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Add EMLAnnotation methods for canonical datasets
- Add methods to add, remove, update, and find sameAs and derivedFrom annotations representing canonical datasets Issue #2542
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‎src/js/collections/metadata/eml/EMLAnnotations.js

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Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@ define(["underscore", "backbone", "models/metadata/eml211/EMLAnnotation"], (
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Backbone,
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EMLAnnotation,
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) => {
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const SCHEMA_ORG_SAME_AS = "http://www.w3.org/2002/07/owl#sameAs";
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const PROV_WAS_DERIVED_FROM = "http://www.w3.org/ns/prov#wasDerivedFrom";
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/**
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* @class EMLAnnotations
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* @classdesc A collection of EMLAnnotations.
@@ -56,6 +58,135 @@ define(["underscore", "backbone", "models/metadata/eml211/EMLAnnotation"], (
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}
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this.add(annotation);
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},
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/**
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* Find all annotations with the given propertyURI.
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* @param {string} propertyURI The propertyURI to search for.
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* @returns {EMLAnnotation[]} An array of EMLAnnotations with the given
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* propertyURI.
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* @since 0.0.0
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*/
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findByProperty(propertyURI) {
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return this.where({ propertyURI });
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},
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/**
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* Adds canonical dataset annotations to this collection. A canonical
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* dataset is the one that is considered the authoritative version; the
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* current EML doc being essentially a duplicate version.
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* @param {string} sourceId The DOI or URL of the canonical dataset.
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* @returns {void}
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* @since 0.0.0
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*/
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addCanonicalDatasetAnnotation(sourceId) {
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if (!sourceId) return null;
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// TODO: Check that sourceId is a valid DOI or URL
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// TODO: Check that there is not already a canonical dataset annotation
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// before adding a new one, since there should only be one.
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return this.add([
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{
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propertyLabel: "derivedFrom",
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propertyURI: PROV_WAS_DERIVED_FROM,
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valueLabel: sourceId,
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valueURI: sourceId,
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},
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{
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propertyLabel: "sameAs",
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propertyURI: SCHEMA_ORG_SAME_AS,
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valueLabel: sourceId,
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valueURI: sourceId,
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},
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]);
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},
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/**
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* Find the annotations that make up the canonical dataset annotation. A
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* canonical dataset is identified by having both a "derivedFrom" and a
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* "sameAs" annotation with the same DOI or URL for the valueURI.
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* @returns {object} An object with the derivedFrom and sameAs
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* annotations.
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* @since 0.0.0
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*/
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findCanonicalDatasetAnnotation() {
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// There must be at least one derivedFrom and one sameAs annotation
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// for this to have a canonical dataset annotation
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if (!this.length) return null;
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const derivedFrom = this.findByProperty(PROV_WAS_DERIVED_FROM);
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if (!derivedFrom?.length) return null;
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const sameAs = this.findByProperty(SCHEMA_ORG_SAME_AS);
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if (!sameAs?.length) return null;
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// Find all pairs that have matching valueURIs
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const pairs = [];
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derivedFrom.forEach((derived) => {
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sameAs.forEach((same) => {
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if (derived.get("valueURI") === same.get("valueURI")) {
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// TODO? Check that the URI is a valid DOI or URL
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pairs.push({ derived, same, uri: derived.get("valueURI") });
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}
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});
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});
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// If there are multiple pairs, we cannot determine which is the
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// canonical dataset.
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if (pairs.length > 1 || !pairs.length) return null;
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// There is only one pair, so return it
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return pairs[0];
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},
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/**
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* Updates the canonical dataset annotations to have the given ID. If
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* there is no canonical dataset annotation, one is added. If the ID is a
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* falsy value, the canonical dataset annotation is removed.
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* @param {string} newSourceId The DOI or URL of the canonical dataset.
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* @returns {object} An object with the derivedFrom and sameAs annotations
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* if the canonical dataset annotations were updated.
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* @since 0.0.0
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*/
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updateCanonicalDataset(newSourceId) {
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if (!newSourceId) {
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this.removeCanonicalDatasetAnnotation();
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return null;
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}
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const canonical = this.findCanonicalDatasetAnnotation();
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if (!canonical) {
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return this.addCanonicalDatasetAnnotation(newSourceId);
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}
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const { derived, same, uri } = canonical;
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if (uri === newSourceId) return null;
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derived.set("valueURI", newSourceId);
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derived.set("valueLabel", newSourceId);
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same.set("valueURI", newSourceId);
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same.set("valueLabel", newSourceId);
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return [derived, same];
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},
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/**
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* Removes the canonical dataset annotations from this collection.
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* @returns {EMLAnnotation[]} The canonical dataset annotations that were
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* removed.
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* @since 0.0.0
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*/
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removeCanonicalDatasetAnnotation() {
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const canonical = this.findCanonicalDatasetAnnotation();
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if (!canonical) return null;
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return this.remove([canonical.derived, canonical.same]);
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},
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/**
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* Returns the URI of the canonical dataset.
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* @returns {string} The URI of the canonical dataset.
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* @since 0.0.0
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*/
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getCanonicalURI() {
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const canonical = this.findCanonicalDatasetAnnotation();
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return canonical?.uri;
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},
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},
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);
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‎src/js/models/metadata/eml211/EMLAnnotation.js

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,8 @@ define(["jquery", "underscore", "backbone"], function ($, _, Backbone) {
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},
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initialize: function (attributes, opions) {
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this.on("change", this.trickleUpChange);
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this.stopListening(this, "change", this.trickleUpChange);
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this.listenTo(this, "change", this.trickleUpChange);
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},
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parse: function (attributes, options) {
@@ -175,7 +176,7 @@ define(["jquery", "underscore", "backbone"], function ($, _, Backbone) {
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/* Let the top level package know of attribute changes from this object */
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trickleUpChange: function () {
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MetacatUI.rootDataPackage.packageModel.set("changed", true);
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MetacatUI.rootDataPackage.packageModel?.set("changed", true);
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},
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},
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);

‎test/js/specs/unit/collections/metadata/eml/EMLAnnotations.spec.js

Lines changed: 67 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,10 @@ define([
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const should = chai.should();
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const expect = chai.expect;
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10-
describe("Accordion Test Suite", () => {
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const SCHEMA_ORG_SAME_AS = "http://www.w3.org/2002/07/owl#sameAs";
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const PROV_WAS_DERIVED_FROM = "http://www.w3.org/ns/prov#wasDerivedFrom";
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describe("EML Annotations Test Suite", () => {
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const state = cleanState(() => {
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const annotations = new EMLAnnotations({
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propertyLabel: "Property Label",
@@ -45,5 +48,68 @@ define([
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state.annotations.remove(state.annotations.at(0));
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state.annotations.length.should.equal(0);
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});
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it("finds annotations by property", () => {
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state.annotations
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.findByProperty("http://example.com/property")
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.length.should.equal(1);
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});
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it("adds canonical dataset annotations", () => {
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const annotations =
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
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state.annotations.length.should.equal(3);
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annotations[0].get("propertyURI").should.equal(PROV_WAS_DERIVED_FROM);
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annotations[0].get("valueURI").should.equal("http://example.com");
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annotations[1].get("propertyURI").should.equal(SCHEMA_ORG_SAME_AS);
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annotations[1].get("valueURI").should.equal("http://example.com");
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});
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68+
it("finds canonical dataset annotations", () => {
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
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const annotations = state.annotations.findCanonicalDatasetAnnotation();
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annotations.should.have.property("derived");
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annotations.should.have.property("same");
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annotations.derived.get("valueURI").should.equal("http://example.com");
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annotations.same.get("valueURI").should.equal("http://example.com");
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annotations.derived
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.get("propertyURI")
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.should.equal(PROV_WAS_DERIVED_FROM);
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annotations.same.get("propertyURI").should.equal(SCHEMA_ORG_SAME_AS);
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});
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it("updates canonical dataset annotations", () => {
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
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state.annotations.updateCanonicalDataset("http://newexample.com");
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state.annotations.getCanonicalURI().should.equal("http://newexample.com");
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});
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87+
it("removes canonical dataset annotations", () => {
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
89+
state.annotations.removeCanonicalDatasetAnnotation();
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state.annotations.length.should.equal(1);
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});
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93+
it("gets the URI of the canonical dataset", () => {
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
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state.annotations.getCanonicalURI().should.equal("http://example.com");
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});
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it("adds annotations if they didn't exist when updating", () => {
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state.annotations.updateCanonicalDataset("http://example.com");
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state.annotations.length.should.equal(3);
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});
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it("removes canonical dataset annotations if the ID is falsy", () => {
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
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state.annotations.updateCanonicalDataset("");
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state.annotations.length.should.equal(1);
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});
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it("does not update canonical dataset annotations if the ID is the same", () => {
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state.annotations.addCanonicalDatasetAnnotation("http://example.com");
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state.annotations.updateCanonicalDataset("http://example.com");
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state.annotations.length.should.equal(3);
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});
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});
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});

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