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package-lock.json
View file @ 9273abf5
......@@ -16,6 +16,7 @@
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......@@ -85,13 +86,14 @@
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......@@ -101,13 +103,14 @@
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......@@ -133,13 +137,14 @@
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......@@ -149,13 +154,14 @@
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......@@ -181,13 +188,14 @@
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......@@ -213,13 +222,14 @@
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......@@ -229,13 +239,14 @@
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......@@ -245,13 +256,14 @@
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......@@ -261,13 +273,14 @@
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......@@ -277,13 +290,14 @@
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......@@ -293,13 +307,14 @@
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......@@ -309,13 +324,14 @@
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......@@ -341,13 +358,14 @@
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......@@ -357,13 +375,14 @@
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......@@ -389,13 +409,14 @@
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"@jridgewell/sourcemap-codec": "^1.5.0",
"@sveltejs/acorn-typescript": "^1.0.5",
"@types/estree": "^1.0.5",
"acorn": "^8.12.1",
"acorn-typescript": "^1.4.13",
"aria-query": "^5.3.1",
"axobject-query": "^4.1.0",
"clsx": "^2.1.1",
......@@ -6131,10 +6159,11 @@
}
},
"node_modules/typescript": {
"version": "5.7.3",
"resolved": "https://registry.npmjs.org/typescript/-/typescript-5.7.3.tgz",
"integrity": "sha512-84MVSjMEHP+FQRPy3pX9sTVV/INIex71s9TL2Gm5FG/WG1SqXeKyZ0k7/blY/4FdOzI12CBy1vGc4og/eus0fw==",
"version": "5.8.2",
"resolved": "https://registry.npmjs.org/typescript/-/typescript-5.8.2.tgz",
"integrity": "sha512-aJn6wq13/afZp/jT9QZmwEjDqqvSGp1VT5GVg+f/t6/oVyrgXM6BY1h9BRh/O5p3PlUPAe+WuiEZOmb/49RqoQ==",
"dev": true,
"license": "Apache-2.0",
"bin": {
"tsc": "bin/tsc",
"tsserver": "bin/tsserver"
......@@ -6315,14 +6344,14 @@
}
},
"node_modules/vite": {
"version": "6.1.0",
"resolved": "https://registry.npmjs.org/vite/-/vite-6.1.0.tgz",
"integrity": "sha512-RjjMipCKVoR4hVfPY6GQTgveinjNuyLw+qruksLDvA5ktI1150VmcMBKmQaEWJhg/j6Uaf6dNCNA0AfdzUb/hQ==",
"version": "6.2.0",
"resolved": "https://registry.npmjs.org/vite/-/vite-6.2.0.tgz",
"integrity": "sha512-7dPxoo+WsT/64rDcwoOjk76XHj+TqNTIvHKcuMQ1k4/SeHDaQt5GFAeLYzrimZrMpn/O6DtdI03WUjdxuPM0oQ==",
"dev": true,
"license": "MIT",
"dependencies": {
"esbuild": "^0.24.2",
"postcss": "^8.5.1",
"esbuild": "^0.25.0",
"postcss": "^8.5.3",
"rollup": "^4.30.1"
},
"bin": {
......
package.json
View file @ 9273abf5
......@@ -54,6 +54,7 @@
"arktype": "^2.0.4",
"date-fns": "^4.1.0",
"fuse.js": "^7.1.0",
"idb": "^8.0.2",
"sveltejs-tippy": "^3.0.0",
"tinykeys": "^3.0.0",
"unplugin-icons": "^22.0.0"
......
src/lib/database.js
View file @ 9273abf5
......@@ -11,7 +11,10 @@ const ID = type(/[\w_]+/).pipe((id) => id.toLowerCase());
const Probability = type('0 <= number <= 1');
const MetadataValue = type({
value: 'string.json.parse',
value: type('string.json.parse').pipe(
(primitive) =>
/** @type {import('./metadata').RuntimeValue<typeof MetadataType.infer>} */ (primitive)
),
confidence: Probability.default(1),
alternatives: {
'[string.json]': Probability
......@@ -131,9 +134,9 @@ const Protocol = table(
);
const Settings = table(
'layer',
'id',
type({
layer: '"defaults" | "user"',
id: '"defaults" | "user"',
protocols: ID.array(),
theme: type.enumerated('dark', 'light', 'auto'),
gridSize: 'number',
......
src/lib/idb.svelte.js 0 → 100644
View file @ 9273abf5
import { openDB } from 'idb';
import { nanoid } from 'nanoid';
import { Tables } from './database';
/** @type {Array<keyof typeof Tables>} */
// @ts-ignore
const tableNames = Object.keys(Tables);
/** @type {{[Table in keyof typeof Tables]: Array<typeof Tables[Table]['infer']>}} */
const tableValues = $state({
Image: [],
Metadata: [],
Observation: [],
Protocol: [],
Settings: []
});
/**
*
* @type {{
* [Name in keyof typeof Tables]: ReturnType<typeof wrangler<Name>>
* } & {
* initialize: () => Promise<void>
* }}
*/
// @ts-ignore
export const tables = {
...Object.fromEntries(tableNames.map((name) => [name, wrangler(name)])),
async initialize() {
await Promise.allSettled(tableNames.map((name) => tables[name].list()));
}
};
/**
*
* @param {Table} table
* @template {keyof typeof Tables} Table
*/
function wrangler(table) {
return {
get state() {
return tableValues[table];
},
/** @param {string} key */
get: async (key) => get(table, key),
/** @param {typeof Tables[Table]['inferIn']} value */
async set(value) {
await set(table, value);
const output = Tables[table].assert(value);
const index = this.state.findIndex((item) => item.id === value.id);
if (index !== -1) tableValues[table][index] = output;
else tableValues[table].push(output);
},
/** @param {Omit<typeof Tables[Table]['inferIn'], 'id'>} value */
async add(value) {
return this.set(
// @ts-ignore
{ ...value, id: `${table}_${nanoid()}` }
);
},
list: async () => list(table),
all: () => iterator(table),
/** @param {string} index */
by: (index) => iterator(table, index),
/** Do not go through validation or type morphing, manipulate the underlying database values directly. Useful for performance reasons, when changing only a property inside of an object and leaving the others unchanged, for example */
raw: {
/** @param {typeof Tables[Table]['inferIn']} value */
async set(value) {
const db = await openDatabase();
return await db.put(table, value);
},
/** @param {string} key */
async get(key) {
const db = await openDatabase();
return await db.get(table, key);
}
}
};
}
/**
*
* @param {TableName} tableName
* @param {typeof Tables[TableName]['inferIn']} value
* @template {keyof typeof Tables} TableName
*/
export async function set(tableName, value) {
console.time(`set ${tableName} ${value.id}`);
const db = await openDatabase();
const validator = Tables[tableName];
validator.assert(value);
return await db.put(tableName, value).then((result) => {
console.timeEnd(`set ${tableName} ${value.id}`);
return result;
});
}
/**
*
* @param {TableName} tableName
* @param {string} key
* @returns {Promise<undefined | typeof Tables[TableName]['infer']>}
* @template {keyof typeof Tables} TableName
*/
export async function get(tableName, key) {
console.time(`get ${tableName} ${key}`);
const db = await openDatabase();
const validator = Tables[tableName];
return await db.get(tableName, key).then((value) => {
const out = value ? validator.assert(value) : undefined;
console.timeEnd(`get ${tableName} ${key}`);
return out;
});
}
/**
*
* @param {TableName} tableName
* @returns {Promise<Array<typeof Tables[TableName]['infer']>>}
* @template {keyof typeof Tables} TableName
*/
export async function list(tableName) {
const db = await openDatabase();
const validator = Tables[tableName];
// @ts-ignore
return await db.getAll(tableName).then((values) => values.map(validator.assert));
}
/**
*
* @param {TableName} tableName
* @param {string} [index]
* @returns {AsyncGenerator<typeof Tables[TableName]['infer'], void, unknown>}
* @template {keyof typeof Tables} TableName
*/
export async function* iterator(tableName, index = undefined) {
const db = await openDatabase();
const validator = Tables[tableName];
const store = db.transaction(tableName).store;
const iter = index ? store.index(index).iterate() : store.iterate();
for await (const cursor of iter) {
yield validator.assert(cursor.value);
}
}
export async function openDatabase() {
if (_database) return _database;
/** @type {Array<{[K in keyof typeof Tables]: [K, typeof Tables[K]]}[keyof typeof Tables]>} */
// @ts-ignore
const tablesByName = Object.entries(Tables);
_database = await openDB('database', 1, {
upgrade(db) {
for (const [tableName, schema] of tablesByName) {
if (!schema.meta.table) continue;
const keyPath = schema.meta.table.indexes[0];
const store = db.createObjectStore(tableName, { keyPath });
for (const index of schema.meta.table.indexes.slice(1)) {
store.createIndex(index, index);
}
}
}
});
return _database;
}
// Magie vodoo Typescript, pas besoin de comprendre
// Si t'es curieuxse, demande à Gwenn qui sera ravie
// de t'expliquer :3
/**
* @type {import('idb').IDBPDatabase<{
* [Name in keyof typeof Tables]: {
* value: (typeof Tables[Name])['inferIn']
* key: string,
* indexes: {
* [IndexName in string]: string;
* }
* }
* }> | undefined}
*/
let _database;
src/lib/metadata.js 0 → 100644
View file @ 9273abf5
import { tables } from './idb';
/**
*
* @param {object} options
* @param {string} options.subjectId id de l'image ou l'observation
* @param {string} options.metadataId id de la métadonnée
* @param {RuntimeValue<import('./database').MetadataType>} options.value la valeur de la métadonnée
* @param {number} [options.confidence=1] la confiance dans la valeur (proba que ce soit la bonne valeur)
* @param {Array<{ value: RuntimeValue<import('./database').MetadataType>; confidence: number }>} [options.alternatives=[]] les autres valeurs possibles
*/
export async function storeMetadataValue({
subjectId,
metadataId,
value,
confidence,
alternatives
}) {
alternatives ??= [];
confidence ??= 1;
const newValue = {
value: JSON.stringify(value),
confidence,
alternatives: Object.fromEntries(
alternatives.map((alternative) => [JSON.stringify(alternative.value), alternative.confidence])
)
};
const image = await tables.Image.raw.get(subjectId);
const observation = await tables.Observation.raw.get(subjectId);
if (image) {
image.metadata[metadataId] = newValue;
await tables.Image.raw.set(image);
} else if (observation) {
observation.metadataOverrides[metadataId] = newValue;
await tables.Observation.raw.set(observation);
} else {
throw new Error(`Aucune image ou observation avec l'ID ${subjectId}`);
}
}
/**
* Gets all metadata for an observation, including metadata derived from merging the metadata values of the images that make up the observation.
* @param {import('./database').Observation} observation
* @returns {Promise<import('./database').MetadataValues>}
*/
export async function observationMetadata(observation) {
// TODO use a transaction instead
const images = await Promise.all(observation.images.map(tables.Image.get)).then(
/**
* @template V
* @param {V[]} images
* @returns {NonNullable<V>[]}
*/
// @ts-ignore
(images) => images.filter(Boolean)
);
const metadataFromImages = await mergeMetadataValues(images);
return {
...metadataFromImages,
...observation.metadataOverrides
};
}
/**
*
* @param {import("./database").Image[]} images
* @returns {Promise<import("./database").MetadataValues>}
*/
export async function mergeMetadataValues(images) {
/** @type {import("./database").MetadataValues} */
const output = {};
const keys = new Set(...images.map((image) => Object.keys(image.metadata)));
for (const key of keys) {
const definition = await tables.Metadata.get(key);
if (!definition) {
console.warn(`Cannot merge metadata values for unknown key ${key}`);
continue;
}
output[key] = mergeMetadata(
definition,
images.flatMap((img) =>
Object.entries(img.metadata)
.filter(([k]) => k === key)
.map(([, v]) => v)
)
);
}
return output;
}
/**
*
* @param {import("./database").Metadata} definition
* @param {import("./database").MetadataValue[]} values
*/
function mergeMetadata(definition, values) {
/**
* @param {(probabilities: number[]) => number} merger
* @param {import('./database').MetadataValue[]} values
* Run merger on array of confidences for every probability of each alternative of each values:
* example: [ { alternatives: { a: 0.8, b: 0.2 } }, { alternatives: { a: 0.6, b: 0.4 } } ]
* turns into: { a: merger([0.8, 0.6]), b: merger([0.2, 0.4]) }
*/
const mergeAlternatives = (merger, values) =>
Object.fromEntries(
values
.flatMap((v) => Object.keys(v.alternatives))
.map((valueAsString) => [
valueAsString,
merger(values.flatMap((v) => v.alternatives[valueAsString] ?? null).filter(Boolean))
])
);
switch (definition.mergeMethod) {
case 'average':
return {
value: mergeAverage(
definition.type,
// @ŧs-ignore
values.map((v) => v.value)
),
confidence: avg(values.map((v) => v.confidence)),
alternatives: mergeAlternatives(avg, values)
};
case 'max':
// return mergeMajority(definition, values);
throw new Error('Pas encore implémenté!');
case 'min':
// return mergeMinority(definition, values);
throw new Error('Pas encore implémenté!');
case 'median':
return {
value: mergeMedian(
definition.type,
values.map((v) => v.value)
),
confidence: median(values.map((v) => v.confidence)),
alternatives: mergeAlternatives(median, values)
};
case 'none':
return {
// TODO use null instead
value: '',
confidence: 0,
alternatives: {}
};
}
}
/** @param {number[]} values */
function avg(values) {
return values.reduce((acc, cur) => acc + cur, 0) / values.length;
}
/**
* Merge values by average.
* @param {Type} type
* @param {Value[]} values
* @returns {Value}
* @template {RuntimeValue<Type>} Value
* @template {import('./database').MetadataType} Type
*/
function mergeAverage(type, values) {
/**
* @param {typeof values} values
*/
const average = (values) => avg(toNumber(type, values));
// @ts-ignore
if (type === 'boolean') return average(values) > 0.5;
// @ts-ignore
if (type === 'integer') return Math.ceil(average(values));
// @ts-ignore
if (type === 'float') return average(values);
// @ts-ignore
if (type === 'date') return new Date(average(values));
if (type === 'location') {
// @ts-ignore
return {
latitude: average(
values.map(
(v) =>
// @ts-ignore
v.latitude
)
),
longitude: average(
values.map(
(
v //@ts-ignore
) => v.longitude
)
)
};
}
throw new Error(`Impossible de fusionner en mode moyenne des valeurs de type ${type}`);
}
/** @param {number[]} values */
const median = (values) => {
const sorted = values.sort((a, b) => a - b);
const middle = Math.floor(sorted.length / 2);
if (sorted.length % 2 === 0) {
return (sorted[middle - 1] + sorted[middle]) / 2;
}
return sorted[middle];
};
/**
* Merge values by median.
* @param {Type} type
* @param {Value[]} values
* @returns {Value}
* @template {RuntimeValue<Type>} Value
* @template {import('./database').MetadataType} Type
*/
function mergeMedian(type, values) {
/** @param {typeof values} values */
const median_ = (values) => median(toNumber(type, values));
// @ts-ignore
if (type === 'boolean') return median_(values) > 0.5;
// @ts-ignore
if (type === 'integer') return Math.ceil(median_(values));
// @ts-ignore
if (type === 'float') return median_(values);
// @ts-ignore
if (type === 'date') return new Date(median_(values));
if (type === 'location') {
// @ts-ignore
return {
latitude: median(
values.map(
(v) =>
// @ts-ignore
v.latitude
)
),
longitude: median(
values.map(
(v) =>
// @ts-ignore
v.longitude
)
)
};
}
throw new Error(`Impossible de fusionner en mode médiane des valeurs de type ${type}`);
}
/**
* Convert series of values to an output number
* @param {Type} type
* @param {Value[]} values
* @template {RuntimeValue<Type>} Value
* @template {import('./database').MetadataType} Type
* @returns {number[]}
*/
function toNumber(type, values) {
// @ts-ignore
if (type === 'integer') return values;
// @ts-ignore
if (type === 'float') return values;
if (type === 'boolean') return values.map((v) => (v ? 1 : 0));
if (type === 'date') return values.map((v) => new Date(/** @type {Date|string} */ (v)).getTime());
throw new Error(`Impossible de convertir des valeurs de type ${type} en nombre`);
}
/**
* @template {import('./database').MetadataType} Type
* @typedef {Type extends 'boolean' ? boolean : Type extends 'integer' ? number : Type extends 'float' ? number : Type extends 'enum' ? string : Type extends 'date' ? Date : Type extends 'location' ? { latitude: number, longitude: number } : string} RuntimeValue
*/
src/lib/settings.svelte.js 0 → 100644
View file @ 9273abf5
import { tables } from './idb.svelte.js';
/** @type {import('./database.js').Settings} */
// @ts-expect-error could be undefined too, but not useful for us
const _settings = $derived(
tables.Settings.state.find((s) => s.id === 'user') ??
tables.Settings.state.find((s) => s.id === 'defaults')
);
/**
* Usage:
* ```svelte
* <script>
* // $derived is important, otherwise the value will not update
* const settings = $derived(getSettings());
* </script>
* ```
* @returns {import('./database.js').Settings} a reactive object that will update when the database changes. Read-only. Use `setSetting` to change values.
*/
export function getSettings() {
return _settings;
}
/**
*
* @param {Key} key
* @param {import("./database.js").Settings[Key]} value
* @template {keyof import("./database.js").Settings} Key
*/
export async function setSetting(key, value) {
const current = (await tables.Settings.get('user')) ?? (await tables.Settings.get('defaults'));
if (!current) {
throw new Error("Les réglages par défaut n'ont pas été initialisés. Rechargez la page.");
}
return tables.Settings.set({
...current,
id: 'user',
[key]: value
});
}
/**
*
* @param {Key} key
* @template {keyof import("./database.js").Settings} Key
*/
export async function getSetting(key) {
const out =
_settings[key] ??
(await tables.Settings.get('user')) ??
(await tables.Settings.get('defaults'));
if (!out) {
throw new Error("Les réglages par défaut n'ont pas été initialisés. Rechargez la page.");
}
return out;
}
src/lib/species.js 0 → 100644
View file @ 9273abf5
import { tables } from './idb.svelte.js';
/**
*
* @param {string} id
*/
export async function defineSpeciesMetadata(id) {
const names = await fetch(
`https://git.inpt.fr/api/v4/projects/cigale%2Fapp/repository/files/models%2Fclass_mapping.txt/raw?lfs=true`
)
.then((res) => res.text())
.then((text) => text.split('\n'));
await tables.Metadata.set({
id,
description: "L'espèce de l'individu",
label: 'Espèce',
learnMore: null,
mergeMethod: 'max',
required: false,
type: 'enum',
options: names.filter(Boolean).map((name, i) => ({
key: i.toString(),
label: name,
description: '',
learnMore: null
}))
});
}
src/routes/+layout.js 0 → 100644
View file @ 9273abf5
import { BUILTIN_METADATA } from '$lib/database.js';
import { tables } from '$lib/idb.svelte.js';
import { getSetting } from '$lib/settings.svelte.js';
import { defineSpeciesMetadata } from '$lib/species.js';
export async function load() {
await fillBuiltinData();
await defineSpeciesMetadata('species');
await tables.initialize();
return {
showInputHints: await getSetting('showInputHints')
};
}
async function fillBuiltinData() {
await Promise.allSettled([
...BUILTIN_METADATA.map(tables.Metadata.set),
tables.Settings.set({
id: 'defaults',
protocols: [],
theme: 'auto',
gridSize: 10,
language: 'fr',
showInputHints: true
})
]);
}
src/routes/+layout.svelte
View file @ 9273abf5
<script>
import { base } from '$app/paths';
import { setContext } from 'svelte';
import { toasts } from '$lib/toasts.svelte';
import Toast from '$lib/Toast.svelte';
import { toasts } from '$lib/toasts.svelte';
import { setContext } from 'svelte';
import './style.css';
import Navigation from './Navigation.svelte';
const { children } = $props();
const { children, data } = $props();
// TODO get value from DB
setContext('showSwitchHints', true);
setContext('showSwitchHints', data.showInputHints);
</script>
<Navigation hasImages={true}></Navigation>
<svelte:head>
<base href={base} />
<base href={base ? `${base}/index.html` : ''} />
</svelte:head>
<section class="toasts">
......