Merge pull request #2551 from NCEAS/feature-2542-add-source-dataset

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

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

@@ -1,75 +1,281 @@
 "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
+       * Find all annotations that have the same property & value URIs & labels.
+       * Only returns the models that are duplicates, not the original. The original
+       * is the first instance found in the collection.
+       * @returns {EMLAnnotation[]} An array of EMLAnnotations that are duplicates.
+       * @since 0.0.0
        */
-      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"));
+      getDuplicates() {
+        const groups = {};
+        let duplicates = [];
+
+        // Group models by their serialized attributes
+        this.each((model) => {
+          // Serialize the model's attributes to create a unique key
+          const key = JSON.stringify(model.attributes);
+
+          // Group models by the serialized key
+          if (groups[key]) {
+            groups[key].push(model);
+          } else {
+            groups[key] = [model];
           }
-          //If this collection is empty or the propertyURI is falsey, return false
-          else {
-            return false;
+        });
+
+        // Identify duplicates in each group
+        Object.values(groups).forEach((group) => {
+          if (group.length > 1) {
+            // Add all but one model from each group to the duplicates array
+            duplicates = duplicates.concat(group.slice(1));
           }
-        } catch (e) {
-          console.error("Could not check for a duplicate annotation: ", e);
-          return false;
+        });
+
+        return duplicates;
+      },
+
+      /**
+       * 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.
+       */
+      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 });
+      },
+
+      /**
+       * 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
+       */
+      addCanonicalDatasetAnnotation(sourceId) {
+        if (!sourceId) return null;
+        return this.add([
+          {
+            propertyLabel: "derivedFrom",
+            propertyURI: PROV_WAS_DERIVED_FROM,
+            valueLabel: sourceId,
+            valueURI: sourceId,
+            isCanonicalDataset: true,
+          },
+          {
+            propertyLabel: "sameAs",
+            propertyURI: SCHEMA_ORG_SAME_AS,
+            valueLabel: sourceId,
+            valueURI: sourceId,
+            isCanonicalDataset: true,
+          },
+        ]);
+      },
+
+      /**
+       * 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")) {
+              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 left in this case
+        const canonAnnos = pairs[0];
+
+        // Make sure each annotation has the isCanonicalDataset flag set,
+        // we will use it later, e.g. in validation
+        canonAnnos.derived.set("isCanonicalDataset", true);
+        canonAnnos.same.set("isCanonicalDataset", true);
+
+        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 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
+       * Removes the canonical dataset annotations from this collection.
+       * @returns {EMLAnnotation[]} The canonical dataset annotations that were
+       * removed.
+       * @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);
+      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;
+      },
+
+      /** @inheritdoc */
+      validate() {
+        // Remove any totally empty annotations
+        this.remove(this.filter((annotation) => annotation.isEmpty()));
+
+        // Remove annotations with the same value URI & property URI
+        const duplicates = this.getDuplicates();
+        if (duplicates.length) {
+          this.remove(duplicates);
+        }
+
+        // Validate each annotation
+        const errors = this.map((annotation) => annotation.validate());
+
+        // Remove any empty errors
+        const filteredErrors = errors.filter((error) => error);
+
+        // Each annotation validation is an array, flatten them to one array
+        const flatErrors = [].concat(...filteredErrors);
+
+        if (!filteredErrors.length) return null;
+
+        // Put canonicalDataset annotation errors in their own category
+        // so they can be displayed in the special canonicalDataset field.
+        const canonicalErrors = [];
+        const errorsToRemove = [];
+        // Check for a canonicalDataset annotation error
+        flatErrors.forEach((annotationError, i) => {
+          if (annotationError.isCanonicalDataset) {
+            canonicalErrors.push(annotationError);
+            errorsToRemove.push(i);
           }
+        });
+
+        // Remove canonicalDataset errors from the annotation errors
+        // backwards so we don't mess up the indexes.
+        errorsToRemove.reverse().forEach((i) => {
+          flatErrors.splice(i, 1);
+        });
 
-          this.add(annotation);
-        } catch (e) {
-          console.error(
-            "Could not replace the EMLAnnotation in the collection: ",
-            e,
-          );
+        if (canonicalErrors.length) {
+          // The two canonicalDataset errors are the same, so just show one.
+          flatErrors.push({
+            attr: "canonicalDataset",
+            message: canonicalErrors[0].message,
+          });
         }
+
+        return flatErrors;
       },
     },
   );