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Parse HDF5 string padding metadata #1659

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Jun 5, 2024
Merged

Parse HDF5 string padding metadata #1659

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16 changes: 16 additions & 0 deletions packages/app/src/providers/h5grove/__snapshots__/h5grove-api.test.ts.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -686,12 +686,14 @@ exports[`test file matches snapshot 1`] = `
"cset": 0,
"dtype": "|O",
"size": 8,
"strpad": 0,
"vlen": true,
},
"shape": null,
"type": {
"charSet": "ASCII",
"class": "String",
"strPad": "null-terminated",
},
"value": null,
},
Expand All @@ -702,12 +704,14 @@ exports[`test file matches snapshot 1`] = `
"cset": 0,
"dtype": "|O",
"size": 8,
"strpad": 0,
"vlen": true,
},
"shape": [],
"type": {
"charSet": "ASCII",
"class": "String",
"strPad": "null-terminated",
},
"value": "Some text",
},
Expand All @@ -718,13 +722,15 @@ exports[`test file matches snapshot 1`] = `
"cset": 0,
"dtype": "|S9",
"size": 9,
"strpad": 1,
"vlen": false,
},
"shape": [],
"type": {
"charSet": "ASCII",
"class": "String",
"length": 9,
"strPad": "null-terminated",
},
"value": "Some text",
},
Expand All @@ -735,12 +741,14 @@ exports[`test file matches snapshot 1`] = `
"cset": 1,
"dtype": "|O",
"size": 8,
"strpad": 0,
"vlen": true,
},
"shape": [],
"type": {
"charSet": "UTF-8",
"class": "String",
"strPad": "null-terminated",
},
"value": "Some text",
},
Expand All @@ -751,6 +759,7 @@ exports[`test file matches snapshot 1`] = `
"cset": 1,
"dtype": "|O",
"size": 8,
"strpad": 0,
"vlen": true,
},
"shape": [
Expand All @@ -759,6 +768,7 @@ exports[`test file matches snapshot 1`] = `
"type": {
"charSet": "UTF-8",
"class": "String",
"strPad": "null-terminated",
},
"value": [
"foo",
Expand All @@ -773,13 +783,15 @@ exports[`test file matches snapshot 1`] = `
"cset": 1,
"dtype": "|S9",
"size": 9,
"strpad": 1,
"vlen": false,
},
"shape": [],
"type": {
"charSet": "UTF-8",
"class": "String",
"length": 9,
"strPad": "null-terminated",
},
"value": "Some text",
},
Expand Down Expand Up @@ -1230,6 +1242,7 @@ exports[`test file matches snapshot 1`] = `
"cset": 1,
"dtype": "|O",
"size": 8,
"strpad": 0,
"vlen": true,
},
},
Expand All @@ -1252,6 +1265,7 @@ exports[`test file matches snapshot 1`] = `
"utf-8": {
"charSet": "UTF-8",
"class": "String",
"strPad": "null-terminated",
},
},
},
Expand Down Expand Up @@ -1289,6 +1303,7 @@ exports[`test file matches snapshot 1`] = `
"cset": 1,
"dtype": "|O",
"size": 8,
"strpad": 0,
"vlen": true,
},
},
Expand All @@ -1313,6 +1328,7 @@ exports[`test file matches snapshot 1`] = `
"utf-8": {
"charSet": "UTF-8",
"class": "String",
"strPad": "null-terminated",
},
},
},
Expand Down
1 change: 1 addition & 0 deletions packages/app/src/providers/h5grove/models.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,7 @@ export interface H5GroveTimeType extends H5GroveBaseType {
export interface H5GroveStringType extends H5GroveBaseType {
class: 3;
cset: number;
strPad?: number; // optional for backwards compatibility with h5grove <= 2.1.0
vlen: boolean;
}

Expand Down
8 changes: 4 additions & 4 deletions packages/app/src/providers/h5grove/utils.test.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { H5T_CSET, H5T_ORDER } from '@h5web/shared/h5t';
import { H5T_CSET, H5T_ORDER, H5T_STR } from '@h5web/shared/h5t';
import {
arrayType,
bitfieldType,
Expand Down Expand Up @@ -42,13 +42,13 @@ describe('parseDType', () => {
it('should convert string types', () => {
expect(
parseDType({ class: 3, size: 6, cset: 0, vlen: false }),
).toStrictEqual(strType(H5T_CSET.ASCII, 6));
).toStrictEqual(strType(H5T_CSET.ASCII, undefined, 6));
expect(
parseDType({ class: 3, size: 6, cset: 0, vlen: true }),
).toStrictEqual(strType(H5T_CSET.ASCII));
expect(
parseDType({ class: 3, size: 6, cset: 1, vlen: false }),
).toStrictEqual(strType(H5T_CSET.UTF8, 6));
parseDType({ class: 3, size: 6, cset: 1, strPad: 1, vlen: false }),
).toStrictEqual(strType(H5T_CSET.UTF8, H5T_STR.NULLPAD, 6));
expect(
parseDType({ class: 3, size: 6, cset: 1, vlen: true }),
).toStrictEqual(strType(H5T_CSET.UTF8));
Expand Down
4 changes: 2 additions & 2 deletions packages/app/src/providers/h5grove/utils.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -149,8 +149,8 @@ export function parseDType(type: H5GroveType): DType {
}

if (h5tClass === H5T_CLASS.STRING) {
const { cset, vlen } = type;
return strType(cset, vlen ? undefined : size);
const { cset, strPad, vlen } = type;
return strType(cset, strPad, vlen ? undefined : size);
}

if (h5tClass === H5T_CLASS.BITFIELD) {
Expand Down
4 changes: 3 additions & 1 deletion packages/app/src/providers/hsds/models.ts
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@@ -1,3 +1,4 @@
import type { H5T_CSET, H5T_STR } from '@h5web/shared/h5t';
import type { Entity } from '@h5web/shared/hdf5-models';

/* --------------------- */
Expand Down Expand Up @@ -104,7 +105,8 @@ export interface HsdsNumericType {

export interface HsdsStringType {
class: 'H5T_STRING';
charSet: `H5T_CSET_${'ASCII' | 'UTF8'}`;
charSet: `H5T_CSET_${keyof typeof H5T_CSET}`;
strPad: `H5T_STR_${keyof typeof H5T_STR}`;
length: number | 'H5T_VARIABLE';
}

Expand Down
10 changes: 7 additions & 3 deletions packages/app/src/providers/hsds/utils.test.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { H5T_CSET, H5T_ORDER } from '@h5web/shared/h5t';
import { H5T_CSET, H5T_ORDER, H5T_STR } from '@h5web/shared/h5t';
import type { DType } from '@h5web/shared/hdf5-models';
import {
arrayType,
Expand Down Expand Up @@ -52,22 +52,26 @@ describe('convertHsdsType', () => {
const asciiStr: HsdsStringType = {
class: 'H5T_STRING',
charSet: 'H5T_CSET_ASCII',
strPad: 'H5T_STR_NULLTERM',
length: 25,
};

expect(convertHsdsType(asciiStr)).toStrictEqual(
strType(H5T_CSET.ASCII, 25),
strType(H5T_CSET.ASCII, H5T_STR.NULLTERM, 25),
);
});

it('should convert variable-length UTF-8 string type', () => {
const unicodeStr: HsdsStringType = {
class: 'H5T_STRING',
charSet: 'H5T_CSET_UTF8',
strPad: 'H5T_STR_NULLPAD',
length: 'H5T_VARIABLE',
};

expect(convertHsdsType(unicodeStr)).toStrictEqual(strType(H5T_CSET.UTF8));
expect(convertHsdsType(unicodeStr)).toStrictEqual(
strType(H5T_CSET.UTF8, H5T_STR.NULLPAD),
);
});

it('should convert integer types', () => {
Expand Down
7 changes: 5 additions & 2 deletions packages/app/src/providers/hsds/utils.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
import { assertArray, isGroup } from '@h5web/shared/guards';
import { H5T_CSET, H5T_ORDER } from '@h5web/shared/h5t';
import { H5T_CSET, H5T_ORDER, H5T_STR } from '@h5web/shared/h5t';
import type {
ArrayShape,
Attribute,
Expand Down Expand Up @@ -138,11 +138,14 @@ export function convertHsdsType(hsdsType: HsdsType): DType {
return convertHsdsCompoundType(hsdsType);

case 'H5T_STRING': {
const { charSet, length } = hsdsType;
const { charSet, strPad, length } = hsdsType;
return strType(
H5T_CSET[
charSet.slice(charSet.lastIndexOf('_') + 1) as keyof typeof H5T_CSET
],
H5T_STR[
strPad.slice(strPad.lastIndexOf('_') + 1) as keyof typeof H5T_STR
],
length === 'H5T_VARIABLE' ? undefined : length,
);
}
Expand Down
4 changes: 2 additions & 2 deletions packages/app/src/providers/mock/mock-file.ts
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { H5T_CSET } from '@h5web/shared/h5t';
import { H5T_CSET, H5T_STR } from '@h5web/shared/h5t';
import type { GroupWithChildren } from '@h5web/shared/hdf5-models';
import {
arrayType,
Expand Down Expand Up @@ -62,7 +62,7 @@ export function makeMockFile(): GroupWithChildren {
}),
scalar('scalar_compound', ['foo', 2], {
type: compoundType({
str: strType(H5T_CSET.ASCII, 3),
str: strType(H5T_CSET.ASCII, H5T_STR.NULLPAD, 3),
int: intType(8),
}),
attributes: [
Expand Down
2 changes: 1 addition & 1 deletion packages/h5wasm/package.json
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Expand Up @@ -47,7 +47,7 @@
},
"dependencies": {
"comlink": "4.4.1",
"h5wasm": "0.7.4",
"h5wasm": "0.7.5",
"nanoid": "5.0.7"
},
"devDependencies": {
Expand Down
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