react-cheminfo 0.3.0 → 0.4.1

package/lib/state/ui/index.d.ts

@@ -0,0 +1,3 @@
+export type { BucketRead, PersistBucketOptions, PersistedBucket, } from './persistBucket.ts';
+export { persistBucket } from './persistBucket.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/state/ui/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/state/ui/index.ts"],"names":[],"mappings":"AAAA,YAAY,EACV,UAAU,EACV,oBAAoB,EACpB,eAAe,GAChB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC"}

package/lib/state/ui/index.js

@@ -0,0 +1,2 @@
+export { persistBucket } from "./persistBucket.js";
+//# sourceMappingURL=index.js.map

package/lib/state/ui/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/state/ui/index.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC"}

package/lib/state/ui/mergeStored.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Merge what came out of storage over the defaults it was stored against.
+ *
+ * A field the defaults name and the payload does not keeps its default, so a
+ * field added after the last save lands as its default rather than as
+ * `undefined`. A field whose stored value no longer has the shape of its
+ * default — a number where a string is expected, an object where an array is —
+ * is discarded, because a payload written by an older version of a page must
+ * never reach the interface as the wrong type. A key the defaults do not name
+ * is kept, so a bucket whose default is an empty dictionary keeps everything
+ * that was ever put in it.
+ *
+ * The result shares no object and no array with `defaults`, so a caller may
+ * write into it.
+ * @param defaults - What every missing or unusable field falls back to.
+ * @param stored - Whatever `JSON.parse` gave back, trusted for nothing.
+ * @returns The defaults, with whatever was stored and is usable on top.
+ */
+export declare function mergeStored<T extends object>(defaults: T, stored: unknown): T;
+/**
+ * Whether a value is a plain object — the shape the JSON payload of a bucket
+ * takes — rather than an array, a primitive or null.
+ * @param value - Value to inspect.
+ * @returns True for a plain object.
+ */
+export declare function isPlainRecord(value: unknown): value is Record<string, unknown>;
+//# sourceMappingURL=mergeStored.d.ts.map

package/lib/state/ui/mergeStored.d.ts.map

@@ -0,0 +1 @@
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package/lib/state/ui/mergeStored.js

@@ -0,0 +1,82 @@
+/**
+ * Merge what came out of storage over the defaults it was stored against.
+ *
+ * A field the defaults name and the payload does not keeps its default, so a
+ * field added after the last save lands as its default rather than as
+ * `undefined`. A field whose stored value no longer has the shape of its
+ * default — a number where a string is expected, an object where an array is —
+ * is discarded, because a payload written by an older version of a page must
+ * never reach the interface as the wrong type. A key the defaults do not name
+ * is kept, so a bucket whose default is an empty dictionary keeps everything
+ * that was ever put in it.
+ *
+ * The result shares no object and no array with `defaults`, so a caller may
+ * write into it.
+ * @param defaults - What every missing or unusable field falls back to.
+ * @param stored - Whatever `JSON.parse` gave back, trusted for nothing.
+ * @returns The defaults, with whatever was stored and is usable on top.
+ */
+export function mergeStored(defaults, stored) {
+    const source = isPlainRecord(stored) ? stored : {};
+    return mergeRecord(defaults, source);
+}
+/**
+ * Whether a value is a plain object — the shape the JSON payload of a bucket
+ * takes — rather than an array, a primitive or null.
+ * @param value - Value to inspect.
+ * @returns True for a plain object.
+ */
+export function isPlainRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function mergeRecord(defaults, stored) {
+    const merged = {};
+    for (const [name, value] of Object.entries(defaults)) {
+        merged[name] = cloneValue(value);
+    }
+    for (const [name, value] of Object.entries(stored)) {
+        if (value === undefined)
+            continue;
+        merged[name] = Object.hasOwn(defaults, name)
+            ? mergeValue(defaults[name], value)
+            : value;
+    }
+    return merged;
+}
+function mergeValue(defaultValue, storedValue) {
+    if (isPlainRecord(defaultValue) && isPlainRecord(storedValue)) {
+        return mergeRecord(defaultValue, storedValue);
+    }
+    return hasSameShape(defaultValue, storedValue)
+        ? storedValue
+        : cloneValue(defaultValue);
+}
+// A default that is `null` or absent accepts anything, since it names no shape
+// of its own.
+function hasSameShape(defaultValue, storedValue) {
+    if (defaultValue === null || defaultValue === undefined)
+        return true;
+    if (storedValue === null)
+        return false;
+    if (Array.isArray(defaultValue) !== Array.isArray(storedValue))
+        return false;
+    return typeof defaultValue === typeof storedValue;
+}
+function cloneValue(value) {
+    if (Array.isArray(value)) {
+        const copy = new Array(value.length);
+        for (let index = 0; index < value.length; index++) {
+            copy[index] = cloneValue(value[index]);
+        }
+        return copy;
+    }
+    if (isPlainRecord(value)) {
+        const copy = {};
+        for (const [name, item] of Object.entries(value)) {
+            copy[name] = cloneValue(item);
+        }
+        return copy;
+    }
+    return value;
+}
+//# sourceMappingURL=mergeStored.js.map

package/lib/state/ui/mergeStored.js.map

@@ -0,0 +1 @@
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package/lib/state/ui/persistBucket.d.ts

@@ -0,0 +1,65 @@
+/**
+ * A bucket of preferences kept in `localStorage` under one versioned key.
+ *
+ * Everything here is best effort. In a page framed by a course, third-party
+ * storage is partitioned in Chrome and blocked in Safari, so a read may find
+ * nothing, a write may be refused, and touching the store may throw before it
+ * is even reached — none of which may ever reach the interface. A visitor whose
+ * quota is full still gets a working site, with their preferences lasting only
+ * as long as the tab.
+ * @param options - See {@link PersistBucketOptions}.
+ * @returns The three ways to use the bucket: read it, write it, forget it.
+ */
+export declare function persistBucket<T extends object>(options: PersistBucketOptions<T>): PersistedBucket<T>;
+/** How a bucket is named, versioned and filled in. */
+export interface PersistBucketOptions<T extends object> {
+    /**
+     * Name of the bucket, namespaced by the site, e.g. `smiles:exercises`. The
+     * version is appended to it, so this never carries one itself.
+     */
+    key: string;
+    /**
+     * Schema version, appended to the key as `:v<version>`. Raise it when a new
+     * shape cannot be reconciled with the old one field by field, and every entry
+     * written by the previous shape is then ignored rather than migrated.
+     * @default 1
+     */
+    version?: number;
+    /**
+     * What a visitor who has stored nothing gets, and what every missing or
+     * unusable field of a stored payload falls back to. Must be JSON
+     * serialisable, since that is how it is stored.
+     */
+    defaults: T;
+    /**
+     * Called when a write was refused because the store is full, with the error
+     * the store threw. The write is swallowed either way; this only exists so a
+     * page can tell its visitor that what they are doing is no longer being kept.
+     * @default undefined
+     */
+    onQuotaExceeded?: (error: unknown) => void;
+}
+/** The three ways a page uses its bucket. */
+export interface PersistedBucket<T extends object> {
+    /** The versioned key the bucket occupies, e.g. `smiles:exercises:v1`. */
+    readonly storageKey: string;
+    /** What was stored, merged over the defaults. */
+    read: () => BucketRead<T>;
+    /** Store the bucket as it now stands, replacing what was there. */
+    write: (value: T) => void;
+    /** Forget the bucket, leaving whatever the page holds in memory untouched. */
+    clear: () => void;
+}
+/** What one read of a bucket found. */
+export interface BucketRead<T> {
+    /** The stored payload merged over the defaults, ready to be used as is. */
+    value: T;
+    /**
+     * True when nothing usable was there: no entry, an unreadable store, or a
+     * payload that is not an object. It tells a first visit from a visitor who
+     * chose exactly the defaults, which is what decides whether a page opens on
+     * its welcome state or writes the bucket straight back.
+     */
+    firstRun: boolean;
+}
+//# sourceMappingURL=persistBucket.d.ts.map

package/lib/state/ui/persistBucket.d.ts.map

@@ -0,0 +1 @@
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package/lib/state/ui/persistBucket.js

@@ -0,0 +1,90 @@
+import { isPlainRecord, mergeStored } from "./mergeStored.js";
+/**
+ * A bucket of preferences kept in `localStorage` under one versioned key.
+ *
+ * Everything here is best effort. In a page framed by a course, third-party
+ * storage is partitioned in Chrome and blocked in Safari, so a read may find
+ * nothing, a write may be refused, and touching the store may throw before it
+ * is even reached — none of which may ever reach the interface. A visitor whose
+ * quota is full still gets a working site, with their preferences lasting only
+ * as long as the tab.
+ * @param options - See {@link PersistBucketOptions}.
+ * @returns The three ways to use the bucket: read it, write it, forget it.
+ */
+export function persistBucket(options) {
+    const { key, version = 1, defaults, onQuotaExceeded } = options;
+    const storageKey = `${key}:v${version}`;
+    return {
+        storageKey,
+        read: () => {
+            const stored = readEntry(storageKey);
+            return {
+                value: mergeStored(defaults, stored),
+                firstRun: stored === undefined,
+            };
+        },
+        write: (value) => {
+            writeEntry(storageKey, value, onQuotaExceeded);
+        },
+        clear: () => {
+            try {
+                globalThis.localStorage?.removeItem(storageKey);
+            }
+            catch {
+                // An unavailable store has nothing to forget.
+            }
+        },
+    };
+}
+function readEntry(storageKey) {
+    let raw;
+    try {
+        raw = globalThis.localStorage?.getItem(storageKey) ?? null;
+    }
+    catch {
+        return undefined;
+    }
+    if (raw === null)
+        return undefined;
+    try {
+        const parsed = JSON.parse(raw);
+        return isPlainRecord(parsed) ? parsed : undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
+function writeEntry(storageKey, value, onQuotaExceeded) {
+    let serialized;
+    try {
+        serialized = JSON.stringify(value);
+    }
+    catch {
+        // A value that cannot be serialised is a bug in the caller, never a reason
+        // to take the page down with it.
+        return;
+    }
+    try {
+        globalThis.localStorage?.setItem(storageKey, serialized);
+    }
+    catch (error) {
+        if (!isQuotaExceeded(error) || onQuotaExceeded === undefined)
+            return;
+        try {
+            onQuotaExceeded(error);
+        }
+        catch {
+            // A callback that throws must not turn a lost preference into a crash.
+        }
+    }
+}
+function isQuotaExceeded(error) {
+    if (typeof error !== 'object' || error === null)
+        return false;
+    const { name, code } = error;
+    return (name === 'QuotaExceededError' ||
+        name === 'NS_ERROR_DOM_QUOTA_REACHED' ||
+        code === 22 ||
+        code === 1014);
+}
+//# sourceMappingURL=persistBucket.js.map

package/lib/state/ui/persistBucket.js.map

@@ -0,0 +1 @@
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package/lib/structure/core/editorValue.d.ts

@@ -0,0 +1,69 @@
+/** One structure of an editor's value, with whatever was written next to it. */
+export interface EditorLine {
+    /**
+     * The structure. On a line-oriented value this is the first blank-separated
+     * token, because a line notation never holds a blank; on a molfile it is the
+     * whole file.
+     */
+    structure: string;
+    /**
+     * What followed the structure on its line, which a Daylight `.smi` file uses
+     * as a name. Empty when nothing did.
+     */
+    label: string;
+    /** 1-based line the structure starts on, so an error can point back at it. */
+    line: number;
+}
+/** An editor's value, classified and cut into the structures it holds. */
+export interface EditorValue {
+    /** How the value is written; `empty` when it holds no structure at all. */
+    kind: 'molfile' | 'smiles' | 'empty';
+    /**
+     * The molfile, exactly as it arrived, when `kind` is `molfile`. Empty
+     * otherwise — a molfile's fixed-width header does not survive being trimmed.
+     */
+    molfile: string;
+    /**
+     * Every structure the value holds, in order: one per meaningful line for a
+     * line-oriented value, a single entry for a molfile, none for an empty one.
+     */
+    entries: EditorLine[];
+}
+/**
+ * Take an editor's value apart.
+ *
+ * A structure box is handed whatever the chemist had: one molfile pasted out
+ * of another tool, or a run of line notations one per line, possibly with a
+ * name after each and with blank and `#` comment lines in between. Both are
+ * read here so a page can take either without asking which it was given.
+ * @param text - The editor's value, as typed, pasted or dropped.
+ * @returns The notation, the molfile when it is one, and the structures.
+ */
+export declare function splitEditorValue(text: string): EditorValue;
+/** An idCode and, when the writer emitted one, the atom layout beside it. */
+export interface IdCodeValue {
+    idCode: string;
+    /** Absent when the value carried no coordinates. */
+    coordinates?: string;
+}
+/**
+ * Take an idCode apart.
+ *
+ * A drawing editor appends the atom coordinates after a space, which
+ * `Molecule.fromIDCode` takes as a second argument rather than as part of the
+ * first, and which two drawings of the same structure differ by.
+ * @param value - The editor value, coordinates included or not.
+ * @returns The idCode and the coordinates, the idCode empty for a blank value.
+ */
+export declare function splitIdCode(value: string): IdCodeValue;
+/**
+ * Whether an idCode describes nothing.
+ *
+ * Erasing a canvas does not leave the editor with an empty string: it leaves
+ * the idCode of the empty molecule, or of the empty fragment in query mode.
+ * Treating either as a structure keeps a filter alive with nothing drawn.
+ * @param value - The editor value, coordinates included or not.
+ * @returns True when there is nothing on the canvas.
+ */
+export declare function isEmptyIdCode(value: string): boolean;
+//# sourceMappingURL=editorValue.d.ts.map

package/lib/structure/core/editorValue.d.ts.map

@@ -0,0 +1 @@
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package/lib/structure/core/editorValue.js

@@ -0,0 +1,72 @@
+import { looksLikeMolfile } from "./molfile.js";
+/**
+ * Take an editor's value apart.
+ *
+ * A structure box is handed whatever the chemist had: one molfile pasted out
+ * of another tool, or a run of line notations one per line, possibly with a
+ * name after each and with blank and `#` comment lines in between. Both are
+ * read here so a page can take either without asking which it was given.
+ * @param text - The editor's value, as typed, pasted or dropped.
+ * @returns The notation, the molfile when it is one, and the structures.
+ */
+export function splitEditorValue(text) {
+    if (text.trim() === '')
+        return { kind: 'empty', molfile: '', entries: [] };
+    if (looksLikeMolfile(text)) {
+        return {
+            kind: 'molfile',
+            molfile: text,
+            entries: [{ structure: text, label: '', line: 1 }],
+        };
+    }
+    const entries = splitLines(text);
+    return entries.length === 0
+        ? { kind: 'empty', molfile: '', entries: [] }
+        : { kind: 'smiles', molfile: '', entries };
+}
+/**
+ * Take an idCode apart.
+ *
+ * A drawing editor appends the atom coordinates after a space, which
+ * `Molecule.fromIDCode` takes as a second argument rather than as part of the
+ * first, and which two drawings of the same structure differ by.
+ * @param value - The editor value, coordinates included or not.
+ * @returns The idCode and the coordinates, the idCode empty for a blank value.
+ */
+export function splitIdCode(value) {
+    const [idCode = '', coordinates] = value.trim().split(' ');
+    return coordinates === undefined ? { idCode } : { idCode, coordinates };
+}
+/**
+ * Whether an idCode describes nothing.
+ *
+ * Erasing a canvas does not leave the editor with an empty string: it leaves
+ * the idCode of the empty molecule, or of the empty fragment in query mode.
+ * Treating either as a structure keeps a filter alive with nothing drawn.
+ * @param value - The editor value, coordinates included or not.
+ * @returns True when there is nothing on the canvas.
+ */
+export function isEmptyIdCode(value) {
+    return EMPTY_ID_CODES.has(splitIdCode(value).idCode);
+}
+/** What openchemlib writes for a structure with no atoms: molecule, fragment. */
+const EMPTY_ID_CODES = new Set(['', 'd@', 'dH']);
+function splitLines(text) {
+    const entries = [];
+    const lines = text.split('\n');
+    for (let index = 0; index < lines.length; index++) {
+        const line = (lines[index] ?? '').trim();
+        if (line === '' || line.startsWith('#'))
+            continue;
+        const blank = line.search(/\s/);
+        entries.push(blank === -1
+            ? { structure: line, label: '', line: index + 1 }
+            : {
+                structure: line.slice(0, blank),
+                label: line.slice(blank).trim(),
+                line: index + 1,
+            });
+    }
+    return entries;
+}
+//# sourceMappingURL=editorValue.js.map

package/lib/structure/core/editorValue.js.map

@@ -0,0 +1 @@
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package/lib/structure/core/fragmentQuery.d.ts

@@ -0,0 +1,33 @@
+import type { StructureKind } from './readStructure.ts';
+/** What a substructure field is currently filtering on. */
+export interface FragmentQuery {
+    /** The notation the query should be read as. */
+    kind: StructureKind;
+    /** The query, ready to hand a parser. Empty when nothing is filtered on. */
+    value: string;
+    /**
+     * True when the field filters on nothing — a blank box, or the idCode an
+     * erased canvas leaves behind.
+     */
+    isEmpty: boolean;
+}
+/**
+ * Read what a substructure field holds.
+ *
+ * A filter is fed from two places that disagree about what "nothing" is: a
+ * text box hands back the empty string, while a drawing canvas hands back the
+ * idCode of the empty molecule. Both mean the filter is off, and a filter that
+ * stays on with nothing drawn quietly hides every result.
+ * @param text - The field's value: an idCode, a molfile or a line notation.
+ * @returns The notation, the query, and whether anything is being filtered on.
+ */
+export declare function fragmentQuery(text: string): FragmentQuery;
+/**
+ * Whether two field values describe the same query, so a search is not run
+ * again for a value that only changed by its surrounding blanks.
+ * @param left - One field value.
+ * @param right - The other field value.
+ * @returns True when both would be read as the same query.
+ */
+export declare function sameFragmentQuery(left: string, right: string): boolean;
+//# sourceMappingURL=fragmentQuery.d.ts.map

package/lib/structure/core/fragmentQuery.d.ts.map

@@ -0,0 +1 @@
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package/lib/structure/core/fragmentQuery.js

@@ -0,0 +1,37 @@
+import { isEmptyIdCode } from "./editorValue.js";
+import { readStructure } from "./readStructure.js";
+/**
+ * Read what a substructure field holds.
+ *
+ * A filter is fed from two places that disagree about what "nothing" is: a
+ * text box hands back the empty string, while a drawing canvas hands back the
+ * idCode of the empty molecule. Both mean the filter is off, and a filter that
+ * stays on with nothing drawn quietly hides every result.
+ * @param text - The field's value: an idCode, a molfile or a line notation.
+ * @returns The notation, the query, and whether anything is being filtered on.
+ */
+export function fragmentQuery(text) {
+    if (isEmptyIdCode(text))
+        return { kind: 'empty', value: '', isEmpty: true };
+    const read = readStructure(text);
+    return {
+        kind: read.kind,
+        value: read.value,
+        isEmpty: read.kind === 'empty',
+    };
+}
+/**
+ * Whether two field values describe the same query, so a search is not run
+ * again for a value that only changed by its surrounding blanks.
+ * @param left - One field value.
+ * @param right - The other field value.
+ * @returns True when both would be read as the same query.
+ */
+export function sameFragmentQuery(left, right) {
+    const first = fragmentQuery(left);
+    const second = fragmentQuery(right);
+    if (first.isEmpty || second.isEmpty)
+        return first.isEmpty === second.isEmpty;
+    return first.kind === second.kind && first.value === second.value;
+}
+//# sourceMappingURL=fragmentQuery.js.map

package/lib/structure/core/fragmentQuery.js.map

@@ -0,0 +1 @@
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package/lib/structure/core/index.d.ts

@@ -0,0 +1,11 @@
+export type { EditorLine, EditorValue } from './editorValue.ts';
+export { splitEditorValue } from './editorValue.ts';
+export type { FragmentQuery } from './fragmentQuery.ts';
+export { fragmentQuery, sameFragmentQuery } from './fragmentQuery.ts';
+export type { MolfileClassification, MolfileVersion } from './molfile.ts';
+export { classifyMolfile, molfileAtomCount } from './molfile.ts';
+export type { ReadStructureResult, StructureKind } from './readStructure.ts';
+export { looksLikeSmarts, readStructure } from './readStructure.ts';
+export type { StructureSource, StructureSourceInput, } from './structureSource.ts';
+export { structureSource } from './structureSource.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/structure/core/index.d.ts.map

@@ -0,0 +1 @@
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package/lib/structure/core/index.js

@@ -0,0 +1,6 @@
+export { splitEditorValue } from "./editorValue.js";
+export { fragmentQuery, sameFragmentQuery } from "./fragmentQuery.js";
+export { classifyMolfile, molfileAtomCount } from "./molfile.js";
+export { looksLikeSmarts, readStructure } from "./readStructure.js";
+export { structureSource } from "./structureSource.js";
+//# sourceMappingURL=index.js.map

package/lib/structure/core/index.js.map

@@ -0,0 +1 @@
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package/lib/structure/core/molfile.d.ts

@@ -0,0 +1,42 @@
+/** Which connection-table dialect a molfile is written in. */
+export type MolfileVersion = 'v2000' | 'v3000' | 'unknown';
+/** What a molfile's counts line says about it. */
+export interface MolfileClassification {
+    /** The dialect, `unknown` when the text carries no version stamp. */
+    version: MolfileVersion;
+    /**
+     * Atoms the counts line declares, `0` when there is no counts line to read.
+     */
+    atomCount: number;
+}
+/**
+ * Read a molfile's version and its declared atom count.
+ *
+ * The two dialects write their counts in unrelated places: V2000 packs them
+ * into the fixed-width fields of the line ending in `V2000`, while a V3000
+ * file leaves those fields at zero and declares the real counts on an
+ * `M  V30 COUNTS` line further down. Reading a V3000 file with the V2000 rule
+ * therefore answers zero atoms without failing, which is what makes a viewer
+ * render an empty scene and report nothing.
+ * @param text - A molfile, or any text that may not be one.
+ * @returns The dialect and the declared atom count.
+ */
+export declare function classifyMolfile(text: string): MolfileClassification;
+/**
+ * How many atoms a molfile declares, whichever dialect it is written in.
+ * @param text - A molfile, or any text that may not be one.
+ * @returns The declared atom count, `0` when the text declares none.
+ */
+export declare function molfileAtomCount(text: string): number;
+/**
+ * Whether a piece of text should be read as a molfile rather than as a line
+ * notation.
+ *
+ * A line notation is a single line and can never carry a version stamp, so a
+ * text holding a header, a counts line and at least one atom line is the one
+ * that is a molfile.
+ * @param text - The structure, as typed, pasted or dropped.
+ * @returns True when it should be read as a molfile.
+ */
+export declare function looksLikeMolfile(text: string): boolean;
+//# sourceMappingURL=molfile.d.ts.map

package/lib/structure/core/molfile.d.ts.map

@@ -0,0 +1 @@
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