@jbrowse/product-core 4.3.0 → 5.0.0-beta.1

package/esm/Session/MultipleViews.js

@@ -1,88 +1,379 @@
-import { localStorageGetBoolean, localStorageSetBoolean, } from '@jbrowse/core/util';
-import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree';
+import { applyOrderWithin, localStorageGetBoolean, localStorageSetBoolean, reorderWithin, } from '@jbrowse/core/util';
+import { addDisposer, applyPatch, cast, detach, getMembers, getParent, hasParent, isReferenceType, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
-import { BaseSessionModel, isBaseSession } from "./BaseSession.js";
-import { DrawerWidgetSessionMixin } from "./DrawerWidgets.js";
+import { scheduleDetachedDestroy } from '../scheduleDetachedDestroy.js';
+import { BaseSessionModel, isBaseSession } from './BaseSession.js';
+import { DrawerWidgetSessionMixin } from './DrawerWidgets.js';
+// Whether `node` IS `view` or lives somewhere under it. A view can CONTAIN
+// views, so `takeOut` matches widgets to the view leaving by containment rather
+// than by `widget.view.id === view.id`. ADR-069 says what that cost.
+//
+// Deliberately not `findParentThat`, which warns and throws when the walk runs
+// out: this asks the question of every reference every widget holds, and most
+// of them point somewhere else entirely, so "no" is an ordinary answer here
+// rather than a fault.
+function isWithin(node, view) {
+    if (!isStateTreeNode(node)) {
+        return false;
+    }
+    let cur = node;
+    while (cur !== view) {
+        if (!hasParent(cur)) {
+            return false;
+        }
+        cur = getParent(cur);
+    }
+    return true;
+}
+function viewIdsWithin(view) {
+    return [view.id, ...(view.views ?? []).flatMap(v => viewIdsWithin(v))];
+}
+// Empty every reference `holder` has into `view`, and say whether it had any.
+//
+// MST invalidates a reference when its TARGET node is detached or destroyed, so
+// a widget's reference to the view itself empties on its way out and one
+// pointing INSIDE it does not: `openFeatureWidget` stores the clicked feature's
+// track, and that node is neither detached nor destroyed — it just leaves the
+// session's identifier cache with the view, which makes reading the reference
+// THROW where `safeReference` promises undefined. The widget's own autoruns go
+// on running whether or not its panel is on screen, so that throw comes out of
+// a reaction, uncatchable by the caller.
+//
+// So do here what `onInvalidated` would have done, while the reference can
+// still be read. Only where the type allows undefined — a required reference
+// has no empty value to move to, and the widget is hidden either way. ADR-069.
+function dropRefsInto(holder, view) {
+    let found = false;
+    for (const [key, prop] of Object.entries(getMembers(holder).properties)) {
+        if (isReferenceType(prop) && isWithin(holder[key], view)) {
+            found = true;
+            if (prop.is(undefined)) {
+                applyPatch(holder, { op: 'replace', path: `/${key}`, value: undefined });
+            }
+        }
+    }
+    return found;
+}
+/**
+ * #stateModel MultipleViewsSessionMixin
+ */
 export function MultipleViewsSessionMixin(pluginManager) {
     return types
         .compose(BaseSessionModel(pluginManager), DrawerWidgetSessionMixin(pluginManager), types.model({
+        /**
+         * #property
+         */
         views: types.array(pluginManager.pluggableMstType('view', 'stateModel')),
+        /**
+         * #property
+         */
         stickyViewHeaders: types.optional(types.boolean, () => localStorageGetBoolean('stickyViewHeaders', true)),
-        useWorkspaces: types.optional(types.boolean, () => localStorageGetBoolean('useWorkspaces', false)),
+        /**
+         * #property
+         * enables the tabbed/tiled workspace layout for this session. Undefined
+         * means unspecified — read `effectiveUseWorkspaces`.
+         */
+        useWorkspaces: types.stripDefault(types.maybe(types.boolean), undefined),
     }))
-        .actions(self => ({
-        moveViewDown(id) {
-            const idx = self.views.findIndex(v => v.id === id);
-            if (idx !== -1 && idx < self.views.length - 1) {
-                self.views.splice(idx, 2, self.views[idx + 1], self.views[idx]);
-            }
-        },
-        moveViewUp(id) {
-            const idx = self.views.findIndex(view => view.id === id);
-            if (idx > 0) {
-                self.views.splice(idx - 1, 2, self.views[idx], self.views[idx - 1]);
-            }
-        },
-        moveViewToTop(id) {
-            const idx = self.views.findIndex(view => view.id === id);
-            self.views = cast([
-                self.views[idx],
-                ...self.views.filter(view => view.id !== id),
-            ]);
+        .views(self => ({
+        /**
+         * #getter
+         * resolved workspaces flag (never undefined): this session's value, else
+         * the user preference over the `configuration.preferences.useWorkspaces`
+         * admin default. Every consumer reads this, not the raw property — only
+         * sessions built from a snapshot or a spec `layout` set that, so the
+         * admin default is what reaches the arrivals that bypass defaultSession.
+         */
+        get effectiveUseWorkspaces() {
+            return (self.useWorkspaces ?? self.getPreference('useWorkspaces') === true);
         },
-        moveViewToBottom(id) {
-            const idx = self.views.findIndex(view => view.id === id);
-            self.views = cast([
-                ...self.views.filter(view => view.id !== id),
-                self.views[idx],
-            ]);
+        /**
+         * #getter
+         * what `effectiveUseWorkspaces` becomes after `resetUseWorkspaces` — the
+         * admin default, with both this session's own value and the user's
+         * override out of the way. The Preferences reset diff needs this rather
+         * than the override map, which can't see a session-scoped value (a spec
+         * `layout`, a "move view to a tab") and so reported nothing to reset.
+         */
+        get defaultUseWorkspaces() {
+            return self.getPreferenceDefault('useWorkspaces') === true;
         },
-        addView(typeName, initialState = {}) {
-            const typeDefinition = pluginManager.getElementType('view', typeName);
-            if (!typeDefinition) {
-                throw new Error(`unknown view type ${typeName}`);
+    }))
+        .actions(self => {
+        // `scopeIds` narrows the move to a subset of the stack: in a tabbed
+        // workspace "move this view up" means up past the previous view IN THIS
+        // PANEL, and the view that happens to precede it in `self.views` may be
+        // in another panel, where moving past it would look like a no-op. Omitted
+        // (the classic stack) every view is in scope and this is a plain reorder.
+        const move = (id, direction, scopeIds) => {
+            const idx = self.views.findIndex(v => v.id === id);
+            const scope = scopeIds && new Set(scopeIds);
+            self.views = cast(reorderWithin(self.views, idx, direction, v => scope ? scope.has(v.id) : true));
+        };
+        // The body of removeView, callable from replaceView below — an action
+        // can't reach a sibling action through `self` from inside the same
+        // .actions() block, since neither is attached yet.
+        //
+        // **Detached, not removed.** `views.remove` destroys the view and
+        // everything under it right here, inside the action, and MobX runs the
+        // action's pending reactions at the `endBatch` closing it — so every
+        // component still mounted over that view gets a final run against nodes
+        // that just died. ADR-069.
+        //
+        // A view is the worse half of that rule rather than the `setSession`
+        // half, because what is mounted over it is a DISPLAY, and a display's
+        // reads reach `getContainingView`, which walks parents and THROWS when
+        // there is none. So this was not only a noisy console: on
+        // `cancer_sv/multihop_split_view` the throw went to an ErrorBoundary with
+        // no view left under it and took the page. Detaching leaves the walk
+        // something to find.
+        const takeOut = (view) => {
+            // Membership first, and before anything reads through `view`. A view
+            // already out of the session reaches here — `replaceView` documents
+            // that case below — and by then it is detached, or destroyed by the
+            // task scheduled at the bottom. MST's `detach` throws on a node with no
+            // parent, and the widgets holding it were emptied when it left.
+            if (!self.views.includes(view)) {
+                return;
             }
-            const length = self.views.push({
-                ...initialState,
-                type: typeName,
-            });
-            return self.views[length - 1];
-        },
-        removeView(view) {
-            for (const [, widget] of self.activeWidgets) {
-                if (widget.view?.id === view.id) {
+            // The focus is a persisted id, not a reference, so nothing drops it
+            // when the view it names goes. Every consumer compares
+            // `focusedViewId === view.id`, so a stale one matches nothing — the
+            // focus ring vanishes and the drawer stops naming a view, with nothing
+            // to say why — and it ships in a saved or shared session. `replaceView`
+            // captures `wasFocused` above this and re-points the focus at the
+            // replacement afterwards, which is the one case where the focus moves
+            // rather than ending.
+            const { focusedViewId } = self;
+            if (focusedViewId !== undefined &&
+                viewIdsWithin(view).includes(focusedViewId)) {
+                self.setFocusedViewId(undefined);
+            }
+            // Every widget, not the active ones: a widget the user closed keeps
+            // its references and its autoruns. One that pointed into the view is
+            // now empty, so hide it rather than leave the panel showing what it no
+            // longer has.
+            for (const [, widget] of self.widgets) {
+                if (dropRefsInto(widget, view)) {
                     self.hideWidget(widget);
                 }
             }
-            self.views.remove(view);
-        },
-        setStickyViewHeaders(sticky) {
-            self.stickyViewHeaders = sticky;
-        },
-        setUseWorkspaces(useWorkspaces) {
-            self.useWorkspaces = useWorkspaces;
-        },
-        afterAttach() {
-            addDisposer(self, autorun(function stickyViewHeadersAutorun() {
-                localStorageSetBoolean('stickyViewHeaders', self.stickyViewHeaders);
-            }, { name: 'StickyViewHeaders' }));
-            addDisposer(self, autorun(function useWorkspacesAutorun() {
-                localStorageSetBoolean('useWorkspaces', self.useWorkspaces);
-            }, { name: 'UseWorkspaces' }));
-        },
-    }))
+            // MST fires the view's `beforeDetach` here, while it is still attached
+            // and the walk to the session still resolves. That matters: anything of
+            // a view's that reaches OUTSIDE its own tree has to move to that hook,
+            // because after this line the view is a root and `getSession` from a
+            // root throws. ADR-069's detach-time disposer, at view scope — the
+            // comparative views' `releaseTemporaryAssemblies` is the one case.
+            detach(view);
+            scheduleDetachedDestroy(view);
+        };
+        return {
+            /**
+             * #action
+             */
+            moveViewDown(id, scopeIds) {
+                move(id, 'down', scopeIds);
+            },
+            /**
+             * #action
+             */
+            moveViewUp(id, scopeIds) {
+                move(id, 'up', scopeIds);
+            },
+            /**
+             * #action
+             */
+            moveViewToTop(id, scopeIds) {
+                move(id, 'top', scopeIds);
+            },
+            /**
+             * #action
+             */
+            moveViewToBottom(id, scopeIds) {
+                move(id, 'bottom', scopeIds);
+            },
+            /**
+             * #action
+             * Put the named views into the given relative order, leaving views not
+             * named in their own slots.
+             *
+             * `session.views` is the one ordering, so this is how a channel that
+             * states an order in some other vocabulary gets it applied: a session
+             * spec's `layout` names views per panel, top to bottom, and that used to
+             * be honoured by the panel assignment array's order. Now the assignment
+             * carries membership only, so the layout says it here instead, once.
+             */
+            orderViews(ids) {
+                self.views = cast(applyOrderWithin(self.views, ids, v => v.id));
+            },
+            /**
+             * #action
+             */
+            addView(typeName, initialState = {}) {
+                const length = self.views.push({
+                    ...initialState,
+                    type: typeName,
+                });
+                return self.views[length - 1];
+            },
+            /**
+             * #action
+             * swap `view` for a new view of `typeName`, in the slot it occupied.
+             *
+             * The launchers that build a view of a DIFFERENT type out of one you are
+             * already looking at — launch synteny view, read-vs-ref, split view —
+             * otherwise append, leaving the source view above the thing it produced
+             * and a stack of two views showing the same locus. This is the "replace"
+             * half of that offer, and a slot swap rather than remove-then-add so the
+             * new view lands where the reader was looking instead of at the bottom of
+             * the session.
+             *
+             * A launcher whose result is the SAME type as its source does not come
+             * here and should not: collapse introns offers "Replace current view" by
+             * navigating the view it was invoked on, which keeps the view's identity
+             * and so lets its snackbar offer an Undo. Swapping in a new node would
+             * leave nothing to undo onto.
+             *
+             * The slot is `session.views`, which is the order views render in under
+             * both layout modes (a tab's `viewIds` says which tab a view is in, not
+             * where in it), so the swap lands in place either way.
+             *
+             * WHICH panel is a separate question and this does not answer it: the
+             * new view arrives in no tab, and `homeUnassignedViews` puts it in the
+             * active panel — the same panel only when the replaced view was in the
+             * active one. In practice it is, since clicking into a view activates
+             * its panel, and the launch that offers a replace is a click on that
+             * view's own menu.
+             */
+            replaceView(view, typeName, initialState = {}) {
+                // read before the removal, which is what makes both stale
+                const idx = self.views.indexOf(view);
+                // `idx` first, so a view already gone from the session short-circuits
+                // before `view.id` is read: that node is detached and, a task later,
+                // destroyed — and MST warns on any read through a destroyed one
+                const { focusedViewId } = self;
+                const wasFocused = idx !== -1 &&
+                    focusedViewId !== undefined &&
+                    viewIdsWithin(view).includes(focusedViewId);
+                takeOut(view);
+                // a view already gone from the session appends, rather than throwing
+                // or silently dropping the launch
+                const at = idx === -1 ? self.views.length : idx;
+                self.views.splice(at, 0, { ...initialState, type: typeName });
+                const created = self.views[at];
+                // The replacement takes the slot, so it takes the focus with it.
+                // Every consumer compares `focusedViewId === view.id`, so a
+                // replacement that left the old id in place would simply match
+                // nothing: the focus ring would vanish and the drawer would stop
+                // naming a view, with nothing to say why.
+                if (wasFocused) {
+                    self.setFocusedViewId(created.id);
+                }
+                return created;
+            },
+            /**
+             * #action
+             */
+            removeView(view) {
+                takeOut(view);
+            },
+            /**
+             * #action
+             * Take out every view the given session snapshot will not keep, before
+             * a whole-tree `applySnapshot` destroys it where it stands.
+             *
+             * Undo and redo are `applySnapshot` on the session
+             * (`core/util/TimeTraveller`, which calls this), and every view carries
+             * an `ElementId` — so MST reconciles by identifier and destroys what the
+             * target lacks, inside the action, with the components still mounted.
+             * Measured on a redo across a closed view, with the restored view
+             * repainted first: 4 liveliness reads of its display before this, 0
+             * after.
+             *
+             * A view that is present but has changed `type` is destroyed by that
+             * same reconciliation (`areSame` runs the type's `is()` before its id
+             * check), so identity here is the pair, not the id.
+             *
+             * **Views, and deliberately not what is under them.** A track or a
+             * display the snapshot drops is still destroyed in place, and that is
+             * not this door being worse than the others: `hideTrackGeneric` is a
+             * plain `tracks.remove` and measures louder (5 reads to undo's 4).
+             * Detaching one would be worse than the destroy it replaced — a
+             * detached display is a LIVE root, and `getContainingView` walks
+             * parents and throws when the walk finds no view, where a dead node
+             * only warns. At or above the view is the only place that walk still
+             * lands, which is why ADR-069's rule stops there.
+             */
+            takeOutViewsMissingFrom(snapshot) {
+                const incoming = snapshot?.views ?? [];
+                const kept = new Map(incoming.map(v => [v.id, v.type]));
+                // a copy, because `takeOut` splices the array it is iterating
+                for (const view of [...self.views]) {
+                    if (kept.get(view.id) !== view.type) {
+                        takeOut(view);
+                    }
+                }
+            },
+            /**
+             * #action
+             */
+            setStickyViewHeaders(sticky) {
+                self.stickyViewHeaders = sticky;
+            },
+            /**
+             * #action
+             * set the workspaces layout for this session only, leaving the user's
+             * personal default untouched. For session-scoped intent — a spec
+             * carrying a `layout`, or an ad-hoc "move view to a tab/split" — where
+             * rewriting the visitor's global preference would be a surprise. The
+             * user-facing default toggle is `setUseWorkspacesPreference`.
+             */
+            setUseWorkspaces(useWorkspaces) {
+                self.useWorkspaces = useWorkspaces;
+            },
+            /**
+             * #action
+             * the user-facing workspaces toggle: applies to this session and
+             * becomes their default for sessions that don't specify one. Persisted
+             * only here, on an explicit toggle — an autorun mirroring the resolved
+             * value would bake the admin default into every visitor's localStorage
+             * on first load, so a later admin change could never reach them.
+             */
+            setUseWorkspacesPreference(useWorkspaces) {
+                self.useWorkspaces = useWorkspaces;
+                self.setPreferenceOverride('useWorkspaces', useWorkspaces);
+            },
+            /**
+             * #action
+             * drop both this session's explicit value and the user's override so
+             * workspaces falls back to the admin default
+             */
+            resetUseWorkspaces() {
+                self.useWorkspaces = undefined;
+                self.clearPreferenceOverride('useWorkspaces');
+            },
+            afterAttach() {
+                addDisposer(self, autorun(function stickyViewHeadersAutorun() {
+                    localStorageSetBoolean('stickyViewHeaders', self.stickyViewHeaders);
+                }, { name: 'StickyViewHeaders' }));
+            },
+        };
+    })
         .postProcessSnapshot(snap => {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }
-        const { stickyViewHeaders, useWorkspaces, ...rest } = snap;
-        return {
-            ...rest,
-            ...(!stickyViewHeaders ? { stickyViewHeaders } : {}),
-            ...(useWorkspaces ? { useWorkspaces } : {}),
-        };
+        // stickyViewHeaders is a personal per-browser UI preference, not shared
+        // view state: destructure it out so it never lands in the snapshot. It
+        // stays localStorage-backed, so each browser keeps its own value.
+        // useWorkspaces stays: it changes layout intent (and pairs with the
+        // `layout` tree the snapshot carries), which is meaningful to share.
+        const { stickyViewHeaders, ...rest } = snap;
+        return rest;
     });
 }
+/** Type guard for SessionWithMultipleViews */
 export function isSessionWithMultipleViews(session) {
     return isBaseSession(session) && 'views' in session;
 }