@arpproject/recrate 0.1.7-test3 → 0.1.7-test6

package/src/crate-builder/CrateManager/crate-manager.ts

@@ -1,2111 +0,0 @@
-import isArray from "lodash/isArray.js";
-import isNumber from "lodash/isNumber.js";
-import isBoolean from "lodash/isBoolean.js";
-import isString from "lodash/isString.js";
-import isEmpty from "lodash/isEmpty.js";
-import isUndefined from "lodash/isUndefined.js";
-import difference from "lodash/difference.js";
-import round from "lodash/round.js";
-import uniq from "lodash/uniq.js";
-import uniqBy from "lodash/uniqBy.js";
-import isPlainObject from "lodash/isPlainObject.js";
-import flattenDeep from "lodash/flattenDeep.js";
-import intersection from "lodash/intersection.js";
-import compact from "lodash/compact.js";
-import isEqual from "lodash/isEqual.js";
-import { normalise, isURL } from "./lib.js";
-import { getContextDefinition } from "./contexts";
-import type {
-    UnverifiedContext,
-    NormalisedContext,
-    UnverifiedCrate,
-    NormalisedCrate,
-    ProfileManagerType,
-    UnverifiedEntityDefinition,
-    NormalisedEntityDefinition,
-    EntityReference,
-    PrimitiveType,
-    NormalisedProfile,
-} from "../types.js";
-
-interface errorsInterface {
-    hasError: Boolean;
-    init: { description: string; messages: string[] };
-    missingIdentifier: { description: string; entity: UnverifiedEntityDefinition[] };
-    missingTypeDefinition: { description: string; entity: UnverifiedEntityDefinition[] };
-    invalidIdentifier: { description: string; entity: UnverifiedEntityDefinition[] };
-    clash: { description: string; messages: string[] };
-}
-
-interface warningsInterface {
-    hasWarning: Boolean;
-    init: { description: string; messages: string[] };
-    invalidIdentifier: { description: string; entity: UnverifiedEntityDefinition[] };
-    clash: { description: string; messages: string[] };
-}
-
-const entityDateCreatedProperty = "hasCreationDate";
-const entityDateUpdatedProperty = "hasModificationDate";
-
-const structuredClone = function (data: any) {
-    return window.structuredClone(data);
-};
-
-/**
- * @class
- *
- * CrateManager
- *
- * A class to work with RO-Crates
- *
- * @param {crate} - an RO Crate to handle
- */
-export class CrateManager {
-    crate: {
-        "@context": NormalisedContext;
-        "@graph": Array<NormalisedEntityDefinition | undefined>;
-    };
-    pm!: ProfileManagerType;
-    reverse: {
-        [key: string]: any;
-    };
-    graphLength: number;
-    rootDescriptor?: number;
-    rootDataset?: number;
-    entityIdIndex: {
-        [key: string]: number;
-    };
-    providedContext: UnverifiedContext;
-    contextDefinitions: { [key: string]: boolean };
-    localContext: { [key: string]: string };
-    entityTypes: { [key: string]: number };
-    entityTimestamps: Boolean;
-    blankNodes: string[];
-    coreProperties: string[];
-    errors: errorsInterface;
-    warnings: warningsInterface;
-
-    constructor({
-        crate,
-        pm,
-        context = undefined,
-        entityTimestamps = false,
-    }: {
-        crate: UnverifiedCrate;
-        pm?: ProfileManagerType;
-        context?: UnverifiedContext;
-        entityTimestamps?: Boolean;
-    }) {
-        // the crate
-        this.crate = {
-            "@context": [{}],
-            "@graph": [],
-        };
-
-        // the profile manager - if you've set a profile
-        if (pm) this.pm = pm;
-
-        // entity reverse associations
-        this.reverse = {};
-
-        // shortcuts to the root descriptor and dataset
-        this.rootDescriptor = undefined;
-        this.rootDataset = undefined;
-
-        // the mapping of entity id to index in this.crate['@graph]
-        this.entityIdIndex = {};
-
-        // reference to a context that has been provided
-        //  this takes precedence over anything else
-        this.providedContext = undefined;
-
-        // otherwise, Crate Manager will manage the context
-        this.contextDefinitions = {};
-        this.localContext = {};
-
-        // entity types in the crate - for browse entities; filter by type
-        this.entityTypes = {};
-
-        // should entity created and updated timestamps be automatically managed / added
-        this.entityTimestamps = entityTimestamps;
-
-        // keep track of blank nodes for when we mint new ones
-        // this.blankNodes = [ '_:Relationship1', '_:Relationship2', '_:CreateAction1', '_:CreateAction2', ... ]
-        this.blankNodes = [];
-
-        this.graphLength = 0;
-
-        // entity core properties
-        this.coreProperties = ["@id", "@type", "@reverse", "name"];
-        this.errors = {
-            hasError: false,
-            init: {
-                description: `Errors encountered on crate load. These need to be fixed manually.`,
-                messages: [],
-            },
-            missingIdentifier: {
-                description: `The entity does not have an identifier (@id).`,
-                entity: [],
-            },
-            missingTypeDefinition: {
-                description: `The entity does not have a defined type (@type).`,
-                entity: [],
-            },
-            invalidIdentifier: {
-                description: `The entity identifier (@id) is not valid. See https://github.com/describo/crate-builder-component/blob/master/README.identifiers.md for more information`,
-                entity: [],
-            },
-            clash: {
-                description: `The entity already exists and has clash errors.`,
-                messages: [],
-            }
-        };
-        this.warnings = {
-            hasWarning: false,
-            init: {
-                description: `Issues encountered on crate load that should be fixed but aren't breaking`,
-                messages: [],
-            },
-            invalidIdentifier: {
-                description: `The entity identifier (@id) has spaces in it that should be encoded. Describo will do this to pass the validate test but the data must be corrected manually.`,
-                entity: [],
-            },
-            clash: {
-                description: `The entity already exists in the graph. It will be ignored.`,
-                messages: [],
-            }
-        };
-        const t0 = performance.now();
-
-        // verify some basic structural elements exist
-        if (!crate["@context"]) {
-            this.__setError("init", `The crate file does not have a '@context'.`);
-            return;
-        }
-        if (!crate["@graph"] || !isArray(crate["@graph"])) {
-            this.__setError("init", `The crate file does not have '@graph' or it's not an array.`);
-            return;
-        }
-
-        // number of entities in the graph
-        this.graphLength = crate["@graph"].length;
-
-        // iterate over the graph find the root descriptor first
-        for (let i = 0; i < this.graphLength; i++) {
-            if (crate["@graph"][i]["@id"] === "ro-crate-metadata.json") {
-                this.rootDescriptor = i;
-
-                // while we're here
-                //  check that about exists and is an object not an array
-                if ("about" in crate["@graph"][i]) {
-                    if (Array.isArray(crate["@graph"][i].about)) {
-                        crate["@graph"][i].about = (crate["@graph"][i].about as any[])[0];
-                    }
-                } else {
-                    this.__setError(
-                        "init",
-                        `This crate is invalid. The root descriptor does not have an about property.`
-                    );
-                }
-
-                // check that conformsTo exists and is an object not an array
-                if (!("conformsTo" in crate["@graph"][i])) {
-                    this.__setWarning(
-                        "init",
-                        `This root descriptor does not specify 'conformsTo'. It will be set to RO Crate v1.1`
-                    );
-                    crate["@graph"][i].conformsTo = { "@id": "https://w3id.org/ro/crate/1.1" };
-                }
-
-                break;
-            }
-        }
-        // if we haven't located a root descriptor; bail - this crate is borked
-        if (this.rootDescriptor === undefined) {
-            this.__setError(
-                "init",
-                `This crate is invalid. A root descriptor can not been identified.`
-            );
-            return;
-        }
-
-        // now locate the root dataset and ensure the id is sensible
-        const rootDescriptor = crate["@graph"][this.rootDescriptor];
-        for (let i = 0; i < this.graphLength; i++) {
-            if (
-                isEntityReference(rootDescriptor.about) &&
-                crate["@graph"][i]["@id"] === rootDescriptor.about["@id"]
-            ) {
-                this.rootDataset = i;
-
-                // set the root dataset @id to './'
-                crate["@graph"][i]["@id"] = "./";
-                rootDescriptor.about["@id"] = "./";
-                break;
-            }
-        }
-
-        if (this.rootDataset === undefined) {
-            this.__setError("init", `This crate is invalid. A root dataset can not be identified.`);
-            return;
-        }
-
-        // as we process the graph, we do our best to normalise the entities
-        //  this includes ensuring the id is valid and sensible
-        //  if it's not, it might get rewritten
-        // if that happens, we need to ensure any links in the graph are also
-        //  rewritten to the new identifier
-        const idMap: { [key: string]: string } = {};
-
-        // process the the graph
-        for (let i = 0; i < this.graphLength; i++) {
-            // if the entity is empty - ignore it
-            if (isPlainObject(crate["@graph"][i]) && isEmpty(crate["@graph"][i])) continue;
-
-            try {
-                const normalisedEntity: NormalisedEntityDefinition = normalise(
-                    crate["@graph"][i],
-                    i
-                );
-                // store the old to new mappings
-                idMap[(crate["@graph"][i] as EntityReference)["@id"]] = normalisedEntity["@id"];
-
-                // is it a blank node? Store it if it is
-                if (normalisedEntity["@id"].match(/^_:/)) {
-                    this.blankNodes.push(normalisedEntity["@id"]);
-                }
-                // copy the entity into the internal structure
-                this.crate["@graph"].push(structuredClone(normalisedEntity));
-
-                // create the id to index reference
-                this.entityIdIndex[normalisedEntity["@id"]] = this.crate["@graph"].length - 1;
-                this.reverse[normalisedEntity["@id"]] = {};
-
-                // store the entity type for lookups by type
-                this.__storeEntityType(normalisedEntity);
-            } catch (error) {
-                this.__setError(
-                    "init",
-                    `Ignoring bad entity ${JSON.stringify({ "@id": crate["@graph"][i]["@id"], "@type": crate["@graph"][i]["@type"] })}`
-                );
-            }
-        }
-        // console.log(this.crate["@graph"]);
-        // console.log(this.entityIdIndex);
-        // console.log(this.reverse);
-        // console.log(this.entityTypes);
-
-        // one final iteration over the crate to record the reverse links
-        for (let i = 0; i < this.graphLength; i++) {
-            const normalisedEntity = this.crate["@graph"][i] as NormalisedEntityDefinition;
-            if (!normalisedEntity) continue;
-
-            for (let property of Object.keys(normalisedEntity)) {
-                if (this.coreProperties.includes(property)) continue;
-
-                (normalisedEntity[property] as any[]).forEach((entry) => {
-                    // remap any id's that were changed
-                    if (entry?.["@id"])
-                        entry["@id"] = idMap[entry["@id"]] ? idMap[entry["@id"]] : entry["@id"];
-
-                    // set up reverse links
-                    if (entry?.["@id"] && this.reverse[entry["@id"]]) {
-                        if (!this.reverse[entry["@id"]][property]) {
-                            this.reverse[entry["@id"]][property] = [];
-                        }
-                        let links = this.reverse[entry["@id"]][property].map(
-                            (l: { "@id": string }) => l["@id"]
-                        );
-                        if (!links.includes(normalisedEntity["@id"])) {
-                            this.reverse[entry["@id"]][property].push({
-                                "@id": normalisedEntity["@id"],
-                            });
-                        }
-                    }
-                });
-            }
-        }
-
-        if (this.errors.hasError) {
-            return;
-        }
-
-        // assemble all the definitions for use managing the local context
-        this.crate["@context"] = this.__normaliseContext(crate["@context"]);
-        this.contextDefinitions = this.__collectAllDefinitions(this.crate["@context"]);
-        if (context) {
-            // if we're given a context, store it for use later
-            this.providedContext = structuredClone(this.__normaliseContext(context));
-        }
-
-        const t1 = performance.now();
-        console.debug(`Crate ingest and prep: ${round(t1 - t0, 1)}ms`);
-    }
-
-    /** Get the context
-     * @returns the crate context
-     */
-    getContext(): NormalisedContext {
-        if (this.providedContext) {
-            return structuredClone(this.providedContext);
-        } else {
-            let context = this.crate["@context"] as UnverifiedContext;
-            if (!isEmpty(this.localContext)) {
-                context = [...context, this.localContext];
-                context = this.__normaliseContext(context);
-            }
-            return structuredClone(context);
-        }
-    }
-
-    /**
-     * Set the context
-     *
-     * This is equivalent to a profile author setting a context. It gets
-     *   used as is and data updates going forward do not get dealth with.
-     * @param {*} context
-     */
-    setContext(context: NormalisedContext) {
-        this.providedContext = this.__normaliseContext(context);
-    }
-
-    /**
-     * Set a profile
-     *
-     * CrateManager can set reverse associations if defined in a profile.
-     *
-     * */
-    setProfileManager(pm: ProfileManagerType) {
-        this.pm = pm;
-
-        if (this.pm.profile.context) {
-            // if we're given a context, store it for use later
-            this.providedContext = structuredClone(
-                this.__normaliseContext(this.pm.profile.context)
-            );
-        }
-    }
-
-    /**
-     * Get the root dataset
-     *
-     * @returns the root dataset entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let rd = cm.getRootDataset()
-
-     */
-    getRootDataset(): NormalisedEntityDefinition {
-        let rootDataset = structuredClone(this.crate["@graph"][this.rootDataset as number]);
-        rootDataset["@reverse"] = structuredClone(this.reverse[rootDataset["@id"]]);
-        return rootDataset;
-    }
-
-    getRootDescriptor(): NormalisedEntityDefinition {
-        let rootDescriptor = structuredClone(this.crate["@graph"][this.rootDescriptor as number]);
-        rootDescriptor["@reverse"] = structuredClone(this.reverse[rootDescriptor["@id"]]);
-        return rootDescriptor;
-    }
-
-    /**
-     * Get an entity
-     *
-     * @param {Object} options
-     * @param {string} options.id - the id of the entity to get
-     * @param {boolean} options.stub - if true, only the `@id, @type and name` prop's will be returned. That is,
-     *                   you get a stub entry not the complete entity data.
-     * @param {boolean} options.link - if true, all the associated entities are filled out as stubs
-     * @param {boolean} options.materialise - if true, the entity will be created if it doesn't exist (consider
-     *                  when URL's point outside the crate, in this case, they will be created as entities inside it)
-     * @returns the entity
-     *
-     * @example
-
-const cm = new CrateManager({ crate })
-
-// get the full entity
-let rd = cm.getEntity({ id: './' })
-
-// return a stub entry
-rd = cm.getEntity({ id: './', stub: true })
-
-     */
-    getEntity({
-        id,
-        stub = false,
-        link = true,
-        materialise = true,
-    }: {
-        id: string;
-        stub?: boolean;
-        link?: boolean;
-        materialise?: boolean;
-    }): NormalisedEntityDefinition | undefined {
-        if (!id) throw new Error(`An id must be provided`);
-        let indexRef = this.entityIdIndex[id];
-
-        if (indexRef === undefined && !materialise) {
-            return undefined;
-        }
-        if (indexRef === undefined && materialise) {
-            // id's pointing outside the crate won't resolve so we
-            //   'materialise' them here
-            return this.__materialiseEntity({ id });
-        }
-
-        // otherwise we found it so return it
-        let entity = structuredClone(this.crate["@graph"][indexRef]);
-
-        // encode the id
-        id = encodeURI(id);
-
-        entity["@reverse"] = structuredClone(this.reverse[entity["@id"]]) ?? {};
-        if (stub) {
-            return { "@id": entity["@id"], "@type": entity["@type"], name: entity.name };
-        }
-        if (link) {
-            for (let property of Object.keys(entity)) {
-                if (this.coreProperties.includes(property)) continue;
-                entity[property] = entity[property].map((value: EntityReference) => {
-                    if (value?.["@id"]) {
-                        return this.getEntity({ id: value["@id"], stub: true });
-                    }
-                    return value;
-                });
-            }
-        }
-        return entity;
-    }
-
-    /**
-     *  Get Entity Types
-     *
-     * @returns an array of entity types, sorted, found in the crate
-     */
-    getEntityTypes(): string[] {
-        return Object.keys(this.entityTypes).sort();
-    }
-
-    /**
-     * @generator
-     *
-     * @param {Object} params
-     * @param {Number} params.limit - how many entities to return
-     * @param {string} params.query - a string to match against @id, @type and name
-     * @param {string} params.type -  a string to match against @type
-     * @yields {entity}
-     * @example
-
-const cm = new CrateManager({crate})
-let entities = cm.getEntities()
-
-for (let entity of entities) {
-    ...
-}
-
-To get an array just spread the return
-let entities = [ ...cm.getEntities() ]
-
-// query @id, @type and name
-entities = cm.getEntities({ query: 'person' })
-
-// query @id, @type and name for entites of type Person
-entities = cm.getEntities({ query: 'person', type: 'Person' })
-
-// query @id, @type and name for entites of type Person - limit 10 matches
-entities = cm.getEntities({ query: 'person', type: 'Person', limit: 10 })
-
-     */
-    *getEntities(
-        params: { limit?: number; query?: string; type?: string } = {
-            limit: undefined,
-            query: undefined,
-            type: undefined,
-        }
-    ): Generator<NormalisedEntityDefinition> {
-        let { limit, query, type } = params;
-
-        if (!isString(query) && !isUndefined(query)) {
-            throw new Error(`query must be a string`);
-        }
-        if (!isString(type) && !isUndefined(type)) {
-            throw new Error(`type must be a string`);
-        }
-        if (query) {
-            query = query.toLowerCase();
-        }
-        if (type === "ANY") type = undefined;
-
-        let count = 0;
-        for (let i = 0; i < this.graphLength; i++) {
-            let entity = this.crate["@graph"][i];
-            if (!entity) continue;
-            if (query || type) {
-                let eid = entity["@id"].toLowerCase();
-                let etype = isArray(entity["@type"])
-                    ? (entity["@type"].join(", ") as string).toLowerCase()
-                    : (entity["@type"] as string).toLowerCase();
-                let name = String(entity.name).toLowerCase();
-                if (type && !query) {
-                    type = type.toLowerCase();
-                    if (etype.match(type)) {
-                        yield structuredClone(entity);
-                        count += 1;
-                    }
-                } else if (query && !type) {
-                    if (eid.match(query) || name.match(query)) {
-                        yield structuredClone(entity);
-                        count += 1;
-                    }
-                } else if (query && type) {
-                    type = type.toLowerCase();
-                    if (etype.match(type) && (eid.match(query) || name.match(query))) {
-                        yield structuredClone(entity);
-                        count += 1;
-                    }
-                }
-            } else {
-                if (entity) {
-                    yield structuredClone(entity);
-                    count += 1;
-                }
-            }
-
-            if (limit && count === limit) return;
-        }
-    }
-
-    /**
-     *
-     * locateEntity
-     *
-     * Given a set of id's, find the entity or entities that link to all of them.
-     *  This is really for finding grouping type entities like Relationships and Actions so that
-     *  you can augment their description.
-     *  @param { object } params
-     *  @param { array } params.entityIds - an array of entity id's that are linked to from another entity
-     *  @param { boolean } params.strict - if true return entities that have exactly entityIds linked. If false,
-     *                          return entities that have at least entityIds linked
-     *  @returns [] entities matching or undefined
-     */
-
-    locateEntity({
-        entityIds,
-        strict = true,
-    }: {
-        entityIds: string[];
-        strict?: boolean;
-    }): NormalisedEntityDefinition[] | undefined {
-        // encode entityIds
-        entityIds = entityIds.map((eid) => encodeURI(eid));
-
-        // console.log(entityIds);
-        // get one id and use that to resolve what it links to
-        let entity = this.getEntity({ id: entityIds[0], materialise: false });
-
-        //   if it doesn't link to anything then there's no match
-        if (!entity) return undefined;
-
-        // if it does, for each match walk the entity forward and find out what it links to
-        // console.log(entity, this.reverse);
-        let thisEntityLinksTo = this.reverse[entity["@id"]];
-
-        let matches: { [key: string]: string[] } = {};
-        for (let property of Object.keys(thisEntityLinksTo)) {
-            for (let e of thisEntityLinksTo[property]) {
-                matches[e["@id"]] = [];
-            }
-        }
-
-        let entityMatches: NormalisedEntityDefinition[] = [];
-        for (let entityId of Object.keys(matches)) {
-            let entity = this.getEntity({ id: entityId });
-            if (entity) {
-                for (let property of Object.keys(entity)) {
-                    if (this.coreProperties.includes(property)) continue;
-                    for (let instance of entity[property]) {
-                        if (!isEntityReference(instance)) continue;
-                        if ((instance as EntityReference)?.["@id"])
-                            matches[entityId].push(instance["@id"]);
-                    }
-                }
-                if (strict) {
-                    // if strict is true then check if the linked entities match exactly
-                    if (isEqual(matches[entityId].sort(), entityIds.sort()))
-                        entityMatches.push(entity);
-                } else {
-                    // otherwise, check that entityIds is a subset of matches
-                    if (intersection(matches[entityId], entityIds).length === entityIds.length) {
-                        entityMatches.push(entity);
-                    }
-                }
-            }
-        }
-        return entityMatches;
-    }
-
-    /**
-     * resolveLinkedEntities
-     *
-     * Given an entity and a profile, if the entity matches a resolve configuration
-     *   this method will populate the entities linked from the resolve properties
-     *   defined in the profile.
-     *
-     * @param {Object} entity
-     * @param {Object} profile
-     *
-     * @returns an array of associations
-     * @example
-
-// given an entity
-let entity = {
-    "@id": "#createAction1",
-    "@type": ["CreateAction"],
-    name: "A very long named create action to demonstrate what happens with display of long names",
-    object: { "@id": "#person2" },
-    participant: { "@id": "#participant1" },
-    agent: { "@id": "#agent1" },
-};
-
-// and a profile with a resolve configuration
-let profile = {
-    ...
-    resolve: [
-        {
-            types: [ 'Relationship', 'Related' ],
-            properties: [ 'source', 'target' ]
-        },
-        {
-            types: [ 'CreateAction', 'EditAction' ],
-            properties: [ 'object', 'participant', 'agent' ]
-        }
-    ]
-    ...
-}
-
-// get a list of the associated entities
-console.log(cm.resolveLinkedEntityAssociations({ entity, profile }))
-
-
-associations === [
-  {
-    property: 'object',
-    '@id': '#person2',
-    '@type': [ 'Thing' ],
-    name: '#person2'
-  },
-  {
-    property: 'participant',
-    '@id': '#participant1',
-    '@type': [ 'Thing' ],
-    name: '#participant1'
-  },
-  {
-    property: 'agent',
-    '@id': '#agent1',
-    '@type': [ 'Thing' ],
-    name: '#agent1'
-  }
-]
-
-     */
-    resolveLinkedEntityAssociations({
-        entity,
-        profile,
-    }: {
-        entity: NormalisedEntityDefinition;
-        profile: NormalisedProfile;
-    }):
-        | {
-              property: string;
-              "@id": string;
-              "@type": string[];
-              name: string;
-          }[]
-        | [] {
-        if (!profile?.resolve) return [];
-        let resolveConfiguration = profile.resolve;
-        const resolvers: { [key: string]: any } = {};
-        resolveConfiguration.forEach((c) => {
-            c.types.forEach((type) => {
-                resolvers[type] = c.properties;
-            });
-        });
-
-        // does the entity @type overlap with a resolve configuration?
-        const match = intersection(Object.keys(resolvers), entity["@type"]);
-        if (!match.length) {
-            // the current entity does match a resolve definition
-            return [];
-        }
-
-        // what properties need to be resolved?
-        const propertiesToResolve = flattenDeep(match.map((type) => resolvers[type]));
-
-        let associations: Array<{
-            property: string;
-            "@id": string;
-            "@type": string[];
-            name: string;
-        }> = [];
-
-        for (let property of Object.keys(entity)) {
-            // skip core prop's and any prop not specifically configured to resolve
-            if (this.coreProperties.includes(property)) continue;
-            if (!propertiesToResolve.includes(property)) continue;
-
-            // resolve away
-            let values = [].concat(entity[property] as any);
-            values.forEach((value) => {
-                if (!isPlainObject(value) || !("@id" in value)) return value;
-                associations.push({
-                    property,
-                    ...(this.getEntity({
-                        id: value["@id"],
-                        stub: true,
-                    }) as NormalisedEntityDefinition),
-                });
-            });
-        }
-        return associations;
-    }
-
-    /**
-     * Add an entity to the graph
-     *
-     *  The entity must have '@id' and '@type' defined.
-     *
-     * @param {Object} entity - an entity definition to add to the crate
-     * @returns the entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let entity = {
-    "@id": '#e1',
-    "@type": "Person",
-    name: 'person1',
-};
-let r = cm.addEntity(entity);
-
-     */
-    addEntity(entity: UnverifiedEntityDefinition): NormalisedEntityDefinition {
-        if (!("@id" in entity)) {
-            throw new Error(`You can't add an entity without an identifier: '@id'.`);
-        }
-        if (!("@type" in entity)) {
-            throw new Error(`You can't add an entity without defining the type : '@type'.`);
-        }
-
-        const e = structuredClone(entity);
-        let normalisedEntity = normalise(e, this.graphLength);
-        const noClashCheck = this.__confirmNoClash({
-            entity: normalisedEntity,
-        }) as NormalisedEntityDefinition;
-        if (!noClashCheck) {
-            this.__setWarning("clash", `The entity ${normalisedEntity["@id"]} already exists. Crate set back to it's original state.`);
-            return this.getEntity({ id: normalisedEntity["@id"] }) as NormalisedEntityDefinition;
-        } else {
-            this.warnings.hasWarning = false;
-            this.warnings.clash.messages = [];
-        }
-
-        // set all properties, other than core props, to array
-        for (let property of Object.keys(normalisedEntity)) {
-            if (this.coreProperties.includes(property)) continue;
-
-            // ensure it's an array
-            entity[property] = [].concat(normalisedEntity[property] as []);
-
-            // then filter out empty properties with empty strings
-            normalisedEntity[property] = (entity[property] as []).filter((p) => p !== "");
-        }
-
-        // manage timestamps
-        if (this.entityTimestamps) {
-            normalisedEntity[entityDateCreatedProperty] = [new Date().toISOString()];
-            normalisedEntity[entityDateUpdatedProperty] = [new Date().toISOString()];
-        }
-
-        // push it into the graph
-        this.crate["@graph"].push(normalisedEntity);
-
-        // create the index and reverse lookup entries
-        this.graphLength = this.crate["@graph"].length;
-        this.entityIdIndex[normalisedEntity["@id"]] = this.graphLength - 1;
-        this.reverse[normalisedEntity["@id"]] = {};
-        this.__storeEntityType(normalisedEntity);
-
-        return normalisedEntity;
-    }
-
-    /**
-     * Add an entity with a blank node id ('_:...') to the graph.
-     *
-     * Use this when you want to add a non contextual entity to the graph. In thoses
-     *   cases providing an `@id` and name don't really make sense even though those properties are still required
-     *   therefore this method simplifies the process of adding those entity types. For example,
-     *   Actions (e.g. CreateAction), Relationships, GeoShape, GeoCoordinates etc
-     *
-     * @param {string} type - the entity type to configure for the new entity
-     * @returns the entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let r = cm.addBlankNode('Relationship);
-
-r === {
-    '@id': '_:Relationship1',
-    '@type': [ 'Relationship' ],
-    name: '_:Relationship1'
-}
-
-     */
-    addBlankNode(type: string): NormalisedEntityDefinition {
-        const blankNodeTypeMatches = this.blankNodes.filter((n) => n.match(type));
-        const id = `_:${type}${blankNodeTypeMatches.length + 1}`;
-        this.blankNodes.push(id);
-        let entity = {
-            "@id": id,
-            "@type": type,
-            name: id,
-        };
-        return this.addEntity(entity as UnverifiedEntityDefinition);
-    }
-
-    /**
-     * Add files or folders - use addFile or addFolder in preference to this
-     *
-     * This is a helper method specifically for adding files and folders in the crate. This method
-     *   will add the intermediate paths as 'Datasets' (as per the spec) and link everything via the hasPart
-     *   property as required. It is assumed that the path is relative to the root of the folder.
-     *
-     * @param {object} params
-     * @param {string} params.path - a file or folder path
-     * @param {string} params.type - the type of thing being added - File or Dataset
-     * @returns the entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let r = cm.addFileOrFolder('/a/b/c/file.txt);
-     */
-    addFileOrFolder({
-        path,
-        type = "File",
-    }: {
-        path: string;
-        type: string;
-    }): NormalisedEntityDefinition {
-        if (!["File", "Dataset"].includes(type)) {
-            throw new Error(`'addFileOrFolder' type must be File or Dataset`);
-        }
-
-        // remove preceding / and ./
-        if (path.match(/^\.\//)) path = path.replace(/^\.\//, "");
-        if (path.match(/^\//)) path = path.replace(/^\//, "");
-
-        // ensure folders end in '/'
-        if (type === "Dataset" && !path.match(/.*\/$/)) {
-            path = `${path}/`;
-        }
-
-        // remove initial slash if there is one
-        if (path.match(/^\//)) {
-            path = path.substring(1);
-        }
-
-        //  create the file path as individual datasets before joining
-        //   the file into the right place
-        let paths: string[] = path.split("/").slice(0, -1);
-        let i = 0;
-        const entities = [];
-        for (let p of paths) {
-            let entity = {
-                "@id": i > 0 ? `${paths.slice(0, i).join("/")}/${p}/` : `${p}/`,
-                "@type": ["Dataset"],
-                name: i > 0 ? `${paths.slice(0, i).join("/")}/${p}/` : `${p}/`,
-            };
-            entity["@id"] = encodeURI(entity["@id"]);
-            if (entity["@id"] === "./") continue;
-            let normalisedEntity = this.addEntity(entity as UnverifiedEntityDefinition);
-            i += 1;
-            entities.push(normalisedEntity);
-        }
-        i = 0;
-        for (let e of entities) {
-            if (i === 0) {
-                this.linkEntity({
-                    id: "./",
-                    property: "hasPart",
-                    propertyId: "https://schema.org/hasPart",
-                    value: { "@id": e["@id"] },
-                });
-            } else {
-                this.linkEntity({
-                    id: entities[i - 1]["@id"],
-                    property: "hasPart",
-                    propertyId: "https://schema.org/hasPart",
-                    value: { "@id": e["@id"] },
-                });
-            }
-            i += 1;
-        }
-
-        let entity = {
-            "@id": encodeURI(path),
-            "@type": [type],
-            name: path,
-        };
-        if (type === "File") {
-            let id = "./";
-            if (entities.length) {
-                id = entities.slice(-1)[0]?.["@id"];
-            }
-
-            const sourceEntity = this.getEntity({
-                id,
-                stub: true,
-            }) as NormalisedEntityDefinition;
-            this.ingestAndLink({
-                id: sourceEntity["@id"],
-                property: "hasPart",
-                propertyId: "https://schema.org/hasPart",
-                json: entity as UnverifiedEntityDefinition,
-            });
-        }
-        return this.getEntity({ id: entity["@id"], stub: true }) as NormalisedEntityDefinition;
-    }
-
-    /**
-     * Add file
-     *
-     * This is a helper method specifically for adding files to the crate. This method
-     *   will add the intermediate paths as 'Datasets' (as per the spec) and link everything via the hasPart
-     *   property as required. It is assumed that the path is relative to the root of the folder.
-     *
-     * @param {string} path - a file path to add - ensure the file path is relative to the folder root
-     * @returns the entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let r = cm.addFile('/a/b/c/file.txt);
-     */
-    addFile(path: string): NormalisedEntityDefinition {
-        return this.addFileOrFolder({ path, type: "File" });
-    }
-
-    /**
-     * Add folder
-     *
-     * This is a helper method specifically for adding folders to the crate. This method
-     *   will add the intermediate paths as 'Datasets' (as per the spec) and link everything via the hasPart
-     *   property as required. It is assumed that the path is relative to the root of the folder.
-     *
-     * @param {string} path - a folder path to add - ensure the folder path is relative to the folder root
-     * @returns the entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let r = cm.addFolder('/a/b/c);
-     */
-    addFolder(path: string): NormalisedEntityDefinition {
-        return this.addFileOrFolder({ path, type: "Dataset" });
-    }
-
-    /**
-     * Delete an entity
-     *
-     * @param {Object} options
-     * @param {string} options.id - the id of the entity to delete from the crate
-     *
-     * @returns true if successful
-     * @example
-
-const cm = new CrateManager({ crate })
-cm.deleteEntity({ id: '#e1' })
-
-     */
-    deleteEntity({ id }: { id: string }) {
-        if (!id) throw new Error(`'deleteEntity' requires 'id' to be defined`);
-        if (
-            [
-                (this.crate["@graph"][this.rootDescriptor as number] as NormalisedEntityDefinition)[
-                    "@id"
-                ],
-                (this.crate["@graph"][this.rootDataset as number] as NormalisedEntityDefinition)[
-                    "@id"
-                ],
-            ].includes(id)
-        ) {
-            throw new Error(`You can't delete the root dataset or the root descriptor.`);
-        }
-
-        const indexRef = this.entityIdIndex[id];
-        const entity = this.crate["@graph"][indexRef];
-        if (!entity) return;
-
-        this.__removeEntityType(entity);
-
-        // get the entity, find what it links to and remove it from the reverse of those linkages
-        for (let [property, instances] of Object.entries(entity as NormalisedEntityDefinition)) {
-            if (this.coreProperties.includes(property)) continue;
-            for (let instance of instances) {
-                if (!isEntityReference(instance)) continue;
-                if (instance?.["@id"] && this.reverse[instance["@id"]]) {
-                    this.reverse[instance["@id"]][property] = this.reverse[instance["@id"]][
-                        property
-                    ].filter((i: any) => i["@id"] !== id);
-
-                    // remove the property if it's empty
-                    if (!this.reverse[instance["@id"]][property].length) {
-                        delete this.reverse[instance["@id"]][property];
-                    }
-                }
-            }
-        }
-
-        // now do the same by walking the reverse links from this entity
-        for (let [property, instances] of Object.entries(
-            this.reverse[entity["@id"]] as NormalisedEntityDefinition
-        )) {
-            if (this.coreProperties.includes(property)) continue;
-            for (let instance of instances) {
-                if (!isEntityReference(instance)) continue;
-                if (instance["@id"]) {
-                    let linkIndexRef = this.entityIdIndex[instance["@id"]];
-                    let linkEntity = this.crate["@graph"][linkIndexRef];
-                    if (linkEntity) {
-                        linkEntity[property] = linkEntity[property].filter((i) => {
-                            if (isEntityReference(i)) {
-                                return i["@id"] !== id;
-                            } else {
-                                return i;
-                            }
-                        });
-
-                        // remove the property if it's empty
-                        if (!linkEntity[property].length) {
-                            delete linkEntity[property];
-                        }
-                    }
-                }
-            }
-        }
-
-        delete this.entityIdIndex[id];
-        delete this.reverse[id];
-        this.crate["@graph"][indexRef] = undefined;
-
-        return true;
-    }
-
-    /**
-     * Set a property on an entity
-     *
-     * @param {Object} options
-     * @param {options.id} options.id - the id of the entity to add the property to
-     * @param {options.property } options.property - the property to add
-     * @param {options.value} options.value - the data to add to that property. Can be string or object with '@id'
-     * @returns true if successful
-     * @example
-
-const cm = new CrateManager({ crate })
-const authorId = chance.url();
-
-//  setting an object reference
-cm.setProperty({ id: "./", property: "author", value: { "@id": authorId } });
-
-//  setting a text string
-cm.setProperty({ id: "./", property: "author", value: "text" });
-
-//  setting a number
-cm.setProperty({ id: "./", property: "author", value: 3 });
-
-     */
-    setProperty({
-        id,
-        property,
-        propertyId,
-        value,
-    }: {
-        id: string;
-        property: string;
-        propertyId?: string;
-        value: PrimitiveType | EntityReference;
-    }): boolean | undefined {
-        if (this.coreProperties.includes(property)) {
-            throw new Error(`This method does not operate on ${this.coreProperties.join(", ")}`);
-        }
-        if (!id) throw new Error(`'setProperty' requires 'id' to be defined`);
-        if (!property) throw new Error(`setProperty' requires 'property' to be defined`);
-        if (value !== false && !value)
-            throw new Error(`'setProperty' requires 'value' to be defined`);
-
-        //  just don't set an empty object on a property
-        if (isPlainObject(value) && isEmpty(value)) return;
-
-        const indexRef = this.entityIdIndex[id];
-        const entity = this.crate["@graph"][indexRef];
-        if (!entity) return;
-
-        if (!(property in entity)) {
-            entity[property] = [];
-        }
-        // validate the value's shape - v. important
-        if (isString(value) || isNumber(value) || isBoolean(value)) {
-            (entity[property] as any[]).push(value);
-        } else if (isPlainObject(value) && "@id" in value) {
-            // value makes sense
-            // but make sure it's only the id and not the whole entity
-            value = { "@id": value["@id"] };
-
-            // and don't add duplicates
-            let ids = entity[property]
-                .filter((v) => (v as EntityReference)?.["@id"])
-                .map((v) => (v as EntityReference)?.["@id"]);
-            if (!ids.includes(value["@id"])) entity[property].push(value as any);
-
-            // and add a @reverse link
-            this.__addReverse({ id, property, value });
-        } else if(isArray(value)) {
-            // In case of handlesMultipleValues inputs, like checkbox select the value is an array itself.
-            // We need to call toRaw() on it to make it a normal array, ie. get rid of the vue array proxy
-            (entity[property] as any[]) = value;
-        } else {
-            // value doesn't make sense - bail
-            throw new Error(`value must be a string, number, boolean or object with '@id'`);
-        }
-        this.__updateContext({ name: property, id: propertyId });
-
-        // manage timestamps
-        if (this.entityTimestamps) {
-            entity[entityDateUpdatedProperty] = [new Date().toISOString()];
-        }
-        return true;
-    }
-
-    /**
-     * Update a property on an entity
-     *
-     * @param {Object} options
-     * @param {string} options.id - the id of the entity to add the property to
-     * @param {string} options.property - the property to add
-     * @param {string} options.idx - the idx of the property array to update
-     * @param {string} options.value - the data to add to that property, string or object with '@id'
-     * @example
-
-const cm = new CrateManager({ crate })
-cm.updateProperty({ id: "./", property: "@id", value: "something else" });
-cm.updateProperty({ id: "./", property: "author", idx: 1, value: "new" });
-
-     */
-    updateProperty({
-        id,
-        property,
-        idx,
-        value,
-    }: {
-        id: string;
-        property: string;
-        idx?: number;
-        value: PrimitiveType | PrimitiveType[] | EntityReference;
-    }): NormalisedEntityDefinition | undefined | string {
-        console.log("updateProperty", { id, property, idx, value });
-        if (!id) throw new Error(`'setProperty' requires 'id' to be defined`);
-        if (!property) throw new Error(`setProperty' requires 'property' to be defined`);
-        if (value !== false && !value)
-            throw new Error(`'setProperty' requires 'value' to be defined`);
-        console.log("updateProperty", { id, property, idx, value });
-        //  just don't set an empty object on a property
-        if (isPlainObject(value) && isEmpty(value)) return;
-
-        let indexRef = this.entityIdIndex[id];
-        const entity = this.crate["@graph"][indexRef];
-        if (!entity) return;
-
-        if (this.coreProperties.includes(property)) {
-            if (property === "@id") {
-                // First verify the new ID won't clash
-                const tempEntity = structuredClone(entity);
-                tempEntity["@id"] = value as string;
-
-                const noClash = this.__confirmNoClash({
-                    entity: tempEntity,
-                    mintNewId: false
-                });
-
-                if (!noClash) {
-                    this.__setWarning("clash", `The entity ${tempEntity["@id"]} already exists. Crate set back to it's original state.`);
-                    return this.getEntity({ id: tempEntity["@id"] }) as NormalisedEntityDefinition;
-                } else {
-                    this.warnings.hasWarning = false;
-                    this.warnings.clash.messages = [];
-                }
-
-                //  update @id
-                this.__updateEntityId({
-                    oldId: (entity as EntityReference)?.["@id"],
-                    newId: value as string,
-                });
-            } else if (property === "@type") {
-                //  update @type
-                //   ensure it's an array first though or weird sh*t happens
-                value = [].concat(value as any);
-
-                //  when updating the type we first need to clear out the
-                //   old types and then set the new so we end up with correct
-                //   reference counts
-                this.__removeEntityType(entity);
-                entity["@type"] = uniq(value) as [];
-                this.__storeEntityType(entity);
-            } else if (property === "name") {
-                // update name
-                // ensure we're setting a string value for the name property
-                if (isArray(value)) value = value.join(", ");
-                entity.name = String(value);
-            }
-        } else {
-            // In case of handlesMultipleValues inputs, like checkbox select the value is an array itself.
-            // We need to call toRaw() on it to make it a normal array, ie. get rid of the vue array proxy
-            if (isArray(value)) {
-                (entity[property] as any[]) = value;
-            } else {
-                if (idx !== 0 && !idx) throw new Error(`setProperty' requires 'idx' to be defined`);
-                (entity[property] as any[])[idx] = value;
-            }
-        }
-
-        // manage timestamps
-        if (this.entityTimestamps) {
-            entity[entityDateUpdatedProperty] = [new Date().toISOString()];
-        }
-        return entity;
-    }
-
-    /**
-     * Delete a specific property from the entity. That is, an instance of a property.
-     *
-     * @param {Object}
-     * @param {string} options.id - the id of the entity to remove the property value from
-     * @param {string} options.property - the property
-     * @param {string} options.idx - the idx of the property array to delete
-     * @example
-
-const cm = new CrateManager({ crate })
-cm.deleteProperty({ id: "./", property: "author", idx: 1 });
-
-     */
-    deleteProperty({ id, property, idx }: { id: string; property: string; idx?: number }) {
-        if (!id) throw new Error(`'deleteProperty' requires 'id' to be defined`);
-        if (!property) throw new Error(`deleteProperty' requires 'property' to be defined`);
-        // if (idx !== 0 && !idx) throw new Error(`deleteProperty' requires 'idx' to be defined`);
-
-        let entity;
-        if (idx || idx === 0) {
-            // delete just that property instance
-            const indexRef = this.entityIdIndex[id];
-            entity = this.crate["@graph"][indexRef];
-            if (isUndefined(entity)) return;
-
-            let { propertyDefinition } = this.pm.getPropertyDefinition({
-                property: property,
-                entity: entity,
-            });
-
-            // In case of input, which handles multiple values on its own, like a checkbox style select, the array is
-            // handled as a single value, so we need to delete all values at once
-            // For other multivalued inputs, we delete one by one.
-            if (propertyDefinition.handlesMultipleValues === true) {
-                delete entity[property];
-            } else {
-                entity[property].splice(idx, 1);
-                if (!entity[property].length) delete entity[property];
-
-            }
-        } else if (idx === undefined) {
-            const indexRef = this.entityIdIndex[id];
-            entity = this.crate["@graph"][indexRef];
-            if (isUndefined(entity)) return;
-
-            if (!entity[property]) return;
-
-            // iterate over the values and unlink any linked properties
-            entity[property].forEach((instance) => {
-                if ((instance as EntityReference)?.["@id"])
-                    this.unlinkEntity({ id, property, value: instance as EntityReference });
-            });
-
-            // now delete whatever is left
-            delete entity[property];
-        }
-
-        // manage timestamps
-        if (this.entityTimestamps && !isUndefined(entity)) {
-            entity[entityDateUpdatedProperty] = [new Date().toISOString()];
-        }
-    }
-
-    /**
-     * Ingest and link a nested json object
-     *
-     * @param {Object} options
-     * @param {string} options.id - the id of the entity to join the data into
-     * @param {string} options.property - the property to join the data into
-     * @param {string} options.propertyId - the propertyId of the property - ie the url to the definition
-     * @param {json} options.json - the data object to join in
-     * @example
-
-const cm = new CrateManager({ crate })
-let json = {
-    ...,
-}
-cm.ingestAndLink({
-    id: "./",
-    property: "language",
-    json,
-});
-
-     */
-    ingestAndLink({
-        id = undefined,
-        property = undefined,
-        propertyId = undefined,
-        json = {},
-    }: {
-        id: string | undefined;
-        property: string | undefined;
-        propertyId: string | undefined;
-        json: UnverifiedEntityDefinition;
-    }) {
-        if (!id) throw new Error(`ingestAndLink: 'id' must be defined`);
-        if (!property) throw new Error(`ingestAndLink: 'property' must be defined`);
-
-        let flattened = this.flatten(json);
-        let entities: NormalisedEntityDefinition[] = flattened.map(
-            (entity: UnverifiedEntityDefinition) => {
-                let normalisedEntity: NormalisedEntityDefinition = normalise(
-                    entity,
-                    this.graphLength
-                );
-                normalisedEntity = this.addEntity(normalisedEntity);
-                return normalisedEntity;
-            }
-        );
-
-        this.linkEntity({ id, property, propertyId, value: { "@id": entities[0]["@id"] } });
-
-        //  go through and set all of the reverse links
-        for (let entity of entities) {
-            for (let property of Object.keys(entity)) {
-                if (this.coreProperties.includes(property)) continue;
-                (entity[property] as []).forEach((instance) => {
-                    if (instance?.["@id"]) {
-                        this.__addReverse({ id: entity["@id"], property, value: instance });
-                    }
-                });
-            }
-        }
-    }
-
-    /**
-     * Flatten a nested json object to an array
-     *
-     * @param {Object} json - a potentially nested data blob to flatten into array
-     * @returns an array of objects
-     * @example
-
-const cm = new CrateManager({ crate })
-let json = {
-    ...,
-}
-let arrayOfObjects = cm.flatten(json)
-
-     */
-    flatten(json: UnverifiedEntityDefinition): NormalisedEntityDefinition[] {
-        if (!isPlainObject(json)) {
-            throw new Error(`flatten only takes an object.`);
-        }
-        json = structuredClone(json);
-        let flattened = [];
-        flattened.push(json);
-        for (let property of Object.keys(json)) {
-            if (["@id", "@type", "name"].includes(property)) continue;
-
-            if (!isArray(json[property])) json[property] = [json[property] as any];
-
-            json[property].forEach((instance) => {
-                if (isPlainObject(instance)) flattened.push(this.flatten(instance as any));
-            });
-            json[property] = json[property].map((instance: any) => {
-                if (isPlainObject(instance)) return { "@id": instance["@id"] };
-                return instance;
-            });
-        }
-        return flattenDeep(flattened as []).map((e) => e);
-    }
-
-    /**
-     * Link two entities
-     *
-     * Link two entities via a property. If there is a profile defined
-     *      and it has reverse associations, then they will be added.
-     *
-     * @param {Object} options
-     * @param {string} options.id - the id of the entity to add the association to
-     * @param {string} options.property - the property to add the association to
-     * @param {string} options.propertyId - the propertyId of the property - ie the url to the definition
-     * @param {object} options.value - an object with '@id' defining the association to create
-     * @example
-
-const cm = new CrateManager({ crate })
-cm.linkEntity({ id: './', property: 'author', value: { '@id': '#e1' }})
-
-     **/
-    linkEntity({
-        id,
-        property,
-        propertyId = undefined,
-        value,
-    }: {
-        id: string;
-        property: string;
-        propertyId?: string;
-        value: { "@id": string };
-    }): void {
-        if (!id) throw new Error(`'linkEntity' requires 'id' to be defined`);
-        if (!property) throw new Error(`'linkEntity' requires 'property' to be defined`);
-        if (!value) throw new Error(`'linkEntity' requires 'value' to be defined`);
-        if (!isPlainObject(value) || !value["@id"]) {
-            throw new Error(`value must be an object with '@id' defined`);
-        }
-        this.setProperty({ id, property, propertyId, value });
-
-        // set inverse association if required
-        const associations = this.pm?.getPropertyAssociations() ?? {};
-        if (associations[property]) {
-            let inverse = associations[property];
-            this.setProperty({
-                id: value["@id"],
-                property: inverse.property,
-                propertyId: inverse.propertyId,
-                value: { "@id": id },
-            });
-        }
-    }
-
-    /**
-     * Unlink two entities
-     *
-     * Remove an association between two entities. If there is a profile defined
-     *      and it has reverse associations, then they will be removed as well.
-     *
-     * @param {Object} options
-     * @param {string} options.id - the id of the entity to remove the association from
-     * @param {string} options.property - the property containing the association
-     * @param {object} options.value - an object with '@id' defining the association to remove
-     * @example
-
-const cm = new CrateManager({ crate })
-const cm = new CrateManager({ crate })
-cm.unlinkEntity({ id: './', property: 'author', value: { '@id': '#e1' }})
-
-     **/
-    unlinkEntity({
-        id = undefined,
-        property = undefined,
-        value = undefined,
-        stop = false,
-    }: {
-        id: string | undefined;
-        property: string | undefined;
-        value: { "@id": string } | undefined;
-        stop?: boolean;
-    }) {
-        if (!id) throw new Error(`'unlinkEntity' requires 'id' to be defined`);
-        if (!property) throw new Error(`'unlinkEntity' requires 'property' to be defined`);
-        if (!value) throw new Error(`'unlinkEntity' requires 'value' to be defined`);
-        if (!isPlainObject(value) || !value["@id"]) {
-            throw new Error(`value must be an object with '@id' defined`);
-        }
-
-        // console.log("START", id, property, value["@id"]);
-        // get the source entity
-        let indexRef = this.entityIdIndex[id];
-        let entity = this.crate["@graph"][indexRef];
-        if (!entity) return;
-        // console.log("SOURCE ENTITY BEFORE ", entity);
-
-        // and remove the linked entity from the specified property
-        entity[property] = (entity[property] as []).filter((v) => {
-            if (v?.["@id"] && v["@id"] === value["@id"]) {
-                // do nothing - we don't want it
-            } else {
-                return v;
-            }
-        });
-        if (!entity[property].length) delete entity[property];
-
-        // manage timestamps
-        if (this.entityTimestamps) {
-            entity[entityDateUpdatedProperty] = [new Date().toISOString()];
-        }
-        // console.log("SOURCE ENTITY AFTER", entity);
-
-        // clean up the reverse mapping back value['@id'] -> id
-
-        // console.log(`TARGET ENTITY BEFORE REVERSE`, this.reverse[value["@id"]]);
-        // console.log();
-        if (this.reverse[value["@id"]]) {
-            this.reverse[value["@id"]][property] = this.reverse[value["@id"]][property].filter(
-                (v: any) => {
-                    if (isEntityReference(v)) return v["@id"] !== id;
-                }
-            );
-            if (!this.reverse[value["@id"]][property].length)
-                delete this.reverse[value["@id"]][property];
-        }
-        // console.log(`TARGET ENTITY AFTER REVERSE`, this.reverse[value["@id"]]);
-        // remove any inverse associations
-        const associations = this.pm?.getPropertyAssociations() ?? {};
-        if (associations[property] && !stop) {
-            const inverse = associations[property];
-            // console.log(inverse, value["@id"], property, id);
-            this.unlinkEntity({
-                id: value["@id"],
-                property: inverse.property,
-                value: { "@id": id },
-                stop: true, // V. IMPORTANT so we don't get into an infinite loop
-            });
-        }
-    }
-
-    /**
-     * Purge unlinked entities from the crate
-     *
-     * Clean up the graph and purge any unlinked entities including disconnected subtrees.
-     * @example
-
-const cm = new CrateManager({ crate })
-cm.purgeUnlinkedEntities()
-
-     */
-    purgeUnlinkedEntities(): void {
-        let walker = (entity: NormalisedEntityDefinition) => {
-            linkedEntities[entity["@id"]] = true;
-            for (let property of Object.keys(entity)) {
-                if (this.coreProperties.includes(property)) continue;
-                for (let instance of entity[property]) {
-                    if (!isEntityReference(instance)) continue;
-                    if (instance?.["@id"] && !linkedEntities[instance["@id"]]) {
-                        let indexRef = this.entityIdIndex[instance["@id"]];
-                        if (indexRef !== undefined) {
-                            let entity = this.crate["@graph"][indexRef];
-                            walker(entity as NormalisedEntityDefinition);
-                        }
-                    }
-                }
-            }
-        };
-
-        walker = walker.bind(this);
-        let linkedEntities: { [key: string]: boolean } = { "ro-crate-metadata.json": true };
-
-        let rootDescriptor = this.getEntity({ id: "ro-crate-metadata.json" });
-        if (!rootDescriptor) return;
-        // let indexRef = this.entityIdIndex["ro-crate-metadata.json"];
-        // we first need to walk the graph from the root descriptor
-        //  and assemble a list of linked entities that we get to by
-        //  following forward looking associations
-        walker(rootDescriptor);
-
-        // then, we walk the entire graph and look for entities
-        //   that are not already linked. When we find one, we walk
-        //   it forwards to see if it links to anything already linked
-        //   and if yes, then we link it
-        // think things like relationships and actions that may link
-        //   to enities in the graph even though they themselves are not linked to
-        for (let i = 0; i < this.graphLength; i++) {
-            let entity = this.crate["@graph"][i];
-            if (!entity) continue;
-            if (!linkedEntities[entity["@id"]]) {
-                for (let property of Object.keys(entity)) {
-                    if (this.coreProperties.includes(property)) continue;
-                    for (let instance of entity[property]) {
-                        if (!isEntityReference(instance)) continue;
-                        if (instance?.["@id"] && linkedEntities[instance["@id"]]) {
-                            linkedEntities[entity["@id"]] = true;
-                        }
-                    }
-                }
-            }
-        }
-
-        // now we can remove everything we couldn't get to
-        for (let i = 0; i < this.graphLength; i++) {
-            let entity = this.crate["@graph"][i];
-            if (entity && !linkedEntities[entity["@id"]]) {
-                let indexRef = this.entityIdIndex[entity["@id"]];
-                delete this.entityIdIndex[entity["@id"]];
-                delete this.reverse[entity["@id"]];
-                this.crate["@graph"][indexRef] = undefined;
-            }
-        }
-    }
-
-    /**
-     * Export the RO-Crate
-     * @returns the complete ro-crate
-     * @example
-
-const cm = new CrateManager({ crate })
-let crate = cm.exportCrate()
-
-     */
-    exportCrate(): NormalisedCrate {
-        const t0 = performance.now();
-        // const crate = structuredClone(this.crate);
-
-        let entities = this.crate["@graph"]
-            .filter((e) => {
-                return !isUndefined(e);
-            })
-            .map((e) => {
-                const entity = structuredClone(e);
-                entity["@reverse"] =
-                    (structuredClone(this.reverse[e["@id"]]) as {
-                        [key: string]: { "@id": string }[];
-                    }) ?? {};
-
-                for (let property of Object.keys(entity)) {
-                    if (property === "@reverse") {
-                        for (let rp of Object.keys(entity["@reverse"])) {
-                            if (isArray(entity[property][rp]) && entity[property][rp].length === 1)
-                                entity[property][rp] = entity[property][rp][0];
-                        }
-                    } else {
-                        if (isArray(entity[property]) && entity[property].length === 1)
-                            entity[property] = entity[property][0];
-                    }
-                }
-                return entity;
-            });
-
-        const context: NormalisedContext = this.getContext();
-        const crate = {
-            "@context": context.length === 1 ? context[0] : context,
-            "@graph": entities,
-        } as NormalisedCrate;
-        const t1 = performance.now();
-        console.debug(`Crate export: ${round(t1 - t0, 1)}ms`);
-        // console.log(JSON.stringify(this.crate, null, 2));
-        return crate;
-    }
-
-    /**
-     * exportEntityTemplate
-     *
-     * Export an entity as a template to be reused.
-     *  1. If resolveDepth = 0 then the entity is returned with all associations removed
-     *  2. If resolveDepth = 1 then the entity is returned with one level of associations populated but
-     *    all of their associations will be removed.
-     *
-     * @param {Object} options
-     * @param {String} options.id - the id of the entity to export as a template
-     * @param {String} options.resolveDepth - 0 or 1. If 1, linked entities will be joined in
-     *
-     * @returns entity
-     * @example
-
-const cm = new CrateManager({ crate })
-let entity = cm.exportEntityTemplate({ id: '#person' })
-let entity = cm.exportEntityTemplate({ id: '#person', resolveDepth: 1 })
-
-     */
-    exportEntityTemplate({
-        id,
-        resolveDepth = 0,
-    }: {
-        id: string;
-        resolveDepth?: number;
-    }): NormalisedEntityDefinition {
-        if (![0, 1].includes(resolveDepth)) {
-            throw new Error(`resolveDepth can only be 0 or 1`);
-        }
-        let indexRef = this.entityIdIndex[id];
-        let entity = structuredClone(this.crate["@graph"][indexRef]);
-
-        for (let property of Object.keys(entity)) {
-            if (this.coreProperties.includes(property)) continue;
-
-            entity[property] = entity[property].map((value: EntityReference) => {
-                if (value?.["@id"]) {
-                    if (resolveDepth === 0) return undefined;
-                    let linkedIndexRef = this.entityIdIndex[value["@id"]];
-                    let linkedEntity = structuredClone(this.crate["@graph"][linkedIndexRef]);
-                    linkedEntity = this.__removeAssociations(linkedEntity);
-                    delete linkedEntity["@reverse"];
-                    return linkedEntity;
-                } else {
-                    return value;
-                }
-            });
-            entity[property] = compact(entity[property]);
-            if (entity[property].length === 0) {
-                delete entity[property];
-            } else if (entity[property].length === 1) {
-                entity[property] = entity[property][0];
-            }
-        }
-        delete entity["@reverse"];
-        return entity;
-    }
-
-    /**
-     * getErrors
-     *
-     * @returns { errors }
-     *
-     */
-    getErrors(): errorsInterface {
-        return this.errors;
-    }
-
-    /**
-     * getWarnings
-     *
-     * @returns { warnings }
-     */
-    getWarnings(): warningsInterface {
-        return this.warnings;
-    }
-
-    __updateContext({ name, id }: { name: string; id?: string }): void {
-        if (id && !(id in this.contextDefinitions)) {
-            // the property or class isn't defined in the context
-            //   add it in the definitions for lookups later
-            //   store it in the local context which gets joined
-            //    in where required.
-            this.contextDefinitions[id] = true;
-            this.localContext[name] = id;
-        }
-    }
-
-    /**
-     * Normalise context
-     *
-     * Collapse all objects into a single object
-     *
-     * @param {*} context
-     * @returns context
-     */
-    __normaliseContext(context: UnverifiedContext): NormalisedContext {
-        context = [].concat(context);
-        let entries = {};
-        for (let entry of context) {
-            if (isPlainObject(entry)) entries = { ...entries, ...entry };
-        }
-        context = context.filter((e: string | {}) => isString(e));
-        if (!isEmpty(entries)) context = [...context, entries];
-        return context;
-    }
-    __storeEntityType(entity: NormalisedEntityDefinition): void {
-        // store the entity type for lookups by type
-        entity["@type"].forEach((type) => {
-            if (!this.entityTypes[type]) {
-                this.entityTypes[type] = 1;
-            } else {
-                this.entityTypes[type] += 1;
-            }
-        });
-    }
-    __removeEntityType(entity: NormalisedEntityDefinition) {
-        // update the entity type's store
-        entity["@type"].forEach((type) => {
-            this.entityTypes[type] -= 1;
-            if (this.entityTypes[type] === 0) delete this.entityTypes[type];
-        });
-    }
-    __collectAllDefinitions(context: NormalisedContext): { [key: string]: boolean } {
-        let definitions: { [key: string]: boolean } = {};
-
-        for (let entry of context) {
-            if (isString(entry)) {
-                // likely the ro-crate context - see if it is
-                let def = getContextDefinition(entry);
-                if (def) {
-                    definitions = { ...definitions, ...def.definitions };
-                } else {
-                    definitions[entry] = true;
-                }
-            } else if (isPlainObject(entry)) {
-                for (let [key, value] of Object.entries(entry)) {
-                    definitions[value as string] = true;
-                }
-            }
-        }
-        // console.log(definitions);
-        return definitions;
-    }
-    __setError(error: keyof typeof this.errors, entity: string | UnverifiedEntityDefinition) {
-        if (error === "init") {
-            this.errors.init.messages.push(entity as string);
-        } else if (error === "clash") {
-            this.errors.clash.messages.push(entity as string);
-        } else if (error in this.errors) {
-            (this.errors[error] as any).entity.push(entity as UnverifiedEntityDefinition);
-        }
-        this.errors.hasError = true;
-    }
-    __setWarning(warning: keyof typeof this.warnings, entity: string | UnverifiedEntityDefinition) {
-        if (warning in this.warnings) {
-            if (isString(entity)) {
-                (this.warnings[warning] as any).messages.push(entity as string);
-            } else {
-                (this.warnings[warning] as any).entity.push(entity as UnverifiedEntityDefinition);
-            }
-        }
-        this.warnings.hasWarning = true;
-    }
-    __materialiseEntity({ id }: { id: string }): NormalisedEntityDefinition {
-        return {
-            "@id": id,
-            "@type": isURL(id) ? ["URL"] : ["Thing"],
-            name: id,
-        } as NormalisedEntityDefinition;
-    }
-    __confirmNoClash({
-        entity,
-        mintNewId = true,
-    }: {
-        entity: NormalisedEntityDefinition;
-        mintNewId?: boolean;
-    }): NormalisedEntityDefinition | boolean {
-        // if it looks like the root dataset - throw an error
-        //  can't have multiple root datasets
-        if (entity["@id"] === "./") {
-            this.__setError("clash", `You can't add an entity with id: './' as that will clash with the root dataset.`);
-            return false;
-            // throw new Error(
-            //     `You can't add an entity with id: './' as that will clash with the root dataset.`
-            // );
-        } else {
-            this.errors.hasError = false;
-            this.errors.clash.messages = [];
-        }
-        // if it looks like the root descriptor - throw an error
-        //  can't have multiple root descriptors
-        if (entity["@id"] === "ro-crate-metadata.json") {
-            throw new Error(
-                `You can't add an entity with id: 'ro-crate-metadata.json' as that will clash with the root descriptor.`
-            );
-        }
-
-        let idx = this.entityIdIndex[entity["@id"]];
-
-        // if there is no id clash, return the entity as is
-        if (idx === undefined) return entity;
-
-        // if the id is already used, check that the type is different
-        //   if it is, change the id and return the entity for inclusion
-        let entityLookup = this.crate["@graph"][idx];
-        if (!difference(entityLookup?.["@type"], entity["@type"]).length) {
-            return false;
-        } else {
-            // if get to here then there's a clash
-
-            if (mintNewId) {
-                const id = `e${this.graphLength + 1}`;
-                entity["@id"] = `#${id}`;
-                return entity;
-            } else {
-                throw new Error("That id is already used on another entity");
-            }
-        }
-    }
-    __updateEntityId({ oldId, newId }: { oldId: string; newId: string }) {
-        if (!oldId) throw new Error(`You must provide the id to change: oldId`);
-        if (!newId) throw new Error(`You must provide the id for the change: newId`);
-        // get the original entity and see if we can set this new id on it
-        //  we clone the original entity as we don't want to set anything yet
-        let indexRef = this.entityIdIndex[oldId];
-        // console.log("ORIGINAL ENTITY", JSON.stringify(this.crate["@graph"][indexRef], null, 2));
-        let entity = structuredClone(this.crate["@graph"][indexRef]);
-        entity["@id"] = newId;
-        entity = normalise(entity, this.graphLength);
-        entity = this.__confirmNoClash({ entity, mintNewId: false });
-        if (!entity) {
-            this.__setWarning("clash", `The entity ${entity["@id"]} already exists. Crate set back to it's original state.`);
-            return this.getEntity({ id: entity[indexRef] }) as NormalisedEntityDefinition;
-        } else {
-            this.warnings.hasWarning = false;
-            this.warnings.clash.messages = [];
-        }
-        // console.log("NEW ENTITY", JSON.stringify(entity, null, 2));
-
-        // get the entity using the original id and then walk the properties forward
-        //  to find what it links to. For each of those, set the reverse link to the new id
-        indexRef = this.entityIdIndex[oldId];
-        let oe = this.crate["@graph"][indexRef];
-        for (let [property, instances] of Object.entries(oe as NormalisedEntityDefinition)) {
-            if (this.coreProperties.includes(property)) continue;
-            // for (let instance of instances) {
-            //     if (instance?.["@id"]) {
-            //         // console.log(
-            //         //     "FORWARD LINKED ENTITY BEFORE",
-            //         //     property,
-            //         //     this.reverse[instance["@id"]][property]
-            //         // );
-            //         this.reverse[instance["@id"]][property].push({ "@id": entity["@id"] });
-            //         this.reverse[instance["@id"]][property] = this.reverse[instance["@id"]][
-            //             property
-            //         ].filter((i) => i["@id"] !== oldId);
-            //         this.reverse[instance["@id"]][property] = uniqBy(
-            //             this.reverse[instance["@id"]][property],
-            //             "@id"
-            //         );
-            //         // console.log(
-            //         //     "FORWARD LINKED ENTITY AFTER",
-            //         //     property,
-            //         //     this.reverse[instance["@id"]][property]
-            //         // );
-            //     }
-            // }
-            (instances as []).forEach((instance: EntityReference) => {
-                if (instance?.["@id"]) {
-                    // console.log(
-                    //     "FORWARD LINKED ENTITY BEFORE",
-                    //     property,
-                    //     this.reverse[instance["@id"]][property]
-                    // );
-                    this.reverse[instance["@id"]][property].push({ "@id": entity["@id"] });
-                    this.reverse[instance["@id"]][property] = this.reverse[instance["@id"]][
-                        property
-                    ].filter((i: EntityReference) => i["@id"] !== oldId);
-                    this.reverse[instance["@id"]][property] = uniqBy(
-                        this.reverse[instance["@id"]][property],
-                        "@id"
-                    );
-                    // console.log(
-                    //     "FORWARD LINKED ENTITY AFTER",
-                    //     property,
-                    //     this.reverse[instance["@id"]][property]
-                    // );
-                }
-            });
-        }
-
-        // walk the reverse links from this entity and update the forrward links
-        // now walk the reverse links of the entity to update the references to it
-        if (this.reverse[oldId]) {
-            for (let [property, links] of Object.entries(this.reverse[oldId])) {
-                // for (let link of links) {
-                //     let linkIndexRef = this.entityIdIndex[link["@id"]];
-                //     let linkedEntity = this.crate["@graph"][linkIndexRef];
-
-                //     // console.log("REVERSE LINKED ENTITY BEFORE", property, linkedEntity[property]);
-                //     linkedEntity[property].push({ "@id": entity["@id"] });
-                //     linkedEntity[property] = linkedEntity[property].filter(
-                //         (i) => i["@id"] !== oldId
-                //     );
-                //     // console.log("REVERSE LINKED ENTITY AFTER", property, linkedEntity[property]);
-                // }
-                (links as []).forEach((link: EntityReference) => {
-                    let linkIndexRef = this.entityIdIndex[link["@id"]];
-                    let linkedEntity = this.crate["@graph"][linkIndexRef];
-
-                    if (
-                        linkedEntity &&
-                        linkedEntity[property] &&
-                        Array.isArray(linkedEntity[property])
-                    ) {
-                        // console.log("REVERSE LINKED ENTITY BEFORE", property, linkedEntity[property]);
-                        linkedEntity[property].push({ "@id": entity["@id"] } as EntityReference);
-                        linkedEntity[property] = linkedEntity[property].filter((i) => {
-                            if (isEntityReference(i)) return i["@id"] !== oldId;
-                        });
-                    }
-                    // console.log("REVERSE LINKED ENTITY AFTER", property, linkedEntity[property]);
-                });
-            }
-        }
-
-        // now we can update the original entity in the graph
-        // set the new id on the entity itself
-        indexRef = this.entityIdIndex[oldId];
-        (this.crate["@graph"][indexRef] as EntityReference)["@id"] = entity["@id"];
-        // console.log("NEW ENTITY IN GRAPH", JSON.stringify(this.crate["@graph"][indexRef], null, 2));
-
-        // update the index ref's
-        delete this.entityIdIndex[oldId];
-        // console.log("OLDID lookup", this.entityIdIndex[oldId]);
-        this.entityIdIndex[entity["@id"]] = indexRef;
-        // console.log("NEWID lookup", this.entityIdIndex[entity["@id"]]);
-        // console.log(
-        //     "NEW ENTITY IN GRAPH",
-        //     JSON.stringify(this.crate["@graph"][this.entityIdIndex[entity["@id"]]], null, 2)
-        // );
-
-        // copy the reverse associations to the new id
-        //   and then remove the original reverse associations
-        this.reverse[entity["@id"]] = structuredClone(this.reverse[oldId]);
-        delete this.reverse[oldId];
-        // console.log(
-        //     "NEW ENTITY REVERSE CONNECTIONS",
-        //     entity["@id"],
-        //     JSON.stringify(this.reverse[entity["@id"]], null, 2)
-        // );
-
-        // console.log(JSON.stringify(this.crate["@graph"], null, 2));
-        // console.log("");
-        // console.log("");
-        // console.log("");
-        // console.log(JSON.stringify(this.reverse, null, 2));
-        // console.log("");
-        // console.log("");
-        // console.log("");
-        // console.log(JSON.stringify(this.entityIdIndex, null, 2));
-    }
-    __addReverse({
-        id,
-        property,
-        value,
-    }: {
-        id: string;
-        property: string;
-        value: EntityReference;
-    }) {
-        const linkIndexRef = this.entityIdIndex[value["@id"]];
-
-        if (linkIndexRef) {
-            if (!this.reverse[value["@id"]][property]) this.reverse[value["@id"]][property] = [];
-
-            let links = this.reverse[value["@id"]][property].map(
-                (l: EntityReference) => l?.["@id"]
-            );
-            if (!links.includes(id)) {
-                this.reverse[value["@id"]][property].push({ "@id": id });
-            }
-            // this.reverse[value["@id"]][property].push({ "@id": id });
-            // this.reverse[value["@id"]][property] = uniqBy(
-            //     this.reverse[value["@id"]][property],
-            //     "@id"
-            // );
-        }
-    }
-    __removeAssociations(entity: NormalisedEntityDefinition): NormalisedEntityDefinition {
-        for (let property of Object.keys(entity)) {
-            if (this.coreProperties.includes(property)) continue;
-            entity[property] = entity[property].filter((value) => {
-                if (isEntityReference(value)) return !value["@id"];
-            });
-            if (!entity[property].length) delete entity[property];
-        }
-        return entity;
-    }
-}
-
-function isEntityReference(obj: any): obj is EntityReference {
-    return (
-        typeof obj === "object" && obj !== null && "@id" in obj && typeof obj["@id"] === "string"
-    );
-}