@jbrowse/core 5.0.0-beta.13 → 5.0.0-beta.14

package/esm/ReExports/names.js

@@ -0,0 +1,3 @@
+// Published as `@jbrowse/core/ReExports/names` for plugin build tooling; the
+// generated file keeps its suffix so the formatter skips it.
+export { default } from './names.generated.js';

package/esm/assemblyManager/assembly.d.ts

@@ -22,6 +22,9 @@ export interface BasicRegion {
 }
 /**
  * #stateModel Assembly
+ * Loads an assembly's reference sequence names, refName aliases and
+ * cytobands, and maps each data file's refNames onto the assembly's canonical
+ * names.
  */
 export default function assemblyFactory(assemblyConfigType: IAnyType, pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
     /**
@@ -294,6 +297,12 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
      */
     isValidRefName(refName: string): boolean;
 } & {
+    /**
+     * #method
+     * Whether the assembly's `circularRefNames` lists this refName, matched
+     * through its aliases.
+     */
+    isCircularRefName(refName: string): boolean;
     /**
      * #method
      * Where a refName — canonical or any alias — sits in this assembly's own

package/esm/assemblyManager/assembly.js

@@ -17,6 +17,9 @@ export { lookupGeneticCodeId } from './geneticCodes.js';
 export { refNameMismatchMessage } from './refNameMismatch.js';
 /**
  * #stateModel Assembly
+ * Loads an assembly's reference sequence names, refName aliases and
+ * cytobands, and maps each data file's refNames onto the assembly's canonical
+ * names.
  */
 export default function assemblyFactory(assemblyConfigType, pluginManager) {
     return types
@@ -542,6 +545,16 @@ export default function assemblyFactory(assemblyConfigType, pluginManager) {
         },
     }))
         .views(self => ({
+        /**
+         * #method
+         * Whether the assembly's `circularRefNames` lists this refName, matched
+         * through its aliases.
+         */
+        isCircularRefName(refName) {
+            const canonical = self.getCanonicalRefName2(refName);
+            const names = self.getConf('circularRefNames') ?? [];
+            return names.some(name => self.getCanonicalRefName2(name) === canonical);
+        },
         /**
          * #method
          * Where a refName — canonical or any alias — sits in this assembly's own

package/esm/assemblyManager/assemblyConfigSchema.d.ts

@@ -1,6 +1,6 @@
 import type PluginManager from '../PluginManager.ts';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-export { expandAssemblySequence, expandAssemblySequenceAdapter, expandAssemblyShorthand, } from './expandAssemblyConfigShorthand.ts';
+export { expandAssemblySequence, expandAssemblySequenceAdapter, expandAssemblyShorthand, expandSidecarShorthand, refNameAliasAdapterType, } from './expandAssemblyConfigShorthand.ts';
 /**
  * #config BaseAssembly
  * #category assemblyManagement
@@ -116,6 +116,11 @@ declare function assemblyConfigSchema(pluginManager: PluginManager): import("../
     } & {
         defaultValue: unknown;
     };
+    readonly circularRefNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
     readonly geneticCodesLocation: {
         type: "maybeFileLocation";
     };

package/esm/assemblyManager/assemblyConfigSchema.js

@@ -1,26 +1,10 @@
 import { ConfigurationSchema } from '../configuration/index.js';
-import { expandAssemblyShorthand } from './expandAssemblyConfigShorthand.js';
-export { expandAssemblySequence, expandAssemblySequenceAdapter, expandAssemblyShorthand, } from './expandAssemblyConfigShorthand.js';
-/**
- * A sidecar sub-schema written as just its file: `'aliases.txt'` or
- * `{ uri: 'aliases.txt' }` becomes `{ adapter: { type, uri } }`, with `type`
- * picked from the uri. baseUri, stamped by addRelativeUris, rides along. An
- * explicit `adapter` passes through untouched.
- */
+import { expandAssemblyShorthand, expandSidecarShorthand, refNameAliasAdapterType, } from './expandAssemblyConfigShorthand.js';
+export { expandAssemblySequence, expandAssemblySequenceAdapter, expandAssemblyShorthand, expandSidecarShorthand, refNameAliasAdapterType, } from './expandAssemblyConfigShorthand.js';
 function fileAdapterShorthand(typeFor) {
     return {
         shorthand: 'uri',
-        preProcessSnapshot: (snap) => {
-            const { uri, baseUri, adapter } = snap;
-            if (adapter) {
-                return snap;
-            }
-            return {
-                adapter: typeof uri === 'string'
-                    ? { type: typeFor(uri), uri, ...(baseUri ? { baseUri } : {}) }
-                    : { type: typeFor('') },
-            };
-        },
+        preProcessSnapshot: (snap) => expandSidecarShorthand(snap, typeFor),
     };
 }
 /**
@@ -172,6 +156,25 @@ function assemblyConfigSchema(pluginManager) {
             defaultValue: {},
             description: 'Map of reference sequence name to NCBI genetic-code (translation table) id for sequences not using the standard code, e.g. { "chrM": 2 }',
         },
+        /**
+         * #slot
+         * The reference sequences that are circular: a plasmid, an organelle, a
+         * bacterial chromosome. The circular view closes a circle of one such
+         * sequence into a ring with no gap at its origin; every other sequence
+         * keeps the gap that marks its two ends. Names are matched through
+         * refName aliasing.
+         *
+         * #example
+         * The human mitochondrion, by its RefSeq accession:
+         * ```js
+         * ['NC_012920.1']
+         * ```
+         */
+        circularRefNames: {
+            type: 'stringArray',
+            defaultValue: [],
+            description: 'Reference sequences that are circular (a plasmid, an organelle, a bacterial chromosome), which the circular view closes into a ring',
+        },
         /**
          * #slot
          * Optional file (tab-separated `refName<TAB>geneticCodeId`, `#` comments
@@ -198,9 +201,7 @@ function assemblyConfigSchema(pluginManager) {
              * commonly a tsv like chromAliases.txt from UCSC or similar
              */
             adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-        }, fileAdapterShorthand(uri => /sequence_report\.tsv(\.gz)?$/i.test(uri)
-            ? 'NcbiSequenceReportAliasAdapter'
-            : 'RefNameAliasAdapter')),
+        }, fileAdapterShorthand(refNameAliasAdapterType)),
         cytobands: ConfigurationSchema('Cytoband', {
             /**
              * #slot cytobands.adapter

package/esm/assemblyManager/assemblyManager.d.ts

@@ -12,6 +12,8 @@ export interface AssemblyBaseOpts {
 }
 /**
  * #stateModel AssemblyManager
+ * Keeps an `Assembly` for each assembly in the config and the session, and
+ * looks one up by name or alias.
  */
 declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
     /**
@@ -81,6 +83,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -192,6 +195,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -259,6 +263,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -346,6 +351,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -413,6 +419,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -532,6 +539,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -599,6 +607,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -682,6 +691,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {
@@ -749,6 +759,7 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         getCanonicalRefName2(refName: string): string;
         isValidRefName(refName: string): boolean;
     } & {
+        isCircularRefName(refName: string): boolean;
         getRefNamePosition(refName: string): number | undefined;
         getAliasesForRefName(refName: string): string[];
         getRefNameMapForAdapter(adapterConf: {

package/esm/assemblyManager/assemblyManager.js

@@ -85,6 +85,8 @@ function createUnrecognizedAssemblyReports() {
 }
 /**
  * #stateModel AssemblyManager
+ * Keeps an `Assembly` for each assembly in the config and the session, and
+ * looks one up by name or alias.
  */
 function assemblyManagerFactory(conf, pm) {
     return types

package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts

@@ -7,6 +7,15 @@ export declare function referenceSequenceTrackId(assemblyName: unknown): string;
  * filled in when omitted. Returns `snap` itself when there is nothing to do.
  */
 export declare function expandAssemblySequence<T>(snap: T): T;
+/**
+ * A sidecar sub-schema written as just its file: `{ uri: 'aliases.txt' }`
+ * becomes `{ adapter: { type, uri } }`, with `type` picked from the uri.
+ * baseUri, stamped by addRelativeUris, rides along. An explicit `adapter`
+ * passes through untouched.
+ */
+export declare function expandSidecarShorthand(snap: Record<string, unknown>, typeFor: (uri: string) => string): Record<string, unknown>;
+/** The alias adapter an assembly's `refNameAliases` file is read with. */
+export declare function refNameAliasAdapterType(uri: string): "NcbiSequenceReportAliasAdapter" | "RefNameAliasAdapter";
 /**
  * Expand an assembly snapshot's own shorthands into the `sequence` an assembly
  * config declares: {@link expandAssemblySequence}, then the sequence adapter's

package/esm/assemblyManager/expandAssemblyConfigShorthand.js

@@ -37,6 +37,29 @@ export function expandAssemblySequence(snap) {
         },
     };
 }
+/**
+ * A sidecar sub-schema written as just its file: `{ uri: 'aliases.txt' }`
+ * becomes `{ adapter: { type, uri } }`, with `type` picked from the uri.
+ * baseUri, stamped by addRelativeUris, rides along. An explicit `adapter`
+ * passes through untouched.
+ */
+export function expandSidecarShorthand(snap, typeFor) {
+    const { uri, baseUri, adapter } = snap;
+    if (adapter) {
+        return snap;
+    }
+    return {
+        adapter: typeof uri === 'string'
+            ? { type: typeFor(uri), uri, ...(baseUri ? { baseUri } : {}) }
+            : { type: typeFor('') },
+    };
+}
+/** The alias adapter an assembly's `refNameAliases` file is read with. */
+export function refNameAliasAdapterType(uri) {
+    return /sequence_report\.tsv(\.gz)?$/i.test(uri)
+        ? 'NcbiSequenceReportAliasAdapter'
+        : 'RefNameAliasAdapter';
+}
 /**
  * Expand an assembly snapshot's own shorthands into the `sequence` an assembly
  * config declares: {@link expandAssemblySequence}, then the sequence adapter's

package/esm/checkPlugins.js

@@ -1,4 +1,4 @@
-import { isStorePluginDefinition, maybePluginUrl, pluginUrl, } from './pluginDefinitions.js';
+import { isStorePluginDefinition, maybePluginUrl, resolvedPluginUrl, } from './pluginDefinitions.js';
 // Whether a set of plugin definitions is safe to load without asking the user.
 // Lives in core rather than a product because every product that can be handed
 // a config by an untrusted party needs the same gate: Web from its address bar,
@@ -66,8 +66,11 @@ function isTrustedUrl(url) {
  * exist to prevent on the loader side.
  */
 function isTrustedDefinition(def) {
-    const url = maybePluginUrl(def);
-    return url === undefined ? isStorePluginDefinition(def) : isTrustedUrl(url);
+    if (maybePluginUrl(def) === undefined) {
+        return isStorePluginDefinition(def);
+    }
+    const url = resolvedPluginUrl(def);
+    return url !== undefined && isTrustedUrl(url);
 }
 // Every url a store entry can resolve to: the top-level fallback plus each
 // version-pinned build. A config plugin is "in the store" if its url is any of
@@ -82,7 +85,10 @@ export function checkPluginsAgainstStore(pluginsToCheck, storePlugins) {
         return true;
     }
     const storeUrls = new Set(storePlugins.plugins.flatMap(storePluginUrls));
-    return pluginsToCheck.every(p => isTrustedDefinition(p) || storeUrls.has(pluginUrl(p)));
+    return pluginsToCheck.every(p => {
+        const url = resolvedPluginUrl(p);
+        return isTrustedDefinition(p) || (url !== undefined && storeUrls.has(url));
+    });
 }
 export async function checkPlugins(pluginsToCheck) {
     // Trusted-by-prefix plugins and store refs are accepted without consulting

package/esm/configuration/configurationSchema.d.ts

@@ -37,9 +37,14 @@ export interface ConfigurationSchemaOptions<BASE_SCHEMA extends AnyConfiguration
      */
     shorthandWith?: Record<string, unknown>;
     /**
-     * Refuse a snapshot key the schema does not declare, where MST would drop
-     * it in silence. Checked after the `shorthand` lift and before
-     * `preProcessSnapshot`, on the same paths.
+     * What a snapshot key the schema does not declare meets, where MST would
+     * drop it in silence: a config loading names the key on the console and
+     * loads without it, so a config written for another version still draws,
+     * and a write (`refusingUndeclaredKeys`) refuses it. Checked after the
+     * `shorthand` lift and the schema's own `preProcessSnapshot`, on the same
+     * paths, and only on the schema's own snapshot where a union runs every
+     * member over an entry. A display, the `explicitlyTyped` schema identified
+     * by `displayId`, is closed unless it says `false`.
      */
     closed?: boolean;
     /**
@@ -49,16 +54,24 @@ export interface ConfigurationSchemaOptions<BASE_SCHEMA extends AnyConfiguration
      * snapshot or a settings bag arrives by, and read by the `displayDefaults`
      * router, so one declaration serves a config entry, the shorthand object, a
      * share link and an agent's bag alike. A spelling the snapshot already
-     * carries wins over the one a lift produces.
+     * carries wins over the one a lift produces, and a name the schema declares
+     * is left alone, so a subclass keeping a slot its base retired still takes
+     * it. A lift reading no value and answering no member (`() => ({})`) drops
+     * the key, which `jbrowse validate` reports as never read.
      */
     retired?: Record<string, RetiredSpelling>;
     /**
-     * A colour object's defaults by `field`, `*` for any other: the scale while
+     * A color object's defaults by `field`, `*` for any other: the scale while
      * `scale` is unset, and the members that scale reads while unwritten.
      */
     fieldPresets?: Readonly<Record<string, {
         readonly scale: string;
     }>>;
+    /**
+     * The field a color object naming neither a field nor a constant maps
+     * (`withImpliedField`).
+     */
+    impliedField?: string;
     preProcessSnapshot?: (snapshot: Record<string, unknown>) => Record<string, unknown>;
     requires?: REQUIREMENT[];
 }

package/esm/configuration/configurationSchema.js

@@ -6,7 +6,7 @@ import ConfigSlot, { slotWriteRefusal } from './configurationSlot.js';
 import { checkRequirements } from './requirements.js';
 import { getConfigurationSchemaMetadata, registerConfigurationSchema, } from './schemaRegistry.js';
 import { isConfigurationSchemaType, isConstantEntry, isSlotDefinitionEntry, shorthandTargetsOf, } from './schemaTypes.js';
-import { preProcessSnapshotWith } from './snapshotPreprocess.js';
+import { preProcessSnapshotWith, refusingUndeclaredKeys, } from './snapshotPreprocess.js';
 function hookList(hook) {
     return hook === undefined ? [] : Array.isArray(hook) ? hook : [hook];
 }
@@ -82,6 +82,9 @@ function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition
             requires: requires.length ? requires : undefined,
         };
     }
+    if (options.explicitlyTyped && options.explicitIdentifier === 'displayId') {
+        options = { ...options, closed: options.closed ?? true };
+    }
     return { schemaDefinition, options };
 }
 function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
@@ -99,7 +102,6 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
     // narrower than `modelDefinition`, which also holds the identifier and the
     // sub-schemas, neither of which setSlot may write
     const slotKeys = new Set();
-    const storesNull = new Set();
     const featureFields = new Set();
     const takesNoCallback = new Map();
     for (const [slotName, slotDefinition] of Object.entries(schemaDefinition)) {
@@ -124,9 +126,6 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
             slotKeys.add(slotName);
             try {
                 modelDefinition[slotName] = ConfigSlot(slotDefinition);
-                if (modelDefinition[slotName].is(null)) {
-                    storesNull.add(slotName);
-                }
                 if (slotDefinition.type === 'featureField') {
                     featureFields.add(slotName);
                 }
@@ -156,6 +155,10 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
         // collection takes the whole list or map, and `null` resets it
         setSubschema(slotName, data) {
             if (collectionKeys.has(slotName)) {
+                // checked on a copy, since the assignment runs patch listeners
+                if (data != null && !isStateTreeNode(data)) {
+                    refusingUndeclaredKeys(() => modelDefinition[slotName].create(data));
+                }
                 self[slotName] = data ?? undefined;
                 return self[slotName];
             }
@@ -164,7 +167,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
             }
             const newSchema = isStateTreeNode(data)
                 ? data
-                : modelDefinition[slotName].create(data);
+                : refusingUndeclaredKeys(() => modelDefinition[slotName].create(data));
             self[slotName] = newSchema;
             return newSchema;
         },
@@ -215,7 +218,6 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
         name: modelName,
         definition: schemaDefinition,
         options,
-        storesNull,
         featureFields,
         takesNoCallback,
     };

package/esm/configuration/configurationSchemaUnion.d.ts

@@ -27,7 +27,8 @@ export type ConfigurationSchemaUnionType<MEMBERS extends Record<string, AnyConfi
  * member, and a `type` naming no member is refused in every build — where a
  * bare `types.union` would load it as its first member. Each member is an
  * `explicitlyTyped`, `closed` schema named by its key, so a key belonging to
- * another member is refused rather than dropped; one that is not throws here.
+ * another member is named on a load and refused on a write rather than
+ * dropped; one that is not throws here.
  */
 export declare function ConfigurationSchemaUnion<const MEMBERS extends Record<string, AnyConfigurationSchemaType>>(name: string, members: MEMBERS): ConfigurationSchemaUnionType<MEMBERS>;
 /**

package/esm/configuration/configurationSchemaUnion.js

@@ -21,7 +21,8 @@ function memberRefusal(key, member) {
  * member, and a `type` naming no member is refused in every build — where a
  * bare `types.union` would load it as its first member. Each member is an
  * `explicitlyTyped`, `closed` schema named by its key, so a key belonging to
- * another member is refused rather than dropped; one that is not throws here.
+ * another member is named on a load and refused on a write rather than
+ * dropped; one that is not throws here.
  */
 export function ConfigurationSchemaUnion(name, members) {
     for (const [key, member] of Object.entries(members)) {

package/esm/configuration/configurationSlot.js

@@ -6,9 +6,9 @@ import { isCallbackValue } from './slotValueUtils.js';
 function notAColor(value) {
     return `${JSON.stringify(value)} is not a color. A color is a CSS color: a name like "red" or "steelblue", "#rgb" / "#rrggbb" / "#rrggbbaa", "rgb()" / "rgba()" / "hsl()" / "hsla()", "transparent" or a BED triple like "255,0,0"; a color computed per feature is a "jexl:" callback, in a slot that takes one`;
 }
-// '' is a color slot's "none", as in `outlineColor`
+// '' is a color slot's "none", as in `rowColor.unknown`
 const CssColorType = types.refinement('CssColor', types.string, value => value === '' || isCssColor(value), notAColor);
-// a colour list's entry has no "none" to spell
+// a color list's entry has no "none" to spell
 const CssColorEntryType = types.refinement('CssColorEntry', types.string, isCssColor, notAColor);
 const MaybeFileLocation = types.snapshotProcessor(types.maybe(FileLocation), {
     preProcessor: (snap) => snap &&
@@ -37,7 +37,7 @@ const slotTypes = {
     integer: { model: types.integer, fallbackDefault: 1 },
     number: { model: types.number, fallbackDefault: 1 },
     // a `maybe*` type's unset is `undefined`, the one value no config spells:
-    // "decide from the data", as an auto-fitted height or a BED itemRgb colour
+    // "decide from the data", as an auto-fitted height or a BED itemRgb color
     maybeNumber: { model: types.maybe(types.number) },
     maybeBoolean: { model: types.maybe(types.boolean) },
     maybeColor: { model: types.maybe(CssColorType) },
@@ -130,7 +130,7 @@ export default function ConfigSlot(definition) {
     if (type === 'featureField' && callback) {
         throw new Error('a "featureField" slot names a field the display reads per feature, and its jexl: expression is evaluated there, never called with a contextVariable. If this slot overrides a base callback slot, state \'contextVariable: undefined\'.');
     }
-    if (!callback && isJexl(defaultValue)) {
+    if (!callback && type !== 'featureField' && isJexl(defaultValue)) {
         throw new Error(`the defaultValue ${JSON.stringify(defaultValue)} is a jexl: callback, so the slot declares the contextVariable names it reads`);
     }
     const value = enumShaped(type, valueModel);

package/esm/configuration/fillLocations.d.ts

@@ -1,7 +1,9 @@
 /**
  * A shorthand snapshot with its location slots filled in: `derived` supplies
  * what the shorthand implies, and any key the config spells out for itself
- * wins.
+ * wins. The shorthand's own keys leave the result, `uri` and `baseUri` and
+ * whichever others `consumed` names, since an adapter's schema is `closed`
+ * and would name one left behind as undeclared.
  *
  * Spread the other way round — derived over the snapshot — a config naming both
  * a `uri` and a location that is not the sibling of it, `{ uri: 'x.fa',
@@ -9,6 +11,6 @@
  * the one the shorthand invents. Every adapter's normalizer had its own copy of
  * the spread, so the precedence had to be got right 30-odd times.
  */
-export declare function fillLocations(snap: Record<string, unknown>, derived: Record<string, unknown>): {
+export declare function fillLocations(snap: Record<string, unknown>, derived: Record<string, unknown>, consumed?: readonly string[]): {
     [x: string]: unknown;
 };

package/esm/configuration/fillLocations.js

@@ -1,7 +1,9 @@
 /**
  * A shorthand snapshot with its location slots filled in: `derived` supplies
  * what the shorthand implies, and any key the config spells out for itself
- * wins.
+ * wins. The shorthand's own keys leave the result, `uri` and `baseUri` and
+ * whichever others `consumed` names, since an adapter's schema is `closed`
+ * and would name one left behind as undeclared.
  *
  * Spread the other way round — derived over the snapshot — a config naming both
  * a `uri` and a location that is not the sibling of it, `{ uri: 'x.fa',
@@ -9,6 +11,10 @@
  * the one the shorthand invents. Every adapter's normalizer had its own copy of
  * the spread, so the precedence had to be got right 30-odd times.
  */
-export function fillLocations(snap, derived) {
-    return { ...derived, ...snap };
+export function fillLocations(snap, derived, consumed = []) {
+    const written = { ...snap };
+    for (const key of ['uri', 'baseUri', ...consumed]) {
+        delete written[key];
+    }
+    return { ...derived, ...written };
 }

package/esm/configuration/formatAboutConfigSchema.d.ts

@@ -1,8 +1,8 @@
 /**
  * #config FormatAbout
  * #category root
- * jexl callbacks that add, rewrite or hide fields in a track's About dialog.
- * The same schema hangs off every track and off the session as
+ * Holds jexl callbacks that add, rewrite or hide fields in a track's About
+ * dialog. Every track has this schema, and so does the root config as
  * `configuration.formatAbout`, which applies to every track at once. Where both
  * are set the track's object is spread over the session's, so a track can
  * override individual keys the global callback added.

package/esm/configuration/formatAboutConfigSchema.js

@@ -2,8 +2,8 @@ import { ConfigurationSchema } from './configurationSchema.js';
 /**
  * #config FormatAbout
  * #category root
- * jexl callbacks that add, rewrite or hide fields in a track's About dialog.
- * The same schema hangs off every track and off the session as
+ * Holds jexl callbacks that add, rewrite or hide fields in a track's About
+ * dialog. Every track has this schema, and so does the root config as
  * `configuration.formatAbout`, which applies to every track at once. Where both
  * are set the track's object is spread over the session's, so a track can
  * override individual keys the global callback added.

package/esm/configuration/formatDetailsConfigSchema.d.ts

@@ -7,8 +7,8 @@ export declare const DEFAULT_FORMAT_DETAILS_DEPTH = 2;
 /**
  * #config FormatDetails
  * #category root
- * jexl callbacks that add, rewrite or hide fields in the feature-details panel.
- * The same schema hangs off every track and off the session as
+ * Holds jexl callbacks that add, rewrite or hide fields in the feature-details
+ * panel. Every track has this schema, and so does the root config as
  * `configuration.formatDetails`, which applies to every track at once. Where
  * both are set, the callbacks merge with the track's object over the session's,
  * so a track can override individual keys the global callback added, and the

package/esm/configuration/formatDetailsConfigSchema.js

@@ -8,8 +8,8 @@ export const DEFAULT_FORMAT_DETAILS_DEPTH = 2;
 /**
  * #config FormatDetails
  * #category root
- * jexl callbacks that add, rewrite or hide fields in the feature-details panel.
- * The same schema hangs off every track and off the session as
+ * Holds jexl callbacks that add, rewrite or hide fields in the feature-details
+ * panel. Every track has this schema, and so does the root config as
  * `configuration.formatDetails`, which applies to every track at once. Where
  * both are set, the callbacks merge with the track's object over the session's,
  * so a track can override individual keys the global callback added, and the
@@ -64,7 +64,7 @@ export function FormatDetailsConfigSchemaFactory() {
         },
         /**
          * #slot formatDetails.depth
-         * how many levels of subfeature the `subfeatures` callback runs on,
+         * The number of subfeature levels the `subfeatures` callback runs on,
          * defaulting to 2, which stops at a gene's transcripts rather than
          * descending into their exons and CDSs. A track's value wins over the
          * session's
@@ -76,8 +76,8 @@ export function FormatDetailsConfigSchemaFactory() {
         },
         /**
          * #slot formatDetails.maxDepth
-         * how many levels of subfeature card the panel renders at all, which is a
-         * separate question from how deep `subfeatures` formats. Unset means no
+         * The number of subfeature card levels the panel renders at all,
+         * independent of how deep `subfeatures` formats. Unset means no
          * limit. A track's value wins over the session's
          */
         maxDepth: {

package/esm/configuration/getConf.js

@@ -1,9 +1,9 @@
-import { getType, isStateTreeNode } from '@jbrowse/mobx-state-tree';
+import { getSnapshot, getType, isStateTreeNode } from '@jbrowse/mobx-state-tree';
 import { isPlainObject } from '../util/objectUtils.js';
 import { readConfObject } from './readConfObject.js';
 import { getConfigurationSchemaDefinition, getConfigurationSchemaMetadata, } from './schemaRegistry.js';
 import { isConfigurationModel, isConfigurationSchemaType, isConstantEntry, } from './schemaTypes.js';
-import { preProcessSnapshotWith } from './snapshotPreprocess.js';
+import { preProcessSnapshotWith, refusingUndeclaredKeys, } from './snapshotPreprocess.js';
 export function getConf(model, slotPath, args = {}) {
     return readConfObject(model.configuration, slotPath, args);
 }
@@ -66,7 +66,14 @@ function writeConfMember(conf, key, value) {
     const member = conf[key];
     const namespace = isPlainObject(value) ? namespaceMetadata(member) : undefined;
     if (namespace) {
-        for (const [k, v] of Object.entries(preProcessSnapshotWith(namespace, value))) {
+        // refused as a whole before any member lands, so a bad member leaves the
+        // namespace as it was rather than half written and reported as rejected
+        const members = refusingUndeclaredKeys(() => {
+            const lifted = preProcessSnapshotWith(namespace, value);
+            getType(member).create({ ...getSnapshot(member), ...lifted });
+            return lifted;
+        });
+        for (const [k, v] of Object.entries(members)) {
             writeConfMember(member, k, v);
         }
     }
@@ -89,7 +96,9 @@ function writeConfMember(conf, key, value) {
 export function applyConfSettings(target, settings) {
     const conf = isConfigurationModel(target) ? target : target.configuration;
     const meta = getConfigurationSchemaMetadata(conf);
-    const values = meta ? preProcessSnapshotWith(meta, settings) : settings;
+    const values = meta
+        ? preProcessSnapshotWith(meta, settings, { routesUndeclared: true })
+        : settings;
     const report = { applied: [], undeclared: {}, failed: [] };
     for (const [key, value] of Object.entries(values)) {
         const declared = Object.hasOwn(meta?.definition ?? {}, key)

package/esm/configuration/index.d.ts

@@ -15,7 +15,7 @@ export { evaluateForFeature, readConfObject, readConfigValue, } from './readConf
 export { applyConfSettings, getConf, setConf } from './getConf.ts';
 export type { ConfSettingsReport } from './getConf.ts';
 export { fillLocations } from './fillLocations.ts';
-export { applyRetiredSpellings, liftRetiredSpellings, preProcessConfigSnapshot, preProcessSnapshotWith, } from './snapshotPreprocess.ts';
+export { applyRetiredSpellings, declaredSnapshot, liftRetiredSpellings, preProcessConfigSnapshot, preProcessSnapshotWith, refusingUndeclaredKeys, } from './snapshotPreprocess.ts';
 export { shorthandTargets, shorthandTargetsOf } from './schemaTypes.ts';
 export type { ShorthandForm } from './schemaTypes.ts';
 export { requirementProblems } from './requirements.ts';