From f50070885b0bba968f1ff5b1e3d871926139730d Mon Sep 17 00:00:00 2001 From: Axel Bocciarelli Date: Thu, 29 Aug 2024 17:34:47 +0200 Subject: [PATCH] Fetch boolean data from h5grove as binary --- .../__snapshots__/h5grove-api.test.ts.snap | 47 +++- .../app/src/providers/h5grove/h5grove-api.ts | 2 +- .../app/src/providers/h5grove/utils.test.ts | 4 +- packages/app/src/providers/hsds/utils.test.ts | 2 +- packages/app/src/providers/mock/mock-file.ts | 4 +- packages/app/src/providers/utils.ts | 7 +- .../src/vis-packs/core/visualizations.test.ts | 6 +- .../src/__snapshots__/h5wasm-api.test.ts.snap | 25 ++ packages/lib/src/vis/models.ts | 12 - packages/shared/src/hdf5-models.ts | 9 +- packages/shared/src/hdf5-utils.ts | 10 +- packages/shared/src/mock-utils.ts | 3 +- support/h5grove/poetry.lock | 251 ++++++++++-------- support/h5grove/pyproject.toml | 2 +- 14 files changed, 229 insertions(+), 155 deletions(-) diff --git a/packages/app/src/providers/h5grove/__snapshots__/h5grove-api.test.ts.snap b/packages/app/src/providers/h5grove/__snapshots__/h5grove-api.test.ts.snap index 78b8d547d..93bddc039 100644 --- a/packages/app/src/providers/h5grove/__snapshots__/h5grove-api.test.ts.snap +++ b/packages/app/src/providers/h5grove/__snapshots__/h5grove-api.test.ts.snap @@ -1431,6 +1431,11 @@ exports[`test file matches snapshot 1`] = ` "size": 64, }, "bool": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "cplx": { @@ -1605,6 +1610,11 @@ exports[`test file matches snapshot 1`] = ` }, "shape": null, "type": { + "base": { + "class": "Integer (unsigned)", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "value": null, @@ -1629,9 +1639,14 @@ exports[`test file matches snapshot 1`] = ` }, "shape": [], "type": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, - "value": false, + "value": 0, }, { "name": "bool_true_scalar", @@ -1653,9 +1668,14 @@ exports[`test file matches snapshot 1`] = ` }, "shape": [], "type": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, - "value": true, + "value": 1, }, { "name": "bool_2D", @@ -1680,17 +1700,22 @@ exports[`test file matches snapshot 1`] = ` 4, ], "type": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, - "value": [ - true, - false, - true, - true, - false, - false, - true, - false, + "value": Int8Array [ + 1, + 0, + 1, + 1, + 0, + 0, + 1, + 0, ], }, { diff --git a/packages/app/src/providers/h5grove/h5grove-api.ts b/packages/app/src/providers/h5grove/h5grove-api.ts index d79726b0d..06dabee82 100644 --- a/packages/app/src/providers/h5grove/h5grove-api.ts +++ b/packages/app/src/providers/h5grove/h5grove-api.ts @@ -30,7 +30,7 @@ import { export class H5GroveApi extends DataProviderApi { private readonly client: AxiosInstance; - /* API compatible with h5grove@2.1.0 */ + /* API compatible with h5grove@2.3.0 */ public constructor( url: string, filepath: string, diff --git a/packages/app/src/providers/h5grove/utils.test.ts b/packages/app/src/providers/h5grove/utils.test.ts index 3b657781c..26e1adca6 100644 --- a/packages/app/src/providers/h5grove/utils.test.ts +++ b/packages/app/src/providers/h5grove/utils.test.ts @@ -89,10 +89,10 @@ describe('parseDType', () => { parseDType({ class: 8, size: 2, - base: { class: 0, size: 1, order: 0, sign: 0 }, + base: { class: 0, size: 1, order: 0, sign: 1 }, members: { FALSE: 0, TRUE: 1 }, }), - ).toStrictEqual(boolType()); + ).toStrictEqual(boolType(intType(8))); }); it('should convert array types', () => { diff --git a/packages/app/src/providers/hsds/utils.test.ts b/packages/app/src/providers/hsds/utils.test.ts index 418091850..088a9167d 100644 --- a/packages/app/src/providers/hsds/utils.test.ts +++ b/packages/app/src/providers/hsds/utils.test.ts @@ -130,7 +130,7 @@ describe('convertHsdsType', () => { mapping: { FALSE: 0, TRUE: 1 }, }; - expect(convertHsdsType(boolEnum)).toStrictEqual(boolType()); + expect(convertHsdsType(boolEnum)).toStrictEqual(boolType(intType(8))); }); it('should convert the complex compound type into Complex type', () => { diff --git a/packages/app/src/providers/mock/mock-file.ts b/packages/app/src/providers/mock/mock-file.ts index 20a46495c..cbdf8c77f 100644 --- a/packages/app/src/providers/mock/mock-file.ts +++ b/packages/app/src/providers/mock/mock-file.ts @@ -120,7 +120,7 @@ export function makeMockFile(): GroupWithChildren { string: strType(), int: intType(), float: floatType(), - bool: boolType(), + bool: boolType(intType(8)), complex: cplxType(floatType()), }), }), @@ -134,7 +134,7 @@ export function makeMockFile(): GroupWithChildren { string: strType(), int: intType(), float: floatType(), - bool: boolType(), + bool: boolType(intType(8)), complex: cplxType(floatType()), }), }), diff --git a/packages/app/src/providers/utils.ts b/packages/app/src/providers/utils.ts index 262d43e90..c9ae3ebcf 100644 --- a/packages/app/src/providers/utils.ts +++ b/packages/app/src/providers/utils.ts @@ -1,4 +1,4 @@ -import { isEnumType, isNumericType } from '@h5web/shared/guards'; +import { isBoolType, isEnumType, isNumericType } from '@h5web/shared/guards'; import type { ArrayShape, Dataset, @@ -8,13 +8,14 @@ import type { import { DTypeClass } from '@h5web/shared/hdf5-models'; import type { OnProgress } from '@h5web/shared/react-suspense-fetch'; import type { AxiosProgressEvent } from 'axios'; +import { isAxiosError } from 'axios'; import type { DataProviderApi } from './api'; export const CANCELLED_ERROR_MSG = 'Request cancelled'; export function typedArrayFromDType(dtype: DType) { - if (isEnumType(dtype)) { + if (isEnumType(dtype) || isBoolType(dtype)) { return typedArrayFromDType(dtype.base); } @@ -72,7 +73,7 @@ export async function getValueOrError( try { return await api.getValue({ dataset }); } catch (error) { - return error; + return isAxiosError(error) ? error.message : error; } } diff --git a/packages/app/src/vis-packs/core/visualizations.test.ts b/packages/app/src/vis-packs/core/visualizations.test.ts index 31e005628..ad92fa49f 100644 --- a/packages/app/src/vis-packs/core/visualizations.test.ts +++ b/packages/app/src/vis-packs/core/visualizations.test.ts @@ -34,17 +34,17 @@ const scalarInt = dataset('int', intType(), []); const scalarUint = dataset('uint', uintType(), []); const scalarFloat = dataset('float', floatType(), []); const scalarStr = dataset('float', strType(), []); -const scalarBool = dataset('bool', boolType(), []); +const scalarBool = dataset('bool', boolType(intType(8)), []); const scalarCplx = dataset('cplx', cplxType(floatType()), []); const scalarCompound = dataset('comp', compoundType({ int: intType() }), []); const oneDInt = dataset('int_1d', intType(), [5]); const oneDUint = dataset('uint_1d', uintType(), [5]); -const oneDBool = dataset('bool_1d', boolType(), [3]); +const oneDBool = dataset('bool_1d', boolType(intType(8)), [3]); const oneDCplx = dataset('cplx_1d', cplxType(floatType()), [10]); const oneDCompound = dataset('comp_1d', compoundType({ int: intType() }), [5]); const twoDInt = dataset('int_2d', intType(), [5, 3]); const twoDUint = dataset('uint_2d', uintType(), [5, 3]); -const twoDBool = dataset('bool_2d', boolType(), [3, 2]); +const twoDBool = dataset('bool_2d', boolType(intType(8)), [3, 2]); const twoDCplx = dataset('cplx_2d', cplxType(floatType()), [2, 2]); const twoDStr = dataset('str_2d', strType(), [5, 3]); const threeDFloat = dataset('float_3d', intType(), [5, 3, 1]); diff --git a/packages/h5wasm/src/__snapshots__/h5wasm-api.test.ts.snap b/packages/h5wasm/src/__snapshots__/h5wasm-api.test.ts.snap index 67f7344a0..81aa9af8e 100644 --- a/packages/h5wasm/src/__snapshots__/h5wasm-api.test.ts.snap +++ b/packages/h5wasm/src/__snapshots__/h5wasm-api.test.ts.snap @@ -1615,6 +1615,11 @@ exports[`test file matches snapshot 1`] = ` "size": 64, }, "bool": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "cplx": { @@ -1812,6 +1817,11 @@ exports[`test file matches snapshot 1`] = ` }, "shape": null, "type": { + "base": { + "class": "Integer (unsigned)", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "value": null, @@ -1836,6 +1846,11 @@ exports[`test file matches snapshot 1`] = ` }, "shape": [], "type": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "value": 0, @@ -1860,6 +1875,11 @@ exports[`test file matches snapshot 1`] = ` }, "shape": [], "type": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "value": 1, @@ -1887,6 +1907,11 @@ exports[`test file matches snapshot 1`] = ` 4, ], "type": { + "base": { + "class": "Integer", + "endianness": "little-endian", + "size": 8, + }, "class": "Boolean", }, "value": Int8Array [ diff --git a/packages/lib/src/vis/models.ts b/packages/lib/src/vis/models.ts index e610a7e7c..3ec843f06 100644 --- a/packages/lib/src/vis/models.ts +++ b/packages/lib/src/vis/models.ts @@ -1,9 +1,3 @@ -import type { - BooleanType, - ComplexType, - NumericType, - StringType, -} from '@h5web/shared/hdf5-models'; import type { AxisScaleType, ColorScaleType, @@ -87,12 +81,6 @@ export interface AxisParams { export type Coords = [x: number, y: number]; -export type PrintableType = - | BooleanType - | NumericType - | ComplexType - | StringType; - export interface HistogramParams { values: NumArray; bins: NumArray; diff --git a/packages/shared/src/hdf5-models.ts b/packages/shared/src/hdf5-models.ts index 3d6980d88..d680c5bb3 100644 --- a/packages/shared/src/hdf5-models.ts +++ b/packages/shared/src/hdf5-models.ts @@ -134,10 +134,6 @@ export type DType = | ReferenceType | UnknownType; -export interface BooleanType { - class: DTypeClass.Bool; -} - export interface NumericType { class: DTypeClass.Integer | DTypeClass.Unsigned | DTypeClass.Float; size: number; @@ -168,6 +164,11 @@ export interface ArrayType { dims?: number[]; } +export interface BooleanType { + class: DTypeClass.Bool; + base: NumericType; // typically int8 with h5py +} + export interface EnumType { class: DTypeClass.Enum; base: NumericType; // technically, only int/uint diff --git a/packages/shared/src/hdf5-utils.ts b/packages/shared/src/hdf5-utils.ts index ae16276f1..d1f3a82c7 100644 --- a/packages/shared/src/hdf5-utils.ts +++ b/packages/shared/src/hdf5-utils.ts @@ -98,10 +98,6 @@ export function strType( }; } -export function boolType(): BooleanType { - return { class: DTypeClass.Bool }; -} - export function cplxType( realType: NumericType, imagType = realType, @@ -139,6 +135,10 @@ export function arrayType( }; } +export function boolType(baseType: NumericType): BooleanType { + return { class: DTypeClass.Bool, base: baseType }; +} + export function enumType( baseType: NumericType, hdf5Mapping: Record, @@ -162,7 +162,7 @@ export function enumOrBoolType( hdf5Mapping.FALSE === 0 && hdf5Mapping.TRUE === 1 ) { - return boolType(); + return boolType(baseType); } return enumType(baseType, hdf5Mapping); diff --git a/packages/shared/src/mock-utils.ts b/packages/shared/src/mock-utils.ts index 90711ec4f..8f3dda33e 100644 --- a/packages/shared/src/mock-utils.ts +++ b/packages/shared/src/mock-utils.ts @@ -20,6 +20,7 @@ import { buildEntityPath, cplxType, floatType, + intType, strType, unknownType, } from './hdf5-utils'; @@ -297,7 +298,7 @@ function guessType(value: unknown): DType { } if (typeof value === 'boolean') { - return boolType(); + return boolType(intType(8)); } if ( diff --git a/support/h5grove/poetry.lock b/support/h5grove/poetry.lock index 4387786e4..87b76a04c 100644 --- a/support/h5grove/poetry.lock +++ b/support/h5grove/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "h5grove" -version = "2.2.0" +version = "2.3.0" description = "Core utilities to serve HDF5 file contents" optional = false python-versions = ">=3.8" files = [ - {file = "h5grove-2.2.0-py3-none-any.whl", hash = "sha256:6320d688c0235edadf9116392491a476fd1a5363668110e85591870f6722bfcd"}, - {file = "h5grove-2.2.0.tar.gz", hash = "sha256:4ff4aed7166931ed71466ebe6ef49871a8ae76d85e4084601362c8a2b7af0c5d"}, + {file = "h5grove-2.3.0-py3-none-any.whl", hash = "sha256:7000a5aa64a6d77997ad18296552ec4def62d4e24aa05219b59c535233017fdf"}, + {file = "h5grove-2.3.0.tar.gz", hash = "sha256:8d438f2a4616d64b176e6ff352d23b39027b9f1ab2c9169fcfd6f5f1caca8728"}, ] [package.dependencies] @@ -20,7 +20,7 @@ tornado = {version = "*", optional = true, markers = "extra == \"tornado\""} typing-extensions = "*" [package.extras] -dev = ["black", "bump2version", "check-manifest", "flake8", "h5grove[fastapi]", "h5grove[flask]", "h5grove[tornado]", "httpx (>=0.23)", "invoke", "mypy", "myst-parser", "pytest", "pytest-benchmark", "pytest-cov", "pytest-tornado", "sphinx", "sphinx-argparse", "sphinx-autobuild", "types-contextvars", "types-dataclasses", "types-orjson", "types-pkg-resources"] +dev = ["black", "bump2version", "check-manifest", "eval-type-backport", "flake8", "h5grove[fastapi]", "h5grove[flask]", "h5grove[tornado]", "httpx (>=0.23)", "invoke", "mypy", "myst-parser", "pytest", "pytest-benchmark", "pytest-cov", "pytest-tornado", "sphinx", "sphinx-argparse", "sphinx-autobuild", "types-contextvars", "types-dataclasses", "types-orjson", "types-setuptools"] fastapi = ["fastapi", "pydantic (>2)", "pydantic-settings", "uvicorn"] flask = ["Flask", "Flask-Compress", "Flask-Cors"] tornado = ["tornado"] @@ -60,113 +60,141 @@ numpy = ">=1.17.3" [[package]] name = "numpy" -version = "1.26.4" +version = "2.1.1" description = "Fundamental package for array computing in Python" optional = false -python-versions = ">=3.9" +python-versions = ">=3.10" files = [ - {file = "numpy-1.26.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9ff0f4f29c51e2803569d7a51c2304de5554655a60c5d776e35b4a41413830d0"}, - {file = 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