Job

class MSMetaEnhancer.libs.utils.Job.Job(data: Tuple[str, str, str])

Bases: object

validate(converters: dict, metadata: Metadata) → Tuple[Converter, Any]

Makes sure to job is supported or possible to execute on given metadata.

Parameters:

converters – available endpoints
metadata – given metadata

Returns:

particular converter and data if conversion is possible

MSMetaEnhancer.libs.utils.Job.convert_to_jobs(jobs: Tuple[str, str, str])

Logger

class MSMetaEnhancer.libs.utils.Logger.Logger

Bases: object

add_coverage_after(metadata_keys: List[str])

Increase counts of annotated attributes

Parameters:: metadata_keys – discovered attributes

add_coverage_before(metadata_keys: List[str])

Increase counts of already present attributes.

Parameters:: metadata_keys – present attributes

add_filehandler(file_name: str = None)

Initialize filehandler for logfile.

Args:: file_name (str, optional): Log filename. Defaults to None.

add_logs(log_record: LogRecord)

Flush logs to log file.

Parameters:: log_record – log record to write and format to file

set_target_attributes(jobs: List[Job], length: int)

Gather all target attributes from specified jobs

Parameters:

jobs – given list of jobs
length – number of analysed spectra

setup(log_level: int, log_file: str)

Initialize log level and log file.

Args:: log_level (int): Log level to set [‘error’: 1, ‘warning’: 2, ‘info’: 3] log_file (str): Path to log file.

write_metrics(): Write obtained statistical values.

Metrics

class MSMetaEnhancer.libs.utils.Metrics.Metrics

Bases: object

set_params(target_attributes, length)

Set all parameters needed to compute metrics.

Parameters:

target_attributes – target attributes to be obtained during annotation
length – number of spectra data

update_after_annotation(metadata_keys)

Increase counts of annotated attributes

Parameters:: metadata_keys – discovered attributes

update_before_annotation(metadata_keys)

Increase counts of already present attributes.

Parameters:: metadata_keys – present attributes

Errors

exception MSMetaEnhancer.libs.utils.Errors.ConversionNotSupported: Bases: Exception

exception MSMetaEnhancer.libs.utils.Errors.DataAlreadyPresent: Bases: Exception

exception MSMetaEnhancer.libs.utils.Errors.InvalidAttributeFormat: Bases: Exception

exception MSMetaEnhancer.libs.utils.Errors.ServiceNotAvailable

Bases: Exception

async static raise_circuitbreaker(*args)

exception MSMetaEnhancer.libs.utils.Errors.SourceAttributeNotAvailable: Bases: Exception

exception MSMetaEnhancer.libs.utils.Errors.TargetAttributeNotRetrieved: Bases: Exception

exception MSMetaEnhancer.libs.utils.Errors.UnknownConverter: Bases: Exception

exception MSMetaEnhancer.libs.utils.Errors.UnknownFileFormat

Bases: Exception

Format not supported.

exception MSMetaEnhancer.libs.utils.Errors.UnknownResponse: Bases: Exception

Throttler

class MSMetaEnhancer.libs.utils.Throttler.Throttler(rate_limit=10, period=1, retry_interval=0.01)

Bases: object

Class to limit number of parallel requests by a rate (number per period of time).

async acquire()

decrease_limit(): Decrease rate (must be always positive).

flush()

increase_limit(): Increase rate up to allow limit.

ConverterBuilder

class MSMetaEnhancer.libs.utils.ConverterBuilder.ConverterBuilder

Bases: object

static build_converters(session, converters: list[str])

Create provided converters.

Parameters:

session – given aiohttp session
converters – list of converters to be built

Returns:

built converters

converters: dict[str, type] = {}

static register(converters: list[type])

static validate_converters(converters)

Check if converters do exist. Raises UnknownConverter if a converter does not exist.

Parameters:: converters – given list of converters names

Monitor

class MSMetaEnhancer.libs.utils.Monitor.Monitor

Bases: Thread

Class to periodically monitor status of used web.

static check_service(url)

Send a GET request to given URL with 5 sec timeout.

Parameters:: url – given URL
Returns:: True if request is successful with status code 200

static get_base_url(converter)

Extract base URL from the converter.

Parameters:: converter – given converter
Returns:: base URL

join(timeout=None)

Wait until the thread terminates.

This blocks the calling thread until the thread whose join() method is called terminates – either normally or through an unhandled exception or until the optional timeout occurs.

When the timeout argument is present and not None, it should be a floating-point number specifying a timeout for the operation in seconds (or fractions thereof). As join() always returns None, you must call is_alive() after join() to decide whether a timeout happened – if the thread is still alive, the join() call timed out.

When the timeout argument is not present or None, the operation will block until the thread terminates.

A thread can be join()ed many times.

join() raises a RuntimeError if an attempt is made to join the current thread as that would cause a deadlock. It is also an error to join() a thread before it has been started and attempts to do so raises the same exception.

run()

Main loop of the Monitor thread.

Monitor checks if GET on base URL of every converter give status code 200. Such a converter is considered available. This is checked periodically to always have up-to-date information.

set_converters(converters)