

static get_now()[source]¶

Get current time from time.time formatted using Utils.DATE_FMT

Returns:	Current time formatted using `Utils.DATE_FMT`
Return type:	`time.time`

static get_subtree(path=None)[source]¶

Get the subtree structure from a root path

E.g.: File system is /t/a1/a2/a3, get_subtree(path=’/t’) -> /a1/a2/a3 :param path: Root path to get subtree structure from :type path: str :return: List of found subtree :rtype: list

static ok(msg)[source]¶

Prints a [OK] msg

Parameters:	msg (str) – Message to print
Returns:	Message to print
Return type:	str

static reset_timer()[source]¶: Reset to 0.0 timer_start() and timer_stop() for a new elapsed_time() count

static start_timer()[source]¶: Set current time at function call

static stop_timer()[source]¶: Set current time at function call

static time2date(otime)[source]¶

Convert a timestamp into a datetime object

Parameters:	otime (time) – Timestamp to convert
Returns:	Formatted time to date
Return type:	`datetime.datetime`

static time2datefmt(otime, fmt='%Y-%m-%d %H:%M:%S')[source]¶

Converts a timestamp into a date following the format fmt, default to Utils.DATE_FMT

Parameters:	otime (time) – Timestamp to convert fmt (str) – Date format to follow for conversion
Returns:	Formatted time to date
Return type:	`datetime.datetime`

static user()[source]¶

Returns the current user running or using the script. Taken from os.env

Returns:	User name
Return type:	str

static verbose(msg)[source]¶

Prints verbose message. Requires Manager.verbose to be True

Parameters:	msg (str) – Verbose message to print
Returns:	Verbose message
Return type:	str

static warn(msg)[source]¶

Prints warning message. Required Utils.show_warn to be set to True

Parameters:	msg (str) – Warning message to print
Returns:	Warning message
Return type:	str

writer API reference¶

Writer class to be used with Jinja2 templates

class biomajmanager.writer.Writer(template_dir=None, config=None, output=None)[source]¶

Writer class for BioMAJ manager to create what’s desired as output

__init__(template_dir=None, config=None, output=None)[source]¶

Create Writer object

Parameters:	template_dir (str) – Root directory where to find templates config (`configparser`) – Global configuration file from BiomajConfig output (str) – Output file. Default STDOUT
Raises:	SystemExit – If ‘template_dir’ is not given SystemExit – If ‘MANAGER’ section not found in `manager.properties` SystemExit – If ‘template.dir’ not set in `manager.properties`

__weakref__¶: list of weak references to the object (if defined)

write(template=None, data=None)[source]¶

Print template ‘data’ to stdout using template file ‘template’.

‘data’ arg can be left None, this way method can be used to render file from scratch

Parameters:	template (str) – Template file name data (dict) – Template data
Returns:	True, throws on error
Return type:	bool
Raises:	SystemExit – If ‘template’ is None SystemExit – If ‘template’ is not found SystemExit – If ‘template’ has a syntax error in it SystemExit – If ‘output’ file cannot be opened