react-cheminfo 0.9.0 → 0.11.0

package/lib/spectra/core/problems.js

@@ -0,0 +1,121 @@
+/**
+ * A problem, spelled out.
+ * @param severity - How much it matters.
+ * @param where - Which part of the settings it is about.
+ * @param message - What is wrong.
+ * @returns The problem.
+ */
+export function problem(severity, where, message) {
+    return { severity, where, message };
+}
+/**
+ * Whether a value is a number the processor can work with.
+ * @param value - What the settings hold.
+ * @returns True when it is a finite number.
+ */
+export function isNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value);
+}
+/**
+ * Whether a value is a whole number.
+ * @param value - What the settings hold.
+ * @returns True when it is a finite integer.
+ */
+export function isWholeNumber(value) {
+    return isNumber(value) && Number.isInteger(value);
+}
+/**
+ * Whether a label can stand as the name of a variable.
+ *
+ * A range's label becomes a parameter of the function the calculations are
+ * compiled into, so a label with a space in it fails far from the field that
+ * caused it — which is why it is checked here instead.
+ * @param label - What the reader typed.
+ * @returns True when the label can be a variable name.
+ */
+export function isUsableLabel(label) {
+    return /^[A-Za-z_$][\w$]*$/.test(label) && !RESERVED_WORDS.has(label);
+}
+/**
+ * What is wrong with an expression, as far as can be told without running it.
+ *
+ * The expression is compiled by the processor, not here, so this catches what
+ * a reader actually mistypes — an empty box, unclosed brackets, a variable that
+ * never appears — and stays silent about the rest rather than pretending to be
+ * a parser.
+ * @param formula - What the reader typed.
+ * @param variable - The one name the expression may read, `x` or `y`.
+ * @returns The complaint, or undefined when nothing obvious is wrong.
+ */
+export function formulaProblem(formula, variable) {
+    const trimmed = formula.trim();
+    if (trimmed === '')
+        return 'The expression is empty.';
+    if (!new RegExp(String.raw `\b${variable}\b`).test(trimmed)) {
+        return `The expression never reads ${variable}, so every point would get the same value.`;
+    }
+    let depth = 0;
+    for (const character of trimmed) {
+        if (character === '(')
+            depth++;
+        if (character === ')')
+            depth--;
+        if (depth < 0)
+            return 'A closing bracket has nothing to close.';
+    }
+    if (depth > 0)
+        return 'A bracket is left open.';
+    return undefined;
+}
+/** The names a range may not take, because a function cannot be given them. */
+const RESERVED_WORDS = new Set([
+    'arguments',
+    'await',
+    'break',
+    'case',
+    'catch',
+    'class',
+    'const',
+    'continue',
+    'debugger',
+    'default',
+    'delete',
+    'do',
+    'else',
+    'enum',
+    'eval',
+    'export',
+    'extends',
+    'false',
+    'finally',
+    'for',
+    'function',
+    'if',
+    'implements',
+    'import',
+    'in',
+    'instanceof',
+    'interface',
+    'let',
+    'new',
+    'null',
+    'package',
+    'private',
+    'protected',
+    'public',
+    'return',
+    'static',
+    'super',
+    'switch',
+    'this',
+    'throw',
+    'true',
+    'try',
+    'typeof',
+    'var',
+    'void',
+    'while',
+    'with',
+    'yield',
+]);
+//# sourceMappingURL=problems.js.map

package/lib/spectra/core/problems.js.map

@@ -0,0 +1 @@
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package/lib/spectra/core/settings.d.ts

@@ -0,0 +1,67 @@
+import type { FilterXYType } from 'ml-signal-processing';
+import type { SpectraProcessor } from 'spectra-processor';
+/** Everything `new SpectraProcessor(…)` is built with. */
+export type SpectraProcessorSettings = NonNullable<ConstructorParameters<typeof SpectraProcessor>[0]>;
+/**
+ * How every spectrum is brought onto one x grid. Until this is settled no two
+ * spectra can be compared, which is why it is the first thing the editor asks.
+ */
+export type NormalizationSettings = NonNullable<SpectraProcessorSettings['normalization']>;
+/** A stretch of x the resampling grid skips. */
+export type ExclusionZone = NonNullable<NormalizationSettings['exclusions']>[number];
+/** What `getPostProcessedData` reads, once every spectrum shares one grid. */
+export type PostProcessingSettings = NonNullable<Parameters<SpectraProcessor['getPostProcessedData']>[0]>;
+/** How every spectrum is scaled onto a reference one. */
+export type ScaleSettings = NonNullable<PostProcessingSettings['scale']>;
+/** A named stretch of x whose integral is reported per spectrum. */
+export type SpectraRange = NonNullable<PostProcessingSettings['ranges']>[number];
+/** A formula over the range integrals, reported per spectrum. */
+export type SpectraCalculation = NonNullable<PostProcessingSettings['calculations']>[number];
+/** One step of the matrix stage, which works across spectra rather than along one. */
+export type MatrixFilter = NonNullable<PostProcessingSettings['filters']>[number];
+/**
+ * One step of the per-spectrum chain.
+ *
+ * `spectra-processor` types the same array as `{ name: string }`, which accepts
+ * names `filterXY` throws on. The editor holds the union `filterXY` actually
+ * dispatches, so a chain that type-checks is a chain that runs.
+ */
+export type SpectrumFilter = FilterXYType;
+/** The name of a chain step — the 23 `filterXY` knows. */
+export type SpectrumFilterName = FilterXYType['name'];
+/** The three names `getPostProcessedData`'s own switch matches. */
+export type MatrixFilterName = 'centerMean' | 'pqn' | 'rescale';
+/** The four scalings `getPostProcessedData` matches, lower-cased. */
+export type ScaleMethod = 'integration' | 'max' | 'min' | 'minmax';
+/** Both settings objects the processor takes, which are independent of each other. */
+export interface SpectraSettings {
+    /** What the constructor is handed. */
+    processor: SpectraProcessorSettings;
+    /** What `getPostProcessedData` is handed. */
+    postProcessing: PostProcessingSettings;
+}
+/** The bytes of original data kept before the processor starts discarding it. */
+export declare const DEFAULT_MAX_MEMORY: number;
+/** Points the injected resampling lands on when the settings name no number. */
+export declare const DEFAULT_NUMBER_OF_POINTS = 1024;
+/** Nothing set: the processor's own defaults, spelled out so a reset is one value. */
+export declare const EMPTY_SETTINGS: SpectraSettings;
+/**
+ * The chain as the editor understands it.
+ *
+ * The single cast in the package. Upstream types the array as
+ * `{ name: string; options?: any }[]` while its own `getNormalized` types the
+ * very same array as `FilterXYType[]`; this reads it back at the narrower type
+ * its consumer already assumes.
+ * @param settings - What the constructor would be handed.
+ * @returns The chain steps, in the order they run.
+ */
+export declare function normalizationFilters(settings: SpectraProcessorSettings): readonly SpectrumFilter[];
+/**
+ * The same settings with a different chain, leaving every other field alone.
+ * @param settings - What the constructor would be handed.
+ * @param filters - The chain to put in its place.
+ * @returns A new settings object.
+ */
+export declare function withNormalizationFilters(settings: SpectraProcessorSettings, filters: readonly SpectrumFilter[]): SpectraProcessorSettings;
+//# sourceMappingURL=settings.d.ts.map

package/lib/spectra/core/settings.d.ts.map

@@ -0,0 +1 @@
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package/lib/spectra/core/settings.js

@@ -0,0 +1,35 @@
+/** The bytes of original data kept before the processor starts discarding it. */
+export const DEFAULT_MAX_MEMORY = 256 * 1024 * 1024;
+/** Points the injected resampling lands on when the settings name no number. */
+export const DEFAULT_NUMBER_OF_POINTS = 1024;
+/** Nothing set: the processor's own defaults, spelled out so a reset is one value. */
+export const EMPTY_SETTINGS = {
+    processor: { normalization: {} },
+    postProcessing: {},
+};
+/**
+ * The chain as the editor understands it.
+ *
+ * The single cast in the package. Upstream types the array as
+ * `{ name: string; options?: any }[]` while its own `getNormalized` types the
+ * very same array as `FilterXYType[]`; this reads it back at the narrower type
+ * its consumer already assumes.
+ * @param settings - What the constructor would be handed.
+ * @returns The chain steps, in the order they run.
+ */
+export function normalizationFilters(settings) {
+    return (settings.normalization?.filters ?? []);
+}
+/**
+ * The same settings with a different chain, leaving every other field alone.
+ * @param settings - What the constructor would be handed.
+ * @param filters - The chain to put in its place.
+ * @returns A new settings object.
+ */
+export function withNormalizationFilters(settings, filters) {
+    return {
+        ...settings,
+        normalization: { ...settings.normalization, filters: [...filters] },
+    };
+}
+//# sourceMappingURL=settings.js.map

package/lib/spectra/core/settings.js.map

@@ -0,0 +1 @@
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package/lib/spectra/core/settingsProblems.d.ts

@@ -0,0 +1,18 @@
+import type { SettingsProblem } from './problems.ts';
+import type { MatrixFilterName, ScaleMethod, SpectraSettings } from './settings.ts';
+/** The only three names `getPostProcessedData` matches; anything else throws. */
+export declare const MATRIX_FILTER_NAMES: readonly MatrixFilterName[];
+/** The only four scalings it matches, which it lower-cases before comparing. */
+export declare const SCALE_METHODS: readonly ScaleMethod[];
+/**
+ * Everything wrong, or probably wrong, with a whole settings object.
+ *
+ * Nothing here blocks: the editor is not a gate, and a reader mid-thought is
+ * allowed to hold settings that would throw. What it does is name the value the
+ * processor will fail on before the reader hands it over and reads a stack
+ * trace instead.
+ * @param settings - Both objects the processor would be handed.
+ * @returns Every problem found, errors and advice together.
+ */
+export declare function settingsProblems(settings: SpectraSettings): SettingsProblem[];
+//# sourceMappingURL=settingsProblems.d.ts.map

package/lib/spectra/core/settingsProblems.d.ts.map

@@ -0,0 +1 @@
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package/lib/spectra/core/settingsProblems.js

@@ -0,0 +1,148 @@
+import { chainProblems } from "./chainProblems.js";
+import { isNumber, isUsableLabel, isWholeNumber, problem } from "./problems.js";
+import { normalizationFilters } from "./settings.js";
+/** The only three names `getPostProcessedData` matches; anything else throws. */
+export const MATRIX_FILTER_NAMES = [
+    'pqn',
+    'centerMean',
+    'rescale',
+];
+/** The only four scalings it matches, which it lower-cases before comparing. */
+export const SCALE_METHODS = [
+    'min',
+    'max',
+    'minmax',
+    'integration',
+];
+/**
+ * Everything wrong, or probably wrong, with a whole settings object.
+ *
+ * Nothing here blocks: the editor is not a gate, and a reader mid-thought is
+ * allowed to hold settings that would throw. What it does is name the value the
+ * processor will fail on before the reader hands it over and reads a stack
+ * trace instead.
+ * @param settings - Both objects the processor would be handed.
+ * @returns Every problem found, errors and advice together.
+ */
+export function settingsProblems(settings) {
+    const problems = [];
+    const normalization = settings.processor.normalization ?? {};
+    const where = 'Resampling';
+    const { from, to, numberOfPoints, exclusions } = normalization;
+    if (isNumber(from) && isNumber(to) && from >= to) {
+        problems.push(problem('error', where, 'From is not below to.'));
+    }
+    if (numberOfPoints !== undefined &&
+        (!isWholeNumber(numberOfPoints) || numberOfPoints < 2)) {
+        problems.push(problem('error', where, 'A grid needs at least two points.'));
+    }
+    const { maxMemory } = settings.processor;
+    if (maxMemory !== undefined && (!isNumber(maxMemory) || maxMemory <= 0)) {
+        problems.push(problem('error', 'Memory', 'The budget must be a number above zero.'));
+    }
+    for (const [index, zone] of (exclusions ?? []).entries()) {
+        const zoneWhere = `Excluded zone ${String(index + 1)}`;
+        if (!isNumber(zone.from) || !isNumber(zone.to) || zone.from >= zone.to) {
+            problems.push(problem('error', zoneWhere, 'From is not below to.'));
+        }
+        if (zone.ignore === true) {
+            problems.push(problem('warning', zoneWhere, 'Hidden only from the chart: the zone is still dropped from the data.'));
+        }
+    }
+    const { applyRangeSelectionFirst } = normalization;
+    problems.push(...chainProblems(normalizationFilters(settings.processor), applyRangeSelectionFirst === true), ...postProcessingProblems(settings));
+    return problems;
+}
+/**
+ * Everything wrong with the stage that works across spectra rather than along one.
+ * @param settings - Both objects the processor would be handed.
+ * @returns Its problems.
+ */
+function postProcessingProblems(settings) {
+    const problems = [];
+    const { filters, scale, ranges, calculations } = settings.postProcessing;
+    for (const [index, step] of (filters ?? []).entries()) {
+        const where = `Matrix step ${String(index + 1)}`;
+        if (step.name !== undefined &&
+            step.name !== '' &&
+            !MATRIX_FILTER_NAMES.includes(step.name)) {
+            problems.push(problem('error', where, `The matrix stage only knows ${MATRIX_FILTER_NAMES.join(', ')}; it throws on anything else.`));
+        }
+    }
+    const method = scale?.method;
+    if (method !== undefined &&
+        method !== '' &&
+        !SCALE_METHODS.includes(method.toLowerCase())) {
+        problems.push(problem('error', 'Scaling', `Unknown scaling: ${method}. It throws on anything but ${SCALE_METHODS.join(', ')}.`));
+    }
+    if (scale?.relative === true && scale.targetID === undefined) {
+        problems.push(problem('warning', 'Scaling', 'The difference is taken against the first spectrum the processor holds, which is not necessarily one of those selected.'));
+    }
+    const labels = new Set();
+    for (const [index, range] of (ranges ?? []).entries()) {
+        const where = `Range ${String(index + 1)}`;
+        const label = range.label ?? '';
+        if (label === '') {
+            problems.push(problem('error', where, 'A range with no name is silently skipped.'));
+        }
+        else if (!isUsableLabel(label)) {
+            problems.push(problem('error', where, `${label} cannot be the name of a variable, and the calculations read it as one.`));
+        }
+        else if (labels.has(label)) {
+            problems.push(problem('error', where, `${label} names two ranges; the second wins.`));
+        }
+        else {
+            labels.add(label);
+        }
+        if (isNumber(range.from) && isNumber(range.to) && range.from >= range.to) {
+            problems.push(problem('error', where, 'From is not below to.'));
+        }
+    }
+    for (const [index, calculation] of (calculations ?? []).entries()) {
+        const where = `Calculation ${String(index + 1)}`;
+        if (!isUsableLabel(calculation.label)) {
+            problems.push(problem('error', where, 'A calculation needs a name that can be a variable.'));
+        }
+        const complaint = calculationProblem(calculation.formula, labels);
+        if (complaint !== undefined) {
+            problems.push(problem('error', where, complaint));
+        }
+    }
+    if ((calculations ?? []).length > 0 && labels.size === 0) {
+        problems.push(problem('error', 'Calculations', 'A calculation reads the range integrals, and no range is named.'));
+    }
+    return problems;
+}
+/**
+ * What is wrong with a calculation, as far as can be told without running it.
+ * @param formula - What the reader typed.
+ * @param labels - The range names it may read.
+ * @returns The complaint, or undefined when nothing obvious is wrong.
+ */
+function calculationProblem(formula, labels) {
+    const trimmed = formula.trim();
+    if (trimmed === '')
+        return 'The formula is empty.';
+    let depth = 0;
+    for (const character of trimmed) {
+        if (character === '(')
+            depth++;
+        if (character === ')')
+            depth--;
+        if (depth < 0)
+            return 'A closing bracket has nothing to close.';
+    }
+    if (depth > 0)
+        return 'A bracket is left open.';
+    // The lookbehind keeps the exponent of a number such as `1e3` from reading
+    // as the name of a range.
+    const named = trimmed.replaceAll(/\.\w+/g, '').match(/(?<![\w$.])[A-Za-z_$][\w$]*/g) ??
+        [];
+    for (const name of named) {
+        if (name !== 'Math' && !labels.has(name)) {
+            return `${name} is not the name of a range, so the formula would throw.`;
+        }
+    }
+    return undefined;
+}
+//# sourceMappingURL=settingsProblems.js.map

package/lib/spectra/core/settingsProblems.js.map

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package/lib/spectra/core/stepProblems.d.ts

@@ -0,0 +1,13 @@
+import type { SettingsProblem } from './problems.ts';
+import type { SpectrumFilter } from './settings.ts';
+/**
+ * Everything wrong with one step's own options.
+ *
+ * Every rule here is one the processor actually fails on, checked against what
+ * `filterXY` does rather than against what the option is called.
+ * @param step - The step.
+ * @param where - How the panel labels it.
+ * @returns Its problems.
+ */
+export declare function stepProblems(step: SpectrumFilter, where: string): SettingsProblem[];
+//# sourceMappingURL=stepProblems.d.ts.map

package/lib/spectra/core/stepProblems.d.ts.map

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package/lib/spectra/core/stepProblems.js

@@ -0,0 +1,133 @@
+import { filterOptions, readFilterOption } from "./filterChain.js";
+import { formulaProblem, isNumber, isWholeNumber, problem, } from "./problems.js";
+/** Where a Savitzky–Golay window and degree can sit inside a step's options. */
+const WINDOW_PREFIXES = ['', 'gsd.sgOptions.'];
+/**
+ * Everything wrong with one step's own options.
+ *
+ * Every rule here is one the processor actually fails on, checked against what
+ * `filterXY` does rather than against what the option is called.
+ * @param step - The step.
+ * @param where - How the panel labels it.
+ * @returns Its problems.
+ */
+export function stepProblems(step, where) {
+    const problems = [];
+    const from = readFilterOption(step, 'from');
+    const to = readFilterOption(step, 'to');
+    if (isNumber(from) && isNumber(to) && from >= to) {
+        problems.push(problem('error', where, 'From is not below to.'));
+    }
+    problems.push(...smoothingProblems(step, where), ...zoneProblems(step, where));
+    const points = readFilterOption(step, 'numberOfPoints');
+    if (points !== undefined && (!isWholeNumber(points) || points < 2)) {
+        problems.push(problem('error', where, 'A grid needs at least two points.'));
+    }
+    const peaks = readFilterOption(step, 'nbPeaks');
+    if (peaks !== undefined && (!isWholeNumber(peaks) || peaks < 1)) {
+        problems.push(problem('error', where, 'At least one peak has to be looked for.'));
+    }
+    const minimum = readFilterOption(step, 'min');
+    const maximum = readFilterOption(step, 'max');
+    if (isNumber(minimum) && isNumber(maximum) && minimum >= maximum) {
+        problems.push(problem('error', where, 'The minimum is not below the maximum.'));
+    }
+    if (step.name === 'xFunction' || step.name === 'yFunction') {
+        const variable = step.name === 'xFunction' ? 'x' : 'y';
+        const written = readFilterOption(step, 'function');
+        const complaint = formulaProblem(typeof written === 'string' ? written : '', variable);
+        if (complaint !== undefined) {
+            problems.push(problem('error', where, complaint));
+        }
+    }
+    if (step.name === 'fromTo' && (from !== undefined || to !== undefined)) {
+        const options = filterOptions(step);
+        if (options.fromIndex !== undefined || options.toIndex !== undefined) {
+            problems.push(problem('warning', where, 'Both an x value and a point number are given; the point number wins and the x value is ignored.'));
+        }
+    }
+    return problems;
+}
+/**
+ * What is wrong with a step's window and polynomial, wherever they sit.
+ *
+ * `calibrateX` carries a second pair under its peak picking, and the processor
+ * throws on an even window there exactly as it does on the plain one.
+ * @param step - The step.
+ * @param where - How the panel labels it.
+ * @returns Its problems.
+ */
+function smoothingProblems(step, where) {
+    const problems = [];
+    for (const prefix of WINDOW_PREFIXES) {
+        const window = readFilterOption(step, `${prefix}windowSize`);
+        const polynomial = readFilterOption(step, `${prefix}polynomial`);
+        if (window !== undefined &&
+            (!isWholeNumber(window) || window < 5 || window % 2 === 0)) {
+            problems.push(problem('error', where, 'The window must be an odd whole number of 5 or more.'));
+        }
+        if (polynomial !== undefined &&
+            (!isWholeNumber(polynomial) || polynomial < 1)) {
+            problems.push(problem('error', where, 'The polynomial degree must be a whole number of 1 or more.'));
+        }
+        if (isWholeNumber(window) &&
+            isWholeNumber(polynomial) &&
+            polynomial >= window) {
+            problems.push(problem('error', where, 'The polynomial degree must stay below the window size.'));
+        }
+    }
+    const derivative = readFilterOption(step, 'derivative');
+    if (derivative !== undefined &&
+        (!isWholeNumber(derivative) || derivative < 0)) {
+        problems.push(problem('error', where, 'The derivative must be a whole number of zero or more.'));
+    }
+    return problems;
+}
+/**
+ * What is wrong with the stretches of x a step names.
+ *
+ * A zone left half filled is not harmless: the processor drops it while
+ * normalizing, then reads the first of the zones that are left — so `filterX`
+ * throws, and `equallySpaced` hands back a spectrum of no points at all.
+ * @param step - The step.
+ * @param where - How the panel labels it.
+ * @returns Its problems.
+ */
+function zoneProblems(step, where) {
+    const problems = [];
+    const zones = readFilterOption(step, 'zones');
+    const exclusions = readFilterOption(step, 'exclusions');
+    for (const [index, zone] of asZones(zones).entries()) {
+        if (!isSpan(zone)) {
+            problems.push(problem('error', where, `Zone to keep ${String(index + 1)} needs both bounds, with from below to; the processor fails on a half-filled one.`));
+        }
+    }
+    for (const [index, zone] of asZones(exclusions).entries()) {
+        if (!isSpan(zone)) {
+            problems.push(problem('warning', where, `Zone to drop ${String(index + 1)} needs both bounds, with from below to; as it stands it is ignored.`));
+        }
+    }
+    if (asZones(zones).length > 0 && asZones(exclusions).length > 0) {
+        problems.push(problem('warning', where, 'Zones to keep and zones to drop are both given; the zones to drop win.'));
+    }
+    return problems;
+}
+/**
+ * A step's option read as a list of stretches.
+ * @param value - What the option holds.
+ * @returns The list, empty when the option holds anything else.
+ */
+function asZones(value) {
+    if (!Array.isArray(value))
+        return [];
+    return value.filter((entry) => typeof entry === 'object' && entry !== null);
+}
+/**
+ * Whether a stretch names both of its ends, the right way round.
+ * @param zone - One entry of a zone list.
+ * @returns True when the processor can use it.
+ */
+function isSpan(zone) {
+    return isNumber(zone.from) && isNumber(zone.to) && zone.from < zone.to;
+}
+//# sourceMappingURL=stepProblems.js.map

package/lib/spectra/core/stepProblems.js.map

@@ -0,0 +1 @@
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package/lib/spectra/ui/CalculationRows.d.ts

@@ -0,0 +1,21 @@
+import type { ReactElement } from 'react';
+import type { SpectraCalculation } from '../core/settings.ts';
+/** What {@link CalculationRows} edits. */
+export interface CalculationRowsProps {
+    /** The named formulas reported per spectrum. */
+    value: readonly SpectraCalculation[];
+    /** Called with the new list on every edit. */
+    onChange: (calculations: SpectraCalculation[]) => void;
+}
+/**
+ * The formulas evaluated once per spectrum, over the range integrals.
+ *
+ * The formula box is monospaced and has spellchecking off because what goes in
+ * it is code, not prose: it is compiled into a function whose parameters are
+ * the range names, so a name that does not match a range throws at the moment
+ * the data is asked for rather than here.
+ * @param props - See {@link CalculationRowsProps}.
+ * @returns The list and the button that adds to it.
+ */
+export declare function CalculationRows(props: CalculationRowsProps): ReactElement;
+//# sourceMappingURL=CalculationRows.d.ts.map

package/lib/spectra/ui/CalculationRows.d.ts.map

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