react-cheminfo 0.27.0 → 0.29.0

package/lib/ir/core/irMode.d.ts

@@ -0,0 +1,160 @@
+/**
+ * Everything that differs between reading a spectrum as absorbance and reading
+ * it as percent transmittance.
+ *
+ * The two are the same measurement drawn upside down, and nearly every
+ * difference between them is one of a handful of facts: what the axis is called,
+ * where its baseline is, whether that baseline is held in the window, which way
+ * a band points, and which zoom gestures are worth answering. Gathering them
+ * here is what keeps the switch from being an `if (mode === …)` in the chart,
+ * the tracker, the band marks, the zoom and the fitting separately, where they
+ * would eventually disagree.
+ *
+ * **No conversion happens here, or anywhere in this package.** `ir-spectrum`
+ * adds both an absorbance and a transmittance variable to every spectrum it
+ * reads, whichever the instrument wrote, so the arithmetic that relates them is
+ * its business and is done once at the point the file is understood. A second
+ * implementation here would be a second answer.
+ */
+import type { YAxisRules, ZoomDragMode, ZoomGestures } from '../../chart/core/chartDomain.ts';
+import type { IrMode } from './irSpectrum.ts';
+/** The two ways a spectrum is read, in the order a control offers them. */
+export declare const IR_MODES: readonly IrMode[];
+/**
+ * How each mode behaves, every fact in one place.
+ *
+ * `transmittance` comes first because it is what the majority of instruments
+ * export and what most chemists picture when they say "the IR": bands hanging
+ * down from a baseline near 100.
+ */
+export declare const IR_MODE_RULES: {
+    readonly transmittance: {
+        /** What the vertical axis is called. */
+        readonly title: "transmittance (%)";
+        /**
+         * The clear baseline a band hangs from, which the wheel scales about.
+         *
+         * A hundred rather than zero, and this is the whole reason `YAxisRules`
+         * exists: scaling percent transmittance about zero walks the entire trace
+         * off the top of the plot, because the trace lives just under 100 and
+         * nothing interesting is near the origin.
+         */
+        readonly baseline: 100;
+        /**
+         * Whether 100 is held inside the window a drag asks for.
+         *
+         * It is not. A band dragged out between 20 and 60 percent is being asked
+         * about between 20 and 60 percent; forcing the baseline back in would undo
+         * the zoom in the act of granting it. This is the opposite of a mass
+         * spectrum, whose sticks are drawn *from* their baseline and are cut off at
+         * the ankles without it.
+         */
+        readonly keepBaseline: false;
+        /** Bands point down, away from the baseline above them. */
+        readonly bandsPointDown: true;
+        /**
+         * A drag is the rectangle it sweeps out, whatever tool is chosen.
+         *
+         * Percent transmittance is bounded at both ends and the trace fills nearly
+         * all of it, so the question this axis is asked is never "between which two
+         * percentages" — it is "look closer at that corner", which is a rectangle
+         * and nothing else. Leaving the reading gesture available here would offer a
+         * choice between one useful answer and one that changes nothing.
+         */
+        readonly boxZoomOnly: true;
+        /**
+         * The wheel is left to the page.
+         *
+         * The axis is bounded — a transmittance is a percentage of the light that
+         * got through, so it lies between 0 and 100 and the trace already fills it.
+         * Scaling it freely about 100 therefore only ever takes the window past one
+         * end or crushes it against the other, which is a poor thing to have a
+         * pointer resting over a chart do by accident. The rectangle asks the same
+         * question properly, by naming the two percentages it lands between.
+         *
+         * The zoom in and zoom out **commands** still scale the axis here: they are
+         * aimed at, they step by a known factor, and the reader who pressed one
+         * knows what it did.
+         */
+        readonly wheelZoom: false;
+    };
+    readonly absorbance: {
+        readonly title: "absorbance";
+        /** Zero absorbance is a real floor: no light absorbed. */
+        readonly baseline: 0;
+        /**
+         * Whether zero is held inside the window a drag asks for.
+         *
+         * It is not, for the same reason as transmittance: a weak band between 0.02
+         * and 0.05 absorbance is unreadable in a window that starts at zero, and
+         * being able to drag to it is the point of the gesture. Zero remains the
+         * baseline the wheel scales about, which is what keeps the trace anchored.
+         */
+        readonly keepBaseline: false;
+        /** Bands point up, out of the baseline under them. */
+        readonly bandsPointDown: false;
+        /**
+         * Both drags are worth having, so the tool decides between them.
+         *
+         * Absorbance is open at the top and its weak bands lie against zero, so "what
+         * is between 1650 and 1750" and "what is in that rectangle" are two different
+         * questions a chemist genuinely asks of the same trace.
+         */
+        readonly boxZoomOnly: false;
+        /**
+         * The wheel scales the axis about zero, which is what brings a weak band up
+         * out of the baseline without narrowing the wavenumbers at all.
+         */
+        readonly wheelZoom: true;
+    };
+};
+/**
+ * What the vertical axis is called in a mode.
+ * @param mode - Which value axis is being drawn.
+ * @returns The axis title.
+ */
+export declare function yAxisTitle(mode: IrMode): string;
+/**
+ * How the vertical axis behaves under a gesture in a mode.
+ * @param mode - Which value axis is being drawn.
+ * @returns The rules to hand to the zoom.
+ */
+export declare function yAxisRules(mode: IrMode): YAxisRules;
+/**
+ * Which zoom gestures a mode answers, and what a drag in it asks for.
+ *
+ * The mode has the last word on the drag rather than the tool, because the tool
+ * is a preference and this is not: percent transmittance has one useful drag,
+ * and a viewer that let a tool button ask for the other would answer with a
+ * gesture that narrows the wavenumbers and leaves the crowded axis exactly as it
+ * was. The tool is still read — in absorbance both drags mean something — so a
+ * chemist who chose the square zoom keeps it across a switch to %T and back.
+ * @param mode - Which value axis is being drawn.
+ * @param tool - What a drag asks for where the mode leaves the choice open.
+ * Defaults to the reading gesture.
+ * @returns The gestures to hand to the zoom.
+ */
+export declare function zoomGestures(mode: IrMode, tool?: ZoomDragMode): Required<ZoomGestures>;
+/**
+ * Whether a mode leaves the square zoom as the only drag there is.
+ *
+ * What the toolbar and the status bar need in order to say so: a tool button
+ * showing `read` as available in percent transmittance would be describing a
+ * gesture the chart will not make.
+ * @param mode - Which value axis is being drawn.
+ * @returns Whether every drag is a rectangle.
+ */
+export declare function boxZoomOnly(mode: IrMode): boolean;
+/**
+ * Which way a band points in a mode, which is which way its label is stacked.
+ * @param mode - Which value axis is being drawn.
+ * @returns Whether bands hang downwards.
+ */
+export declare function bandsPointDown(mode: IrMode): boolean;
+/**
+ * The other mode, for a control that toggles between the two.
+ * @param mode - The mode in force.
+ * @returns The one to switch to.
+ */
+export declare function otherIrMode(mode: IrMode): IrMode;
+//# sourceMappingURL=irMode.d.ts.map

package/lib/ir/core/irMode.d.ts.map

@@ -0,0 +1 @@
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package/lib/ir/core/irMode.js

@@ -0,0 +1,175 @@
+/**
+ * Everything that differs between reading a spectrum as absorbance and reading
+ * it as percent transmittance.
+ *
+ * The two are the same measurement drawn upside down, and nearly every
+ * difference between them is one of a handful of facts: what the axis is called,
+ * where its baseline is, whether that baseline is held in the window, which way
+ * a band points, and which zoom gestures are worth answering. Gathering them
+ * here is what keeps the switch from being an `if (mode === …)` in the chart,
+ * the tracker, the band marks, the zoom and the fitting separately, where they
+ * would eventually disagree.
+ *
+ * **No conversion happens here, or anywhere in this package.** `ir-spectrum`
+ * adds both an absorbance and a transmittance variable to every spectrum it
+ * reads, whichever the instrument wrote, so the arithmetic that relates them is
+ * its business and is done once at the point the file is understood. A second
+ * implementation here would be a second answer.
+ */
+/** The two ways a spectrum is read, in the order a control offers them. */
+export const IR_MODES = ['transmittance', 'absorbance'];
+/**
+ * How each mode behaves, every fact in one place.
+ *
+ * `transmittance` comes first because it is what the majority of instruments
+ * export and what most chemists picture when they say "the IR": bands hanging
+ * down from a baseline near 100.
+ */
+export const IR_MODE_RULES = {
+    transmittance: {
+        /** What the vertical axis is called. */
+        title: 'transmittance (%)',
+        /**
+         * The clear baseline a band hangs from, which the wheel scales about.
+         *
+         * A hundred rather than zero, and this is the whole reason `YAxisRules`
+         * exists: scaling percent transmittance about zero walks the entire trace
+         * off the top of the plot, because the trace lives just under 100 and
+         * nothing interesting is near the origin.
+         */
+        baseline: 100,
+        /**
+         * Whether 100 is held inside the window a drag asks for.
+         *
+         * It is not. A band dragged out between 20 and 60 percent is being asked
+         * about between 20 and 60 percent; forcing the baseline back in would undo
+         * the zoom in the act of granting it. This is the opposite of a mass
+         * spectrum, whose sticks are drawn *from* their baseline and are cut off at
+         * the ankles without it.
+         */
+        keepBaseline: false,
+        /** Bands point down, away from the baseline above them. */
+        bandsPointDown: true,
+        /**
+         * A drag is the rectangle it sweeps out, whatever tool is chosen.
+         *
+         * Percent transmittance is bounded at both ends and the trace fills nearly
+         * all of it, so the question this axis is asked is never "between which two
+         * percentages" — it is "look closer at that corner", which is a rectangle
+         * and nothing else. Leaving the reading gesture available here would offer a
+         * choice between one useful answer and one that changes nothing.
+         */
+        boxZoomOnly: true,
+        /**
+         * The wheel is left to the page.
+         *
+         * The axis is bounded — a transmittance is a percentage of the light that
+         * got through, so it lies between 0 and 100 and the trace already fills it.
+         * Scaling it freely about 100 therefore only ever takes the window past one
+         * end or crushes it against the other, which is a poor thing to have a
+         * pointer resting over a chart do by accident. The rectangle asks the same
+         * question properly, by naming the two percentages it lands between.
+         *
+         * The zoom in and zoom out **commands** still scale the axis here: they are
+         * aimed at, they step by a known factor, and the reader who pressed one
+         * knows what it did.
+         */
+        wheelZoom: false,
+    },
+    absorbance: {
+        title: 'absorbance',
+        /** Zero absorbance is a real floor: no light absorbed. */
+        baseline: 0,
+        /**
+         * Whether zero is held inside the window a drag asks for.
+         *
+         * It is not, for the same reason as transmittance: a weak band between 0.02
+         * and 0.05 absorbance is unreadable in a window that starts at zero, and
+         * being able to drag to it is the point of the gesture. Zero remains the
+         * baseline the wheel scales about, which is what keeps the trace anchored.
+         */
+        keepBaseline: false,
+        /** Bands point up, out of the baseline under them. */
+        bandsPointDown: false,
+        /**
+         * Both drags are worth having, so the tool decides between them.
+         *
+         * Absorbance is open at the top and its weak bands lie against zero, so "what
+         * is between 1650 and 1750" and "what is in that rectangle" are two different
+         * questions a chemist genuinely asks of the same trace.
+         */
+        boxZoomOnly: false,
+        /**
+         * The wheel scales the axis about zero, which is what brings a weak band up
+         * out of the baseline without narrowing the wavenumbers at all.
+         */
+        wheelZoom: true,
+    },
+};
+/**
+ * What the vertical axis is called in a mode.
+ * @param mode - Which value axis is being drawn.
+ * @returns The axis title.
+ */
+export function yAxisTitle(mode) {
+    return IR_MODE_RULES[mode].title;
+}
+/**
+ * How the vertical axis behaves under a gesture in a mode.
+ * @param mode - Which value axis is being drawn.
+ * @returns The rules to hand to the zoom.
+ */
+export function yAxisRules(mode) {
+    const { baseline, keepBaseline, bandsPointDown } = IR_MODE_RULES[mode];
+    // `pointsDown` is what tells the zoom which way "released past the baseline"
+    // points: percent transmittance hangs from 100 at the top of the plot, so the
+    // gesture is a drag released above it rather than below.
+    return { baseline, keepBaseline, pointsDown: bandsPointDown };
+}
+/**
+ * Which zoom gestures a mode answers, and what a drag in it asks for.
+ *
+ * The mode has the last word on the drag rather than the tool, because the tool
+ * is a preference and this is not: percent transmittance has one useful drag,
+ * and a viewer that let a tool button ask for the other would answer with a
+ * gesture that narrows the wavenumbers and leaves the crowded axis exactly as it
+ * was. The tool is still read — in absorbance both drags mean something — so a
+ * chemist who chose the square zoom keeps it across a switch to %T and back.
+ * @param mode - Which value axis is being drawn.
+ * @param tool - What a drag asks for where the mode leaves the choice open.
+ * Defaults to the reading gesture.
+ * @returns The gestures to hand to the zoom.
+ */
+export function zoomGestures(mode, tool = 'xAxis') {
+    const { boxZoomOnly, wheelZoom } = IR_MODE_RULES[mode];
+    return { drag: boxZoomOnly ? 'box' : tool, wheel: wheelZoom };
+}
+/**
+ * Whether a mode leaves the square zoom as the only drag there is.
+ *
+ * What the toolbar and the status bar need in order to say so: a tool button
+ * showing `read` as available in percent transmittance would be describing a
+ * gesture the chart will not make.
+ * @param mode - Which value axis is being drawn.
+ * @returns Whether every drag is a rectangle.
+ */
+export function boxZoomOnly(mode) {
+    return IR_MODE_RULES[mode].boxZoomOnly;
+}
+/**
+ * Which way a band points in a mode, which is which way its label is stacked.
+ * @param mode - Which value axis is being drawn.
+ * @returns Whether bands hang downwards.
+ */
+export function bandsPointDown(mode) {
+    return IR_MODE_RULES[mode].bandsPointDown;
+}
+/**
+ * The other mode, for a control that toggles between the two.
+ * @param mode - The mode in force.
+ * @returns The one to switch to.
+ */
+export function otherIrMode(mode) {
+    return mode === 'absorbance' ? 'transmittance' : 'absorbance';
+}
+//# sourceMappingURL=irMode.js.map

package/lib/ir/core/irMode.js.map

@@ -0,0 +1 @@
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package/lib/ir/core/irReducer.d.ts

@@ -0,0 +1,101 @@
+/**
+ * Every change the viewer can undergo, as one function over one object.
+ *
+ * A reducer rather than a graph of signals, for the reason
+ * `docs/decisions.md` gives about the glycan editor: a published component must
+ * not impose a state library on the page that mounts it, and two viewers on one
+ * page must not share a module-level singleton. The state is a plain object, so a
+ * host can save it, restore it and compare it.
+ *
+ * Every case returns the state **itself** when it has nothing to do, so a render
+ * memoised on the state is not defeated by an action that changed nothing —
+ * selecting the spectrum already selected, closing an error that is already
+ * closed.
+ */
+import type { IrSidePanelId } from './irSidePanels.ts';
+import type { IrDomain, IrSpectrum } from './irSpectrum.ts';
+import type { IrSettings, IrState, IrTool, PartialIrState } from './irState.ts';
+/** Everything that can be asked of the viewer. */
+export type IrAction = {
+    type: 'addSpectra';
+    spectra: IrSpectrum[];
+} | {
+    type: 'setSpectra';
+    spectra: IrSpectrum[];
+} | {
+    type: 'removeSpectrum';
+    id: string;
+} | {
+    type: 'renameSpectrum';
+    id: string;
+    name: string;
+} | {
+    type: 'setSpectrumColor';
+    id: string;
+    color: string;
+} | {
+    type: 'setSpectrumVisible';
+    id: string;
+    visible: boolean;
+} | {
+    type: 'selectSpectrum';
+    id: string | null;
+} | {
+    type: 'setDomain';
+    domain: IrDomain;
+} | {
+    type: 'resetDomain';
+} | {
+    type: 'setTool';
+    tool: IrTool;
+} | {
+    type: 'togglePanel';
+    panelId: IrSidePanelId;
+} | {
+    type: 'setError';
+    error: string | null;
+} | {
+    type: 'setSettings';
+    settings: Partial<IrSettings>;
+} | {
+    type: 'loadState';
+    state: PartialIrState;
+} | {
+    type: 'clear';
+};
+/** What a viewer opens on. */
+export interface CreateIrStateOptions {
+    /**
+     * The spectra to open on.
+     * @default []
+     */
+    spectra?: IrSpectrum[];
+    /**
+     * The workspace to open in.
+     * @default DEFAULT_SETTINGS
+     */
+    settings?: Partial<IrSettings>;
+    /**
+     * The panels open to begin with.
+     * @default DEFAULT_SIDE_PANELS
+     */
+    panelIds?: IrSidePanelId[];
+}
+/**
+ * The state a viewer opens with.
+ *
+ * The panel list is spread rather than stored by reference: a caller's array is
+ * the caller's to mutate, and a viewer holding it would find its open panels
+ * changing under it.
+ * @param options - What it opens on.
+ * @returns The state.
+ */
+export declare function createIrState(options?: CreateIrStateOptions): IrState;
+/**
+ * Fold one action into the state.
+ * @param state - The state in force.
+ * @param action - What is being asked.
+ * @returns The new state, or the old one when nothing changed.
+ */
+export declare function irReducer(state: IrState, action: IrAction): IrState;
+//# sourceMappingURL=irReducer.d.ts.map

package/lib/ir/core/irReducer.d.ts.map

@@ -0,0 +1 @@
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package/lib/ir/core/irReducer.js

@@ -0,0 +1,207 @@
+/**
+ * Every change the viewer can undergo, as one function over one object.
+ *
+ * A reducer rather than a graph of signals, for the reason
+ * `docs/decisions.md` gives about the glycan editor: a published component must
+ * not impose a state library on the page that mounts it, and two viewers on one
+ * page must not share a module-level singleton. The state is a plain object, so a
+ * host can save it, restore it and compare it.
+ *
+ * Every case returns the state **itself** when it has nothing to do, so a render
+ * memoised on the state is not defeated by an action that changed nothing —
+ * selecting the spectrum already selected, closing an error that is already
+ * closed.
+ */
+import { DEFAULT_SETTINGS, DEFAULT_SIDE_PANELS, isIrWindow, mergeIrSettings, } from "./irState.js";
+/**
+ * The state a viewer opens with.
+ *
+ * The panel list is spread rather than stored by reference: a caller's array is
+ * the caller's to mutate, and a viewer holding it would find its open panels
+ * changing under it.
+ * @param options - What it opens on.
+ * @returns The state.
+ */
+export function createIrState(options = {}) {
+    const { spectra = [], settings, panelIds } = options;
+    return {
+        data: { spectra: [...spectra] },
+        view: {
+            selectedId: spectra[0]?.id ?? null,
+            domain: null,
+            tool: 'read',
+            openPanelIds: [...(panelIds ?? DEFAULT_SIDE_PANELS)],
+            error: null,
+        },
+        settings: mergeIrSettings(DEFAULT_SETTINGS, settings),
+    };
+}
+/**
+ * Fold one action into the state.
+ * @param state - The state in force.
+ * @param action - What is being asked.
+ * @returns The new state, or the old one when nothing changed.
+ */
+export function irReducer(state, action) {
+    switch (action.type) {
+        case 'addSpectra': {
+            if (action.spectra.length === 0)
+                return state;
+            const spectra = [...state.data.spectra, ...action.spectra];
+            return {
+                ...state,
+                data: { spectra },
+                view: {
+                    ...state.view,
+                    // Whatever arrived is what somebody wants to look at, so it takes the
+                    // selection — but only when nothing was selected, since a spectrum
+                    // added for comparison must not steal the panels from the one being
+                    // read.
+                    selectedId: state.view.selectedId ?? action.spectra[0]?.id ?? null,
+                    error: null,
+                },
+            };
+        }
+        case 'setSpectra': {
+            return {
+                ...state,
+                data: { spectra: [...action.spectra] },
+                view: {
+                    ...state.view,
+                    selectedId: action.spectra[0]?.id ?? null,
+                    // Replacing what is drawn is the one change that throws the window
+                    // away: a window over one spectrum's wavenumbers means nothing over
+                    // another's, and the chart refits when it is handed `null`.
+                    domain: null,
+                    error: null,
+                },
+            };
+        }
+        case 'removeSpectrum': {
+            const spectra = state.data.spectra.filter((spectrum) => spectrum.id !== action.id);
+            if (spectra.length === state.data.spectra.length)
+                return state;
+            return {
+                ...state,
+                data: { spectra },
+                view: {
+                    ...state.view,
+                    selectedId: state.view.selectedId === action.id
+                        ? (spectra[0]?.id ?? null)
+                        : state.view.selectedId,
+                },
+            };
+        }
+        case 'renameSpectrum': {
+            const name = action.name.trim();
+            if (name === '') {
+                return withError(state, 'A spectrum needs a name to be called by.');
+            }
+            return mapSpectrum(state, action.id, (spectrum) => spectrum.name === name ? spectrum : { ...spectrum, name });
+        }
+        case 'setSpectrumColor': {
+            return mapSpectrum(state, action.id, (spectrum) => spectrum.color === action.color
+                ? spectrum
+                : { ...spectrum, color: action.color });
+        }
+        case 'setSpectrumVisible': {
+            return mapSpectrum(state, action.id, (spectrum) => spectrum.visible === action.visible
+                ? spectrum
+                : { ...spectrum, visible: action.visible });
+        }
+        case 'selectSpectrum': {
+            if (state.view.selectedId === action.id)
+                return state;
+            return { ...state, view: { ...state.view, selectedId: action.id } };
+        }
+        case 'setDomain': {
+            if (!isIrWindow(action.domain))
+                return state;
+            return { ...state, view: { ...state.view, domain: action.domain } };
+        }
+        case 'resetDomain': {
+            if (state.view.domain === null)
+                return state;
+            return { ...state, view: { ...state.view, domain: null } };
+        }
+        case 'setTool': {
+            if (state.view.tool === action.tool)
+                return state;
+            return { ...state, view: { ...state.view, tool: action.tool } };
+        }
+        case 'togglePanel': {
+            const { openPanelIds } = state.view;
+            const open = openPanelIds.includes(action.panelId);
+            return {
+                ...state,
+                view: {
+                    ...state.view,
+                    openPanelIds: open
+                        ? openPanelIds.filter((id) => id !== action.panelId)
+                        : [...openPanelIds, action.panelId],
+                },
+            };
+        }
+        case 'setError': {
+            if (state.view.error === action.error)
+                return state;
+            return { ...state, view: { ...state.view, error: action.error } };
+        }
+        case 'setSettings': {
+            const settings = mergeIrSettings(state.settings, action.settings);
+            return { ...state, settings };
+        }
+        case 'loadState': {
+            const { data, view, settings } = action.state;
+            return {
+                data: data === undefined ? state.data : { spectra: [...data.spectra] },
+                view: { ...state.view, ...view },
+                settings: mergeIrSettings(state.settings, settings),
+            };
+        }
+        case 'clear': {
+            if (state.data.spectra.length === 0 && state.view.error === null) {
+                return state;
+            }
+            return {
+                ...state,
+                data: { spectra: [] },
+                view: { ...state.view, selectedId: null, domain: null, error: null },
+            };
+        }
+        /* Every action is handled above, and TypeScript is what keeps that true
+           when one is added — so there is nothing for a fallback to do. */
+        // no default
+    }
+}
+/**
+ * Change one spectrum, leaving the state alone when it did not change.
+ * @param state - The state in force.
+ * @param id - Which spectrum.
+ * @param change - What to make of it; return it unchanged for no change.
+ * @returns The new state, or the old one.
+ */
+function mapSpectrum(state, id, change) {
+    let changed = false;
+    const spectra = state.data.spectra.map((spectrum) => {
+        if (spectrum.id !== id)
+            return spectrum;
+        const next = change(spectrum);
+        if (next !== spectrum)
+            changed = true;
+        return next;
+    });
+    if (!changed)
+        return state;
+    return { ...state, data: { spectra }, view: { ...state.view, error: null } };
+}
+/**
+ * Refuse an action, saying why.
+ * @param state - The state in force.
+ * @param error - The sentence to show whoever asked.
+ * @returns The state carrying the refusal.
+ */
+function withError(state, error) {
+    return { ...state, view: { ...state.view, error } };
+}
+//# sourceMappingURL=irReducer.js.map

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