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Class: HDF5TableDataProvider

Defined in: @tissuumaps-storage/src/hierarchical/hdf5/HDF5TableDataProvider.ts:20

Reads tables from HDF5 files, including AnnData .h5ad files

h5wasm reads synchronously, so the file is opened in a Web Worker that lives as long as the table.

Extends​

Constructors​

Constructor​

new HDF5TableDataProvider(): HDF5TableDataProvider

Returns​

HDF5TableDataProvider

Inherited from​

HierarchicalTableDataProviderBase< HDF5TableDataSource, HDF5TableData, NormalizedHDF5TableDataSource >.constructor

Properties​

name​

readonly name: "HDF5" = "HDF5"

Defined in: @tissuumaps-storage/src/hierarchical/hdf5/HDF5TableDataProvider.ts:28

Overrides​

HierarchicalTableDataProviderBase.name

schema​

readonly schema: object

Defined in: @tissuumaps-storage/src/hierarchical/HierarchicalTableDataProviderBase.ts:34

The JSON schema for the data source

properties​

properties: object

properties.idColumn​

idColumn: object

properties.idColumn.type​

type: string = "string"

properties.nameColumn​

nameColumn: object

properties.nameColumn.type​

type: string = "string"

properties.source​

source: object

properties.source.type​

type: string = "string"

required​

required: string[]

type​

type: string = "object"

Inherited from​

HierarchicalTableDataProviderBase.schema

uischema​

readonly uischema: object

Defined in: @tissuumaps-storage/src/hierarchical/HierarchicalTableDataProviderBase.ts:50

The JSON Forms UI schema for the data source

It must not contain a control for the data source's source, which the application renders itself if the schema declares it, as a string.

elements​

elements: object[]

type​

type: string = "VerticalLayout"

Inherited from​

HierarchicalTableDataProviderBase.uischema

Methods​

createTableData()​

protected createTableData(table, numRows, ids, names): HDF5TableData

Defined in: @tissuumaps-storage/src/hierarchical/hdf5/HDF5TableDataProvider.ts:82

Wraps an open table in the data class of the container format

Parameters​

table​

HierarchicalTable

The open table, which the data owns and closes

numRows​

number

The number of rows

ids​

IDArray | undefined

The row IDs, undefined for sequential IDs

names​

string[] | undefined

The row names, if any

Returns​

HDF5TableData

The data, which owns the table

Overrides​

HierarchicalTableDataProviderBase.createTableData

load()​

load(normalizedDataSource, options?): Promise<HDF5TableData>

Defined in: @tissuumaps-storage/src/hierarchical/HierarchicalTableDataProviderBase.ts:72

Opens a data source and returns the loaded data accessor

The data source has to have been normalized by DataProvider.normalize beforehand.

Parameters​

normalizedDataSource​

NormalizedHDF5TableDataSource

The normalized data source to open

options?​

DataProviderLoadOptions

See DataProviderLoadOptions

Returns​

Promise<HDF5TableData>

A promise that resolves to the loaded data accessor

Inherited from​

HierarchicalTableDataProviderBase.load

normalize()​

normalize(dataSource, workspace, projectSource): NormalizedHDF5TableDataSource

Defined in: @tissuumaps-storage/src/hierarchical/hdf5/HDF5TableDataProvider.ts:30

Parameters​

dataSource​

HDF5TableDataSource

workspace​

FileSystemDirectoryHandle | null

projectSource​

string | null

Returns​

NormalizedHDF5TableDataSource

Overrides​

HierarchicalTableDataProviderBase.normalize

openHierarchicalTable()​

protected openHierarchicalTable(normalizedSource, options): Promise<HierarchicalTable>

Defined in: @tissuumaps-storage/src/hierarchical/hdf5/HDF5TableDataProvider.ts:61

Opens the hierarchical table a normalized source points to

Parameters​

normalizedSource​

string

The normalized source of the data source

options​

signal aborts the load; workspace is the directory handle of the open workspace, required for workspace-relative sources

signal?​

AbortSignal

workspace​

FileSystemDirectoryHandle | null

Returns​

Promise<HierarchicalTable>

The open table; closed by the returned HierarchicalTableDataBase

Overrides​

HierarchicalTableDataProviderBase.openHierarchicalTable

supports()​

supports(normalizedSource): Promise<boolean>

Defined in: @tissuumaps-storage/src/hierarchical/hdf5/HDF5TableDataProvider.ts:53

Returns whether a source has an HDF5 file extension (see HDF5TableDataProvider._extensions)

Parameters​

normalizedSource​

string

The normalized source to check

Returns​

Promise<boolean>

A promise that resolves to whether the source is supported