Support phylogenies and phyloreferences that cannot be parsed

src/components/modals/AdvancedOptionsModal.vue

@@ -115,11 +115,15 @@ export default {
       // Exports the PHYX file as an OWL/JSON-LD file, which can be opened in
       // Protege or converted into OWL/XML or other formats.
       const wrapped = new PhyxWrapper(this.$store.state.phyx.currentPhyx);
-      const content = [JSON.stringify([wrapped.asJSONLD()], undefined, 4)];
+      try {
+        const content = [JSON.stringify([wrapped.asJSONLD()], undefined, 4)];
 
-      // Save to local hard drive.
-      const jsonldFile = new File(content, 'download.jsonld', { type: 'application/json;charset=utf-8' });
-      saveAs(jsonldFile);
+        // Save to local hard drive.
+        const jsonldFile = new File(content, `${this.$store.getters.getDownloadFilenameForPhyx}.jsonld`, { type: 'application/json;charset=utf-8' });
+        saveAs(jsonldFile, `${this.$store.getters.getDownloadFilenameForPhyx}.jsonld`);
+      } catch (err) {
+        alert(`Could not convert Phyx to JSON-LD: ${err}`);
+      }
     },
   },
 };

src/components/phylogeny/PhylogenyView.vue

@@ -239,9 +239,13 @@ export default {
 
       // Look for an unbalanced Newick string.
       let parenLevels = 0;
+      let singleQuoteCount = 0;
+      let doubleQuoteCount = 0;
       for (let x = 0; x < newickTrimmed.length; x += 1) {
         if (newickTrimmed[x] === '(') parenLevels += 1;
         if (newickTrimmed[x] === ')') parenLevels -= 1;
+        if (newickTrimmed[x] === '\'') singleQuoteCount += 1;
+        if (newickTrimmed[x] === '"') doubleQuoteCount += 1;
       }
 
       if (parenLevels !== 0) {
@@ -254,6 +258,24 @@ export default {
         });
       }
 
+      if (singleQuoteCount % 2 > 0) {
+        errors.push({
+          title: "Unbalanced single quotes (') in Newick string",
+          message:
+            `Every single quote should be closed by another single quote, but this Newick string has ` +
+            `${singleQuoteCount} single quotes. Try doubling the single quote to escape it.`,
+        });
+      }
+
+      if (doubleQuoteCount % 2 > 0) {
+        errors.push({
+          title: 'Unbalanced double quotes (") in Newick string',
+          message:
+            `Every double quote should be closed by another double quote, but this Newick string has ` +
+            `${doubleQuoteCount} double quotes. Try doubling the double quote to escape it.`,
+        });
+      }
+
       // Finally, try parsing it with parseNewick and see if we get an error.
       try {
         parseNewick(newickTrimmed);

src/components/phylogeny/Phylotree.vue

@@ -75,10 +75,14 @@ export default {
       return this.phylogeny.newick || "()";
     },
     parsedNewick() {
-      return new PhylogenyWrapper(this.phylogeny).getParsedNewickWithIRIs(
-        this.$store.getters.getPhylogenyId(this.phylogeny),
-        newickParser
-      );
+      try {
+        return new PhylogenyWrapper(this.phylogeny).getParsedNewickWithIRIs(
+          this.$store.getters.getPhylogenyId(this.phylogeny),
+          newickParser
+        );
+      } catch {
+        return undefined;
+      }
     },
     newickErrors() {
       // Check to see if the newick could actually be parsed.

src/components/phyloref/PhylorefView.vue

@@ -648,14 +648,18 @@ export default {
     },
     getNodeLabels(phylogeny, nodeType) {
       // Return a list of node labels in a particular phylogeny.
-      return new PhylogenyWrapper(phylogeny).getNodeLabels(nodeType).sort();
+      try {
+        return new PhylogenyWrapper(phylogeny).getNodeLabels(nodeType).sort();
+      } catch {
+        return [];
+      }
     },
     getExpectedNodeLabel(phylogeny) {
       // Return the node label we expect this phyloref to resolve to on the
       // specified phylogeny.
       return this.$store.getters.getExpectedNodeLabel(
-        this.selectedPhyloref,
-        phylogeny,
+          this.selectedPhyloref,
+          phylogeny,
       );
     },
     getSpecifierLabel(specifier) {

src/components/phyx/PhyxView.vue

@@ -340,16 +340,21 @@ export default {
     getPhylorefExpectedNodeLabel(phyloref, phylogeny) {
       // Return a list of nodes that a phyloreference is expected to resolve to.
       return this.$store.getters.getExpectedNodeLabel(
-        phyloref,
-        phylogeny,
+          phyloref,
+          phylogeny,
       );
     },
     getNodesById(phylogeny, nodeId) {
       // Return all node labels with this nodeId in this phylogeny.
-      const parsed = new PhylogenyWrapper(phylogeny).getParsedNewickWithIRIs(
-        this.$store.getters.getPhylogenyId(phylogeny),
-        newickParser,
-      );
+      let parsed;
+      try {
+        parsed = new PhylogenyWrapper(phylogeny).getParsedNewickWithIRIs(
+            this.$store.getters.getPhylogenyId(phylogeny),
+            newickParser,
+        );
+      } catch {
+        return [];
+      }
 
       function searchNode(node, results = []) {
         if (has(node, '@id') && node['@id'] === nodeId) {

src/components/sidebar/Sidebar.vue

@@ -277,12 +277,26 @@ export default {
           url: 'examples/fisher_et_al_2007.json',
           title: 'Fisher et al, 2007',
         },
-	{
-	  url: 'examples/testudinata_phylonym.json',
-	  title: 'Testudinata from Phylonym',
-	},
+        {
+          url: "examples/testudinata_phylonym.json",
+          title: "Testudinata from Phylonym",
+        },
       ];
     },
+    wrappedPhyx() {
+      return new PhyxWrapper(
+        this.$store.state.phyx.currentPhyx,
+        newickParser
+      );
+    },
+    wrappedPhyxAsJSONLD() {
+      try {
+        return this.wrappedPhyx.asJSONLD();
+      } catch (err) {
+        alert(`Could not convert Phyx to JSON-LD: ${err}`);
+        return undefined;
+      }
+    },
     ...mapGetters([
       'phyxTitle',
     ]),
@@ -416,8 +430,9 @@ export default {
     downloadAsJSONLD() {
       // Exports the PHYX file as an OWL/JSON-LD file, which can be opened in
       // Protege or converted into OWL/XML or other formats.
-      const wrapped = new PhyxWrapper(this.$store.state.phyx.currentPhyx);
-      const content = [JSON.stringify([wrapped.asJSONLD()], undefined, 4)];
+      const jsonld = this.wrappedPhyxAsJSONLD;
+      if (!jsonld) return;
+      const content = [JSON.stringify([jsonld], undefined, 4)];
 
       // Save to local hard drive.
       const jsonldFile = new File(content, `${this.downloadFilenameForPhyx}.jsonld`, { type: 'application/json;charset=utf-8' });
@@ -427,15 +442,19 @@ export default {
     downloadAsNQuads() {
       // Exports the PHYX file as an OWL/N-Quads file, which can be opened in
       // Protege or converted into other RDF formats.
-      const wrapped = new PhyxWrapper(this.$store.state.phyx.currentPhyx);
+      const wrapped = this.wrappedPhyx;
 
       // 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`);
-      });
+      try {
+        wrapped.toRDF('https://example.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`);
+        });
+      } catch (err) {
+        alert(`Could not convert phylogeny to ontology: ${err}`);
+      }
     },
 
     reasonOverPhyloreferences() {
@@ -456,13 +475,15 @@ export default {
       const outerThis = this;
       Vue.nextTick(() => {
         // Prepare JSON-LD file for submission.
-        const jsonld = JSON.stringify([new PhyxWrapper(
-          outerThis.$store.state.phyx.currentPhyx,
-          newickParser,
-        ).asJSONLD()]);
+        const jsonld = outerThis.wrappedPhyxAsJSONLD;
+        if (!jsonld) {
+          outerThis.reasoningInProgress = false;
+          return;
+        }
+        const jsonldAsStr = JSON.stringify([jsonld]);
 
         // To improve upload speed, let's Gzip the file before upload.
-        const jsonldGzipped = pako.gzip(jsonld);
+        const jsonldGzipped = pako.gzip(jsonldAsStr);
 
         // Prepare request for submission.
         const query = $.param({

src/store/modules/resolution.js

@@ -89,9 +89,13 @@ export default {
       }
 
       // Is there a node on the phylogeny with the same label as this phyloreference?
-      const allNodeLabels = new PhylogenyWrapper(phylogeny).getNodeLabels();
-      if (phyloref.label && allNodeLabels.includes(phyloref.label)) {
-        return phyloref.label;
+      try {
+        const allNodeLabels = new PhylogenyWrapper(phylogeny).getNodeLabels();
+        if (phyloref.label && allNodeLabels.includes(phyloref.label)) {
+          return phyloref.label;
+        }
+      } catch {
+        return undefined;
       }
 
       // No expected node labels!