Merge pull request #230 from phyloref/export-as-nquads

This PR upgrades @phyloref/phyx.js to the latest version, allowing us to use reference-based (model 2.0) expectations (#65) and to export the ontology in n-Quads (#222). A few phyx.js methods have been renamed or replaced since this code was written; this PR updates them so that phyloref resolution works again.

See #231 and #232 for some follow-up changes that will be needed after this PR.

Closes #65, closes #204, closes #222.

package.json

@@ -17,7 +17,7 @@
     "@fortawesome/fontawesome-svg-core": "^1.2.29",
     "@fortawesome/free-solid-svg-icons": "^5.13.1",
     "@fortawesome/vue-fontawesome": "^0.1.10",
-    "@phyloref/phyx": "^0.2.1",
+    "@phyloref/phyx": "^1.0.1",
     "bootstrap": "^4.5.0",
     "bootstrap-vue": "^2.15.0",
     "filesaver.js-npm": "^1.0.1",

src/components/sidebar/Sidebar.vue

@@ -66,6 +66,14 @@
           class="list-group-item list-group-item-action"
           href="javascript: void(0)"
           @click="downloadAsJSONLD()"
+        >
+          Export as JSON-LD
+        </a>
+
+        <a
+          class="list-group-item list-group-item-action"
+          href="javascript: void(0)"
+          @click="downloadAsNQuads()"
         >
           Export as ontology
         </a>
@@ -272,14 +280,6 @@ export default {
     examplePHYXURLs() {
       // Returns a list of example files to display in the "Examples" menu.
       return [
-        {
-          url: 'examples/fisher_et_al_2007.json',
-          title: 'Fisher et al, 2007',
-        },
-        {
-          url: 'examples/hillis_and_wilcox_2005.json',
-          title: 'Hillis and Wilcox, 2005',
-        },
         {
           url: 'examples/brochu_2003.json',
           title: 'Brochu 2003',
@@ -427,6 +427,20 @@ export default {
       saveAs(jsonldFile, `${this.downloadFilenameForPhyx}.jsonld`);
     },
 
+    downloadAsNQuads() {
+      // Exports the PHYX file as an OWL/N-Quads file, which can be opened in
+      // Protege or converted into other RDF formats.
+      const wrapped = new PhyxWrapper(this.$store.state.phyx.currentPhyx);
+
+      // TODO: we need a baseIRI here because of https://github.com/phyloref/phyx.js/issues/113
+      // Once that is fixed in phyx.js, we can remove it here.
+      wrapped.toRDF('https://example.phyloref.org/phyx#').then((content) => {
+        // Save to local hard drive.
+        const nqFile = new File([content], `${this.downloadFilenameForPhyx}.owl`, { type: 'application/n-quads;charset=utf-8' });
+        saveAs(nqFile, `${this.downloadFilenameForPhyx}.owl`);
+      });
+    },
+
     reasonOverPhyloreferences() {
       // Reason over all the phyloreferences and store the results on
       // the Vue model at vm.reasoningResults so we can access them.

src/components/specifiers/Specifier.vue

@@ -407,7 +407,7 @@ export default {
   computed: {
     nomenCodes: () => TaxonNameWrapper.getNomenclaturalCodes(),
     nomenclaturalCodeObj() {
-      return TaxonNameWrapper.getNomenCodeAsObject(this.enteredNomenclaturalCode);
+      return TaxonNameWrapper.getNomenCodeDetails(this.enteredNomenclaturalCode);
     },
     specifier() {
       // Check the specifierClass before we figure out how to construct the

src/store/modules/resolution.js

@@ -14,10 +14,14 @@ export default {
     reasoningResults: undefined,
   },
   getters: {
+    // TODO: the following base URIs need to be in this form because that's how they are rendered in the Phyx file.
+    // We previously used methods in phyx.js to coordinate these, but they were removed during a previous cleanup.
+    // So we should probably put them back.
+
     // Return a base URI for a given phylogeny.
-    getBaseURIForPhylogeny: (state, getters, rootState) => phylogeny => PhyxWrapper.getBaseURIForPhylogeny(rootState.phyx.currentPhyx.phylogenies.indexOf(phylogeny)),
+    getBaseURIForPhylogeny: (state, getters, rootState) => phylogeny => `#phylogeny${rootState.phyx.currentPhyx.phylogenies.indexOf(phylogeny)}`,
     // Return a base URI for a given phyloreference.
-    getBaseURIForPhyloref: (state, getters, rootState) => phyloref => PhyxWrapper.getBaseURIForPhyloref(rootState.phyx.currentPhyx.phylorefs.indexOf(phyloref)),
+    getBaseURIForPhyloref: (state, getters, rootState) => phyloref => `#phyloref${rootState.phyx.currentPhyx.phylorefs.indexOf(phyloref)}`,
     // Return the identifier for a given phylogeny. We will use getBaseURIForPhylogeny()
     // unless one has already been set.
     getPhylogenyId: (state, getters) => (phylogeny) => {