@jbrowse/core 5.0.0-beta.1 → 5.0.0-beta.11

package/esm/util/withFeatureDetails.js

@@ -1,4 +1,5 @@
 import { isAlive } from '@jbrowse/mobx-state-tree';
+import { isAbortException } from './aborting.js';
 import { notifyFeatureDetailsMiss } from './openFeatureWidget.js';
 import { getNotificationSink } from './sessionServices.js';
 /**
@@ -48,6 +49,9 @@ export async function withFeatureDetails(self, fetch, onFeat, onMiss = () => {
         }
     }
     catch (e) {
+        if (isAbortException(e)) {
+            return;
+        }
         // Logged whatever happened, and only toasted while the display is still
         // there: `getSession` throws on a detached node, and a message naming a
         // track the user has already closed is noise they cannot act on.

package/esm/util/withLaunchInput.d.ts

@@ -0,0 +1,174 @@
+export { legacyInitMessage, unknownKeysMessage } from './unknownSnapshotKeys.ts';
+import type { IAnyModelType, IModelType, SnapshotIn, SnapshotOut } from '@jbrowse/mobx-state-tree';
+/**
+ * The slice of a PluginManager the partition reads: which view type a
+ * snapshot's `type` names, and that type's state model as REGISTERED — the
+ * one `extendViewType` may have composed more properties onto after the
+ * factory wrapped its own.
+ */
+export interface ViewTypeLookup {
+    viewTypes: {
+        has: (name: string) => boolean;
+    };
+    getViewType: (name: string) => {
+        isStateModelLoaded: boolean;
+        stateModel: IAnyModelType;
+    };
+}
+export interface LaunchInputOptions<M extends IAnyModelType> {
+    /** the PluginManager; without it the partition sees only the wrapped model */
+    registry?: ViewTypeLookup;
+    /**
+     * Whether a snapshot shows the launch applied — rows built, regions set. The
+     * blob persists only until then: a snapshot taken mid-load (an autosave
+     * firing before the launch autorun navigates) has to rebuild the view rather
+     * than drop it to the import form, and a materialized view has nothing left
+     * to rebuild. `installInitAutorun` keys its failure policy off the same line,
+     * read from the live node. `Partial` because a `stripDefault` property is
+     * absent from the snapshot when empty, whatever its declared type says.
+     */
+    materialized: (snap: Partial<SnapshotOut<M>>) => boolean;
+}
+/**
+ * How a launch key's value is told apart from the state property of the same
+ * name. A key whose name collides with nothing is `launch`; the rest name the
+ * discriminator that splits one authored array into the recipe entries the
+ * launcher resolves and the built snapshots MST restores.
+ *
+ * `replay` is the one that is not remapped at all: the value lands on its
+ * property, and a copy rides in the blob so the launcher can run the ordered
+ * imperative step the property write alone does not produce.
+ */
+export type LaunchKeyKind = 'launch' | 'trackEntries' | 'rows' | 'replay';
+export interface LaunchKeySpec {
+    kind: LaunchKeyKind;
+}
+export interface LaunchKeyRegistration<Commands, PassThrough extends string = never> {
+    keys: Record<string, LaunchKeySpec>;
+    passThrough: readonly PassThrough[];
+    /** never assigned; it carries `Commands` to `withLaunchInput`'s return type */
+    commands?: Commands;
+}
+/**
+ * The launch keys a view captured, plus what it has to report.
+ *
+ * `Commands` is not made partial: hand-authored JSON is what fills this, so a
+ * key the interface marks required is not a guarantee here either way, and the
+ * launcher already guards the ones it cannot proceed without.
+ */
+export type LaunchInput<Commands> = Commands & {
+    unknown?: Record<string, unknown>;
+    malformed?: Record<string, unknown>;
+    legacyInit?: boolean;
+};
+/**
+ * The blob when it still holds something to apply, else undefined. A view's
+ * gates ask this rather than the raw property: a snapshot whose only launch
+ * content was a typo has nothing to launch, and a view that thinks otherwise
+ * waits on an assembly nobody named and never leaves the spinner.
+ *
+ * Returns the blob itself, never a copy — the launch autorun clears by
+ * identity, and a fresh object per read strands the init it just applied.
+ */
+export declare function pendingLaunch<C>(launch: LaunchInput<C> | undefined): LaunchInput<C> | undefined;
+/**
+ * A view's snapshot type, widened to the authored shape: every launch key is
+ * accepted beside the declared properties, and a key that is both takes either
+ * meaning. Excess-property checking then makes a misspelled key an error at
+ * every literal site — a `defaultSession` view, an `addView` call, a
+ * `createViewState` spec.
+ */
+export type LaunchSnapshotIn<M extends IAnyModelType, Commands, PassThrough extends string = never> = Omit<SnapshotIn<M>, keyof Commands> & {
+    [K in keyof Commands]?: K extends keyof SnapshotIn<M> ? Commands[K] | SnapshotIn<M>[K] : Commands[K];
+} & {
+    [K in PassThrough]?: unknown;
+} & {
+    /**
+     * @deprecated v4's nesting. Write every setting directly on the view object;
+     * this is unwrapped on the way in and warns.
+     */
+    init?: Commands;
+};
+type ReservedKey = 'id' | 'type' | 'launch';
+/**
+ * What a view can be launched with, derived: the keys its launcher interprets
+ * (`Commands`) plus every declared property of its state model, optional, in
+ * the property's own snapshot type. Nothing is restated, so a property is
+ * authorable — and TYPED — from the line that declares it.
+ *
+ * ```ts
+ * export type LinearSyntenyViewInit = ViewInit<
+ *   LinearSyntenyViewStateModel,
+ *   LinearSyntenyViewCommands
+ * >
+ * ```
+ *
+ * The twin of `LaunchSnapshotIn` above, from the other end: that one widens a
+ * snapshot type for a literal MST site, this one is what a caller BUILDING a
+ * spec annotates, so its commands stay required and its properties optional.
+ */
+export type ViewInit<M extends IAnyModelType, Commands> = Commands & Partial<Omit<SnapshotIn<M>, keyof Commands | ReservedKey>>;
+export type LaunchInputModel<M extends IAnyModelType, Commands, PassThrough extends string = never> = M extends IModelType<infer P, infer O, any, infer S> ? IModelType<P, O, LaunchSnapshotIn<M, Commands, PassThrough>, S> : never;
+/**
+ * Declare one view's launch keys. The argument is
+ * `Record<keyof Commands, LaunchKeySpec>`, so a command the view interprets and
+ * nobody registered is a compile error rather than a key that partitions as a
+ * typo and warns.
+ *
+ * `passThrough` names keys that are neither a launch key nor a declared
+ * property and still belong on the snapshot — a legacy spelling the view's own
+ * `preProcessSnapshot` converts.
+ */
+export declare function defineLaunchKeys<Commands>(): <const P extends readonly string[] = readonly never[]>(keys: Record<keyof Commands, LaunchKeySpec>, { passThrough }?: {
+    passThrough?: P;
+}) => LaunchKeyRegistration<Commands, P[number]>;
+/**
+ * The part of a launch spec that belongs on the snapshot: everything but the
+ * launch keys, and the identity and `launch` keys no spec may set. For a caller
+ * that applies the launch itself and builds the view from a snapshot — a
+ * synteny row, whose parent navigates it and opens its tracks — so what it
+ * hands MST is settings only, and the view's own partition sorts those into
+ * properties and reported typos.
+ */
+export declare function snapshotSettings(spec: Record<string, unknown>, registration: LaunchKeyRegistration<unknown, string> | undefined): {
+    [k: string]: unknown;
+};
+/**
+ * A track recipe rather than a built track snapshot: a built one cannot carry
+ * `trackId`, which BaseTrackModel does not declare. `type` does not
+ * discriminate, because a spec writes display types inline.
+ */
+export declare function isTrackRecipe(entry: unknown): boolean;
+/**
+ * Accept a view's settings written directly on the view object, and move the
+ * ones a launcher has to resolve into the internal `launch` property.
+ *
+ * The partition is a `preProcessSnapshot` and is PURE. A session's view type is
+ * a `types.union`, so MST runs every member's preprocessor against every
+ * candidate snapshot while deciding which one matches, and runs it about twice
+ * more per instantiation; a warning from in here fires against snapshots that
+ * are about to be rejected. `afterAttach` — reached only by a snapshot that won
+ * — reports what the partition captured.
+ *
+ * `registry` is the PluginManager. With it the partition classifies against
+ * the view type as registered, `extendViewType`'s added properties included;
+ * without it, against the model as wrapped here. `materialized` draws the line
+ * past which the blob is no longer persisted; see `LaunchInputOptions`.
+ *
+ * ORDER: MST runs preprocessors in the reverse of the order they were added, so
+ * this belongs on the chain BEFORE a view's own legacy-key preprocessor, where
+ * it partitions the snapshot MST finally consumes rather than a key that remap
+ * is about to convert.
+ *
+ * The widening cast is the LAST link that may change the creation type: it
+ * replaces `CustomC`, so a `.props()` added after it is invisible to
+ * `SnapshotIn`. Further `preProcessSnapshot`/`postProcessSnapshot` links are
+ * fine — both carry `CustomC` through.
+ *
+ * Not `types.snapshotProcessor`, which carries the same widened input and stops
+ * being a `ModelType`. `PluginManager.pluggableMstType` filters union members on
+ * `isModelType`, so a wrapped view is dropped from the session's view union
+ * without a word, and `ViewType.stateModel` and every `.properties`
+ * introspection site break with it.
+ */
+export declare function withLaunchInput<M extends IAnyModelType, Commands, PassThrough extends string>(model: M, registration: LaunchKeyRegistration<Commands, PassThrough>, { registry, materialized }: LaunchInputOptions<M>): LaunchInputModel<M, Commands, PassThrough>;

package/esm/util/withLaunchInput.js

@@ -0,0 +1,274 @@
+import { reportLegacyInit, reportMalformedRows, reportUnknownKeys, } from './unknownSnapshotKeys.js';
+// re-exported here because the surfaces that classify their own keys — a
+// session spec, which launches without ever building a snapshot — reach the
+// partition's vocabulary through this module
+export { legacyInitMessage, unknownKeysMessage } from './unknownSnapshotKeys.js';
+// What afterAttach reports rather than applies. They live in the blob so the
+// partition has one place to put everything, and `pendingLaunch` is what keeps
+// them from reading as work to do.
+const REPORTED = new Set(['unknown', 'malformed', 'legacyInit']);
+/**
+ * The blob when it still holds something to apply, else undefined. A view's
+ * gates ask this rather than the raw property: a snapshot whose only launch
+ * content was a typo has nothing to launch, and a view that thinks otherwise
+ * waits on an assembly nobody named and never leaves the spinner.
+ *
+ * Returns the blob itself, never a copy — the launch autorun clears by
+ * identity, and a fresh object per read strands the init it just applied.
+ */
+export function pendingLaunch(launch) {
+    return launch && Object.keys(launch).some(k => !REPORTED.has(k))
+        ? launch
+        : undefined;
+}
+/**
+ * Declare one view's launch keys. The argument is
+ * `Record<keyof Commands, LaunchKeySpec>`, so a command the view interprets and
+ * nobody registered is a compile error rather than a key that partitions as a
+ * typo and warns.
+ *
+ * `passThrough` names keys that are neither a launch key nor a declared
+ * property and still belong on the snapshot — a legacy spelling the view's own
+ * `preProcessSnapshot` converts.
+ */
+export function defineLaunchKeys() {
+    return (keys, { passThrough } = {}) => ({
+        keys,
+        passThrough: passThrough ?? [],
+    });
+}
+// `id` picks up MST's optional identifier and `type` picks the view, so neither
+// is ever a setting and neither can be lifted off the snapshot.
+const IDENTITY = new Set(['id', 'type']);
+const LAUNCH = 'launch';
+/**
+ * The part of a launch spec that belongs on the snapshot: everything but the
+ * launch keys, and the identity and `launch` keys no spec may set. For a caller
+ * that applies the launch itself and builds the view from a snapshot — a
+ * synteny row, whose parent navigates it and opens its tracks — so what it
+ * hands MST is settings only, and the view's own partition sorts those into
+ * properties and reported typos.
+ */
+export function snapshotSettings(spec, registration) {
+    const keys = registration?.keys ?? {};
+    return Object.fromEntries(Object.entries(spec).filter(([key]) => !(key in keys) && !IDENTITY.has(key) && key !== LAUNCH));
+}
+function isObject(value) {
+    return !!value && typeof value === 'object';
+}
+/**
+ * A track recipe rather than a built track snapshot: a built one cannot carry
+ * `trackId`, which BaseTrackModel does not declare. `type` does not
+ * discriminate, because a spec writes display types inline.
+ */
+export function isTrackRecipe(entry) {
+    return typeof entry === 'string' || (isObject(entry) && 'trackId' in entry);
+}
+// Each per-entry kind says only which entries are an authored recipe. A recipe
+// goes to the blob for the launcher to resolve; everything else is a built
+// snapshot and stays on the property, so a mixed array splits rather than
+// picking one meaning for the whole thing.
+function isRecipeEntry(kind, entry) {
+    switch (kind) {
+        case 'trackEntries':
+            return isTrackRecipe(entry);
+        case 'rows':
+            // a built row is a view snapshot, and every view's `type` is a required
+            // literal
+            return !(isObject(entry) && 'type' in entry);
+        default:
+            return true;
+    }
+}
+function splitEntries(kind, value) {
+    const entries = Array.isArray(value) ? value : [value];
+    const recipes = entries.filter(e => isRecipeEntry(kind, e));
+    const built = entries.filter(e => !isRecipeEntry(kind, e));
+    return {
+        launch: recipes.length
+            ? Array.isArray(value)
+                ? recipes
+                : value
+            : undefined,
+        state: built.length ? (Array.isArray(value) ? built : value) : undefined,
+    };
+}
+// The properties a snapshot's keys are classified against are the REGISTERED
+// view type's, read at preprocess time: `extendViewType` composes onto the
+// model after `withLaunchInput` wrapped it, and a set frozen at wrap time sent
+// every added property to `unknown` — restored at its default, with a warning
+// naming it a typo. The wrapped model's own properties are the answer when no
+// registry is given, or the snapshot names a type it does not hold, which is
+// how a factory-built model in a test behaves.
+function knownPropsResolver(model, registry) {
+    let cachedProps;
+    let cachedKeys = new Set();
+    return (snap) => {
+        const name = snap.type;
+        const registered = registry && typeof name === 'string' && registry.viewTypes.has(name)
+            ? registry.getViewType(name)
+            : undefined;
+        const props = registered?.isStateModelLoaded
+            ? registered.stateModel.properties
+            : model.properties;
+        if (props !== cachedProps) {
+            cachedProps = props;
+            cachedKeys = new Set(Object.keys(props));
+        }
+        return cachedKeys;
+    };
+}
+function classify(snap, { keys, passThrough }, known, out) {
+    for (const [key, value] of Object.entries(snap)) {
+        const spec = keys[key];
+        if (IDENTITY.has(key)) {
+            out.state[key] = value;
+        }
+        else if (spec?.kind === 'launch') {
+            out.launch[key] = value;
+        }
+        else if (spec?.kind === 'replay') {
+            out.state[key] = value;
+            out.launch[key] = value;
+        }
+        else if (spec) {
+            const { launch, state } = splitEntries(spec.kind, value);
+            if (spec.kind === 'rows' && launch !== undefined && state !== undefined) {
+                // A row list indexes against `levels` and `tracks[i]`, so lifting half
+                // of it renumbers the other half. Nothing here can throw — a pure
+                // preprocessor runs against snapshots the union is about to reject — so
+                // the whole list goes to the bucket afterAttach reports and the view
+                // comes up on its import form rather than on a silently misaligned
+                // stack.
+                out.malformed[key] = value;
+            }
+            else {
+                if (launch !== undefined) {
+                    out.launch[key] = launch;
+                }
+                if (state !== undefined) {
+                    out.state[key] = state;
+                }
+            }
+        }
+        else if (known.has(key) || passThrough.includes(key)) {
+            out.state[key] = value;
+        }
+        else {
+            out.unknown[key] = value;
+        }
+    }
+}
+// BreakpointSplitView's v4 `init` was a bare array of panels rather than an
+// object of settings. A positional list can only be the view's row list, and a
+// view declares at most one, so it is read as that key rather than classified
+// per index — which would name "0" and "1" as unknown keys.
+function legacyInitSnapshot(init, { keys }) {
+    const rows = Object.entries(keys).find(([, spec]) => spec.kind === 'rows')?.[0];
+    return Array.isArray(init) && rows ? { [rows]: init } : init;
+}
+/**
+ * Accept a view's settings written directly on the view object, and move the
+ * ones a launcher has to resolve into the internal `launch` property.
+ *
+ * The partition is a `preProcessSnapshot` and is PURE. A session's view type is
+ * a `types.union`, so MST runs every member's preprocessor against every
+ * candidate snapshot while deciding which one matches, and runs it about twice
+ * more per instantiation; a warning from in here fires against snapshots that
+ * are about to be rejected. `afterAttach` — reached only by a snapshot that won
+ * — reports what the partition captured.
+ *
+ * `registry` is the PluginManager. With it the partition classifies against
+ * the view type as registered, `extendViewType`'s added properties included;
+ * without it, against the model as wrapped here. `materialized` draws the line
+ * past which the blob is no longer persisted; see `LaunchInputOptions`.
+ *
+ * ORDER: MST runs preprocessors in the reverse of the order they were added, so
+ * this belongs on the chain BEFORE a view's own legacy-key preprocessor, where
+ * it partitions the snapshot MST finally consumes rather than a key that remap
+ * is about to convert.
+ *
+ * The widening cast is the LAST link that may change the creation type: it
+ * replaces `CustomC`, so a `.props()` added after it is invisible to
+ * `SnapshotIn`. Further `preProcessSnapshot`/`postProcessSnapshot` links are
+ * fine — both carry `CustomC` through.
+ *
+ * Not `types.snapshotProcessor`, which carries the same widened input and stops
+ * being a `ModelType`. `PluginManager.pluggableMstType` filters union members on
+ * `isModelType`, so a wrapped view is dropped from the session's view union
+ * without a word, and `ViewType.stateModel` and every `.properties`
+ * introspection site break with it.
+ */
+export function withLaunchInput(model, registration, { registry, materialized }) {
+    const knownProps = knownPropsResolver(model, registry);
+    const partitioned = model
+        .preProcessSnapshot((snap) => {
+        if (!isObject(snap)) {
+            return snap;
+        }
+        const known = knownProps(snap);
+        const { init, ...rest } = snap;
+        const out = {
+            state: {},
+            launch: {},
+            unknown: {},
+            malformed: {},
+        };
+        if (isObject(init)) {
+            // v4's nesting, unwrapped rather than refused: a nested key sorts the
+            // same three ways a flat one does, so honoring it costs one more pass
+            // and a deprecation warning, where dropping it opens an admin's
+            // `defaultSession` on its defaults. First, so a snapshot spelling one
+            // key both ways resolves to the flat one the docs teach.
+            classify(legacyInitSnapshot(init, registration), registration, known, out);
+            out.launch.legacyInit = true;
+        }
+        classify(rest, registration, known, out);
+        if (Object.keys(out.unknown).length) {
+            out.launch.unknown = out.unknown;
+        }
+        if (Object.keys(out.malformed).length) {
+            out.launch.malformed = out.malformed;
+        }
+        const persisted = out.state[LAUNCH];
+        return Object.keys(out.launch).length
+            ? {
+                ...out.state,
+                [LAUNCH]: {
+                    ...(isObject(persisted) ? persisted : {}),
+                    ...out.launch,
+                },
+            }
+            : out.state;
+    })
+        .actions(self => ({
+        afterAttach() {
+            const { launch } = self;
+            if (launch?.legacyInit) {
+                reportLegacyInit(self);
+            }
+            reportUnknownKeys(self, Object.keys(launch?.unknown ?? {}));
+            reportMalformedRows(self, Object.keys(launch?.malformed ?? {}));
+        },
+    }))
+        // Whole while the view has yet to materialize, since the pending launch is
+        // then the only thing a reload can rebuild the view from, and gone once it
+        // has — the report keys with it, so a saved session never carries a
+        // typo report about content it no longer holds. `legacyInit` goes either
+        // way: it names the SPELLING of the snapshot this view was opened from,
+        // and the saved one does not use it, so persisting it would report nesting
+        // on every restore forever (`pendingLaunch` excludes the report keys, so
+        // no launch run ever clears it).
+        .postProcessSnapshot((snap) => {
+        const launch = snap[LAUNCH];
+        if (!isObject(launch)) {
+            return snap;
+        }
+        const { legacyInit, ...kept } = launch;
+        return Object.keys(kept).length &&
+            !materialized(snap)
+            ? { ...snap, [LAUNCH]: kept }
+            : Object.fromEntries(Object.entries(snap).filter(([key]) => key !== LAUNCH));
+    });
+    return partitioned;
+}