TGA

MassSpecBlock ¶

MassSpecBlock(item_id: str | None = None, init_data: dict | None = None, unique_id: str | None = None)

Bases: DataBlock

Parameters:

Name	Type	Description	Default
`item_id`	`str \| None`	The item to which the block is attached.	`None`
`init_data`	`dict \| None`	A dictionary of data to initialise the block with.	`None`
`unique_id`	`str \| None`	A unique id for the block, used in the DOM and database.	`None`

accepted_file_extensions ¶

accepted_file_extensions = ('.asc', '.txt')

A list of file extensions that the block will attempt to read.

block_db_model ¶

block_db_model = DataBlockResponse

block_id ¶

block_id = unique_id or generate_random_id()

blocktype ¶

blocktype = 'ms'

A short (unique) string key specifying the type of block.

data ¶

data = {'item_id': item_id, 'blocktype': self.blocktype, 'block_id': self.block_id, None: self.defaults}

defaults ¶

defaults: dict[str, Any] = {}

Any default values that should be set if they are not supplied during block init.

description ¶

description = 'Read and visualize mass spectrometry data as a grid plot per channel'

A longer description outlining the purpose and capability of the block.

multi_file ¶

multi_file: bool = False

Whether this block can accept multiple files as input.

name ¶

name = 'Mass spectrometry'

The human-readable block name specifying which technique or file format it pertains to.

plot_functions ¶

plot_functions

A list of methods that will generate plots for this block.

version ¶

version: str = __version__

The implementation version of this particular block.

event_names ¶

event_names() -> set[str]

Return a list of event names supported by this block.

events_by_name ¶

events_by_name() -> dict[str, Callable]

Returns a dict of registered events for this block.

from_web ¶

from_web(data: dict, stored_data: dict | None = None)

Initialise the block state from data passed via web request with a given item and block ID.

Parameters:

Name	Type	Description	Default
`data`	`dict`	The block data to initialiaze the block with.	required
`stored_data`	`dict \| None`	The stored database state of the block, if any, used to preserve server-authoritative fields that cannot be set from the web.	`None`

generate_ms_plot ¶

generate_ms_plot()

null_event ¶

null_event(**kwargs)

A null debug event that does nothing but logs its kwargs and overwrites the data dict with the args.

process_events ¶

process_events(events: list[dict] | dict)

Handle any supported events passed to the block.

to_db ¶

to_db() -> dict

returns a dictionary with the data for this block, ready to be input into mongodb

to_web ¶

to_web() -> dict[str, Any]

Returns a JSON serializable dictionary to render the data block on the web.

update_from_web ¶

update_from_web(data: dict, stored_data: dict | None = None)

Update the block with validated data received from a web request. Will strip any fields that are "computed" or otherwise not controllable by the user, restoring their stored database values where available.

Parameters:

Name	Type	Description	Default
`data`	`dict`	A dictionary of data to update the block with.	required
`stored_data`	`dict \| None`	The stored database state of the block, if any.	`None`

parse_mt_mass_spec_ascii ¶

parse_mt_mass_spec_ascii(path: Path) -> dict[str, DataFrame | dict]

Parses an .asc file containing MS results from a Mettler-Toledo spectrometer and returns a dictionary with keys data and meta, which themselves contain a dictionary of dataframes for each species with the species names/masses as keys, and a dictionary of metadata fields respectively.

Parameters:

Name	Type	Description	Default
`path`	`Path`	The path of the file to parse.	required