Annotator

class MSMetaEnhancer.libs.Annotator.Annotator

Bases: object

Annotator is responsible for annotation process of single spectra.

async annotate(metadata, jobs, repeat=False)

Runs all jobs to add annotations to given dictionary containing metadata

The method goes through specified jobs of form (Source, Target, Converter) and tries to obtain ‘Target’ attribute based on ‘Source’ attribute using ‘Converter’ converter.

Parameters:

  • metadata – given metadata

  • jobs – specified list of jobs to be executed

  • repeat – if some metadata was added, all jobs are executed again

Returns:

annotated dictionary

async execute_job_with_cache(job, metadata, cache, warning)

Execute given job in cached mode. Cache is converter specific and spectra specific.

Raises TargetAttributeNotRetrieved

Parameters:

  • job – given job to be executed

  • metadata – data to be annotated by the job

  • cache – given cache for this spectra

  • warning – object storing warnings related to current metadata

Returns:

updated metadata and cache

set_converters(converters)

Curator

class MSMetaEnhancer.libs.Curator.Curator

Bases: object

Curator makes sure that all data is curated before the actual annotation can proceed. Currently, fixing CAS numbers to correct format is supported.

Additionally, it supports metadata validation to make sure the produced data are correct.

curate_casno(metadata)

Curate metadata of particular spectra.

Parameters:

metadata – given metadata

Returns:

curated metadata

curate_metadata(metadata_list)

Iterates over given metadata and curates individual entries.

Parameters:

metadata_list – given metadata

Returns:

curated metadata

static filter_invalid_metadata(metadata, log, job)

Validates metadata and filters out invalid ones.

Parameters:

  • metadata – metadata content

  • log – object storing logs related to current metadata

  • job – executed job

Returns:

only valid metadata

static fix_cas_number(cas_number)

Adds dashes to CAS number.

Parameters:

cas_number – given CAS number

Returns:

CAS number enriched by dashes (if needed)

Converter

class MSMetaEnhancer.libs.Converter.Converter

Bases: ABC

General class for conversions.

abstract async convert(source, target, data)

Converts specified {source} attribute (provided in {data}) to {target} attribute.

Parameters:

  • source – given attribute name

  • target – required attribute name

  • data – given attribute value

Returns:

obtained value of target attribute

property converter_name
create_top_level_conversion_methods(conversions, asynch=True)

Method to create and set dynamic methods defined in conversions

Parameters:

  • conversions – triples of form (from, to, method)

  • asynch – whether to create asynchronous methods

get_conversion_functions() → list

Method to compute all available conversion functions.

Assumes that the functions always have from {source}_to_{target}

Returns:

a list of available conversion functions

MSMetaEnhancer.libs.Converter.create_top_level_method(obj: Converter, source: str, target: str, method: str, asynch: bool = True)

Assign a new method to {obj} called {source}_to_{target} which calls {method}.

Parameters:

  • obj – given object (typically a Converter)

  • source – attribute name used as source of data

  • target – attribute name obtained using this dynamic method

  • method – method which is called in the object with single argument

  • asynch – whether to create asynchronous methods