Allow adding, removing, and changing the "canonical dataset" in the Editor

src/js/collections/metadata/eml/EMLAnnotations.js

@@ -1,75 +1,191 @@
 "use strict";
 
-define([
-  "jquery",
-  "underscore",
-  "backbone",
-  "models/metadata/eml211/EMLAnnotation",
-], function ($, _, Backbone, EMLAnnotation) {
+define(["underscore", "backbone", "models/metadata/eml211/EMLAnnotation"], (
+  _,
+  Backbone,
+  EMLAnnotation,
+) => {
+  const SCHEMA_ORG_SAME_AS = "http://www.w3.org/2002/07/owl#sameAs";
+  const PROV_WAS_DERIVED_FROM = "http://www.w3.org/ns/prov#wasDerivedFrom";
   /**
    * @class EMLAnnotations
    * @classdesc A collection of EMLAnnotations.
    * @classcategory Collections/Metadata/EML
    * @since 2.19.0
-   * @extends Backbone.Collection
+   * @augments Backbone.Collection
    */
-  var EMLAnnotations = Backbone.Collection.extend(
+  const EMLAnnotations = Backbone.Collection.extend(
     /** @lends EMLAnnotations.prototype */
     {
+      /** @inheritdoc */
+      model: EMLAnnotation,
+
       /**
-       * The reference to the model class that this collection is made of.
-       * @type EMLAnnotation
-       * @since 2.19.0
+       * Checks if this collection already has an annotation for the same
+       * property URI.
+       * @param {EMLAnnotation} annotation The EMLAnnotation to compare against
+       * the annotations already in this collection.
+       * @returns {boolean} Returns true is this collection already has an
+       * annotation for this property.
        */
-      model: EMLAnnotation,
+      hasDuplicateOf(annotation) {
+        // If there is at least one model in this collection and there is a
+        // propertyURI set on the given model,
+        if (this.length && annotation.get("propertyURI")) {
+          // Return whether or not there is a duplicate
+          const properties = this.pluck("propertyURI");
+          return properties.includes(annotation.get("propertyURI"));
+        }
+        // If this collection is empty or the propertyURI is falsey, return
+        // false
+        return false;
+      },
 
       /**
-       * Checks if this collection already has an annotation for the same property URI.
-       * @param {EMLAnnotation} annotation The EMLAnnotation to compare against the annotations already in this collection.
-       * @returns {Boolean} Returns true is this collection already has an annotation for this property.
-       * @since 2.19.0
+       * Removes the EMLAnnotation from this collection that has the same
+       * propertyURI as the given annotation. Then adds the given annotation to
+       * the collection. If no duplicate is found, the given annotation is still
+       * added to the collection.
+       * @param {EMLAnnotation} annotation The EMLAnnotation to replace
+       * duplicates with.
        */
-      hasDuplicateOf: function (annotation) {
-        try {
-          //If there is at least one model in this collection and there is a propertyURI set on the given model,
-          if (this.length && annotation.get("propertyURI")) {
-            //Return whether or not there is a duplicate
-            let properties = this.pluck("propertyURI");
-            return properties.includes(annotation.get("propertyURI"));
-          }
-          //If this collection is empty or the propertyURI is falsey, return false
-          else {
-            return false;
-          }
-        } catch (e) {
-          console.error("Could not check for a duplicate annotation: ", e);
-          return false;
+      replaceDuplicateWith(annotation) {
+        if (this.length && annotation.get("propertyURI")) {
+          const duplicates = this.findWhere({
+            propertyURI: annotation.get("propertyURI"),
+          });
+          this.remove(duplicates);
         }
+        this.add(annotation);
+      },
+
+      /**
+       * Find all annotations with the given propertyURI.
+       * @param {string} propertyURI The propertyURI to search for.
+       * @returns {EMLAnnotation[]} An array of EMLAnnotations with the given
+       * propertyURI.
+       * @since 0.0.0
+       */
+      findByProperty(propertyURI) {
+        return this.where({ propertyURI });
       },
 
       /**
-       * Removes the EMLAnnotation from this collection that has the same propertyURI as the given annotation.
-       * Then adds the given annotation to the collection. If no duplicate is found, the given annotation is still added
-       * to the collection.
-       * @param {EMLAnnotation} annotation
-       * @since 2.19.0
+       * Adds canonical dataset annotations to this collection. A canonical
+       * dataset is the one that is considered the authoritative version; the
+       * current EML doc being essentially a duplicate version.
+       * @param {string} sourceId The DOI or URL of the canonical dataset.
+       * @returns {void}
+       * @since 0.0.0
        */
-      replaceDuplicateWith: function (annotation) {
-        try {
-          if (this.length && annotation.get("propertyURI")) {
-            let duplicates = this.findWhere({
-              propertyURI: annotation.get("propertyURI"),
-            });
-            this.remove(duplicates);
-          }
-
-          this.add(annotation);
-        } catch (e) {
-          console.error(
-            "Could not replace the EMLAnnotation in the collection: ",
-            e,
-          );
+      addCanonicalDatasetAnnotation(sourceId) {
+        if (!sourceId) return null;
+        // TODO: Check that sourceId is a valid DOI or URL
+
+        // TODO: Check that there is not already a canonical dataset annotation
+        // before adding a new one, since there should only be one.
+        return this.add([
+          {
+            propertyLabel: "derivedFrom",
+            propertyURI: PROV_WAS_DERIVED_FROM,
+            valueLabel: sourceId,
+            valueURI: sourceId,
+          },
+          {
+            propertyLabel: "sameAs",
+            propertyURI: SCHEMA_ORG_SAME_AS,
+            valueLabel: sourceId,
+            valueURI: sourceId,
+          },
+        ]);
+      },
+
+      /**
+       * Find the annotations that make up the canonical dataset annotation. A
+       * canonical dataset is identified by having both a "derivedFrom" and a
+       * "sameAs" annotation with the same DOI or URL for the valueURI.
+       * @returns {object} An object with the derivedFrom and sameAs
+       * annotations.
+       * @since 0.0.0
+       */
+      findCanonicalDatasetAnnotation() {
+        // There must be at least one derivedFrom and one sameAs annotation
+        // for this to have a canonical dataset annotation
+        if (!this.length) return null;
+        const derivedFrom = this.findByProperty(PROV_WAS_DERIVED_FROM);
+        if (!derivedFrom?.length) return null;
+        const sameAs = this.findByProperty(SCHEMA_ORG_SAME_AS);
+        if (!sameAs?.length) return null;
+
+        // Find all pairs that have matching valueURIs
+        const pairs = [];
+        derivedFrom.forEach((derived) => {
+          sameAs.forEach((same) => {
+            if (derived.get("valueURI") === same.get("valueURI")) {
+              // TODO? Check that the URI is a valid DOI or URL
+              pairs.push({ derived, same, uri: derived.get("valueURI") });
+            }
+          });
+        });
+
+        // If there are multiple pairs, we cannot determine which is the
+        // canonical dataset.
+        if (pairs.length > 1 || !pairs.length) return null;
+
+        // There is only one pair, so return it
+        return pairs[0];
+      },
+
+      /**
+       * Updates the canonical dataset annotations to have the given ID. If
+       * there is no canonical dataset annotation, one is added. If the ID is a
+       * falsy value, the canonical dataset annotation is removed.
+       * @param {string} newSourceId The DOI or URL of the canonical dataset.
+       * @returns {object} An object with the derivedFrom and sameAs annotations
+       * if the canonical dataset annotations were updated.
+       * @since 0.0.0
+       */
+      updateCanonicalDataset(newSourceId) {
+        if (!newSourceId) {
+          this.removeCanonicalDatasetAnnotation();
+          return null;
         }
+        const canonical = this.findCanonicalDatasetAnnotation();
+        if (!canonical) {
+          return this.addCanonicalDatasetAnnotation(newSourceId);
+        }
+
+        const { derived, same, uri } = canonical;
+        if (uri === newSourceId) return null;
+
+        derived.set("valueURI", newSourceId);
+        derived.set("valueLabel", newSourceId);
+        same.set("valueURI", newSourceId);
+        same.set("valueLabel", newSourceId);
+
+        return [derived, same];
+      },
+
+      /**
+       * Removes the canonical dataset annotations from this collection.
+       * @returns {EMLAnnotation[]} The canonical dataset annotations that were
+       * removed.
+       * @since 0.0.0
+       */
+      removeCanonicalDatasetAnnotation() {
+        const canonical = this.findCanonicalDatasetAnnotation();
+        if (!canonical) return null;
+        return this.remove([canonical.derived, canonical.same]);
+      },
+
+      /**
+       * Returns the URI of the canonical dataset.
+       * @returns {string} The URI of the canonical dataset.
+       * @since 0.0.0
+       */
+      getCanonicalURI() {
+        const canonical = this.findCanonicalDatasetAnnotation();
+        return canonical?.uri;
       },
     },
   );

src/js/models/metadata/eml211/EML211.js

@@ -86,6 +86,7 @@ define([
           methods: new EMLMethods(), // An EMLMethods objects
           project: null, // An EMLProject object,
           annotations: null, // Dataset-level annotations
+          canonicalDataset: null,
           dataSensitivityPropertyURI:
             "http://purl.dataone.org/odo/SENSO_00000005",
           nodeOrder: [
@@ -143,6 +144,13 @@ define([
           this.set("synced", true);
         });
 
+        this.stopListening(this, "change:canonicalDataset");
+        this.listenTo(
+          this,
+          "change:canonicalDataset",
+          this.updateCanonicalDataset,
+        );
+
         //Create a Unit collection
         if (!this.units.length) this.createUnits();
       },
@@ -160,6 +168,17 @@ define([
         );
       },
 
+      updateCanonicalDataset() {
+        let uri = this.get("canonicalDataset");
+        uri = uri?.length ? uri[0] : null;
+        let annotations = this.get("annotations");
+        if (!annotations) {
+          annotations = new EMLAnnotations();
+          this.set("annotations", annotations);
+        }
+        annotations.updateCanonicalDataset(uri);
+      },
+
       /*
        * Maps the lower-case EML node names (valid in HTML DOM) to the camel-cased EML node names (valid in EML).
        * Used during parse() and serialize()
@@ -734,6 +753,16 @@ define([
           }
         }
 
+        // Once all the nodes have been parsed, check if any of the annotations
+        // make up a canonical dataset reference
+        const annotations = modelJSON["annotations"];
+        if (annotations) {
+          const canonicalDataset = annotations.getCanonicalURI();
+          if (canonicalDataset) {
+            modelJSON["canonicalDataset"] = canonicalDataset;
+          }
+        }
+
         return modelJSON;
       },
 

src/js/models/metadata/eml211/EMLAnnotation.js

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

src/js/templates/metadata/metadataOverview.html

@@ -94,3 +94,11 @@ <h5>Alternate Identifiers <i class="required-icon hidden" data-category="alterna
     list any additional identifiers that can be used to locate or label the dataset here.</p>
 	<p class="notification" data-category="alternateIdentifier"></p>
 </div>
+
+<div class="canonical-id basic-text-container" data-category="canonicalDataset">
+	<h5>Canonical Dataset <i class="required-icon hidden" data-category="canonicalDataset"></i></h5>
+	<p class="subtle">If this dataset is essentially a duplicate of a version
+	stored elsewhere, provide the ID of the original dataset here. This must be a
+	DOI or URL</p>
+	<p class="notification" data-category="canonicalDataset"></p>
+</div>

src/js/views/metadata/EML211View.js

@@ -302,6 +302,13 @@ define([
         );
         $(overviewEl).find(".altids").append(altIdsEls);
 
+        // Canonical Identifier
+        const canonicalIdEl = this.createBasicTextFields(
+          "canonicalDataset",
+          "Add a new canonical identifier",
+        );
+        $(overviewEl).find(".canonical-id").append(canonicalIdEl);
+
         //Usage
         //Find the model value that matches a radio button and check it
         // Note the replace() call removing newlines and replacing them with a single space
@@ -1909,7 +1916,7 @@ define([
                   .addClass("basic-text");
               textRow.append(input.clone().val(value));
 
-              if (category != "title")
+              if (category !== "title" && category !== "canonicalDataset")
                 textRow.append(
                   this.createRemoveButton(
                     null,
@@ -1922,7 +1929,11 @@ define([
               textContainer.append(textRow);
 
               //At the end, append an empty input for the user to add a new one
-              if (i + 1 == allModelValues.length && category != "title") {
+              if (
+                i + 1 == allModelValues.length &&
+                category !== "title" &&
+                category !== "canonicalDataset"
+              ) {
                 var newRow = $(
                   $(document.createElement("div")).addClass("basic-text-row"),
                 );
@@ -2006,7 +2017,12 @@ define([
         }
 
         //Add another blank text input
-        if ($(e.target).is(".new") && value != "" && category != "title") {
+        if (
+          $(e.target).is(".new") &&
+          value != "" &&
+          category != "title" &&
+          category !== "canonicalDataset"
+        ) {
           $(e.target).removeClass("new");
           this.addBasicText(e);
         }
@@ -2036,12 +2052,12 @@ define([
           allBasicTexts = $(
             ".basic-text.new[data-category='" + category + "']",
           );
-
         //Only show one new row at a time
         if (allBasicTexts.length == 1 && !allBasicTexts.val()) return;
         else if (allBasicTexts.length > 1) return;
         //We are only supporting one title right now
-        else if (category == "title") return;
+        else if (category === "title" || category === "canonicalDataset")
+          return;
 
         //Add another blank text input
         var newRow = $(document.createElement("div")).addClass(