Merge branch 'master' into improve-documentation

.github/workflows/deploy-to-github-pages.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Build Vue page in /docs
         run: |
           npm install
-          VUE_APP_VERSION=$GITHUB_REF_NAME npm run build
+          VITE_APP_VERSION=$GITHUB_REF_NAME npm run build
           
       - name: Deploy /docs to branch gh-pages
         uses: JamesIves/github-pages-deploy-action@v4

package.json

@@ -27,7 +27,7 @@
     "lodash": "^4.17.19",
     "newick-js": "^1.2.1",
     "pako": "^2.1.0",
-    "phylotree": "^1.4.0",
+    "phylotree": "^2.0.1",
     "popper.js": "^1.16.1",
     "vue": "^2.7.7",
     "vue-cookies": "^1.8.1",

src/App.vue

@@ -61,7 +61,7 @@ export default {
     AdvancedOptionsModal,
   },
   data: () => ({
-    version: process.env.VUE_APP_VERSION,
+    version: import.meta.env.VITE_APP_VERSION,
   }),
   computed: mapState({
     display: state => state.ui.display,

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

@@ -290,9 +290,13 @@ 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) {
@@ -305,6 +309,24 @@ 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

@@ -16,6 +16,16 @@
     <div v-else class="phylotreeContainer">
       <div :id="'phylogeny' + phylogenyIndex" class="col-md-12 phylogeny" />
       <ResizeObserver @notify="redrawTree" />
+      <button
+        type="button"
+        class="btn btn-primary"
+        @click="exportAsNexus()"
+        data-toggle="tooltip"
+        data-placement="bottom"
+        title="Download Nexus file with annotations of where phyloreferences resolve"
+      >
+        Download as Nexus
+      </button>
     </div>
   </div>
 </template>
@@ -30,7 +40,8 @@ import { uniqueId, has } from "lodash";
 import { phylotree, newickParser } from "phylotree";
 import jQuery from "jquery";
 import { PhylogenyWrapper, PhylorefWrapper } from "@phyloref/phyx";
-import {addCustomMenu} from "phylotree/src/render/menus";
+import { addCustomMenu } from "phylotree/src/render/menus";
+import { saveAs } from "filesaver.js-npm";
 
 /*
  * Note that this requires the Phylotree Javascript to be loaded in the HTML
@@ -75,10 +86,14 @@ 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.
@@ -130,6 +145,121 @@ export default {
     this.redrawTree();
   },
   methods: {
+    exportAsNexus() {
+      // Store a list of annotations containing both double quotes and single quotes.
+      let annotations_containing_single_and_double_quotes = [];
+
+      // Export this phylogeny as a Nexus string in a .nex file for download.
+      const newickStr = this.tree.getNewick((node) => {
+        // Is the resolved node for this phyloref? If so, let's make an annotation.
+        if (
+          this.phyloref !== undefined &&
+          has(node, "data") &&
+          has(node.data, "@id")
+        ) {
+          const annotations = [];
+          const data = node.data;
+
+          const convertToNexusAnnotationValue = (str) => {
+            // We really just need to wrap this in double-quotes, which means we need to filter out existing double
+            // quotes. We can do that by replacing them with a single quote. However, if there are already single
+            // quotes in the string, then this is a non-reversible action, so we should warn the user before doing
+            // that. If we need to do that, we add the annotations to annotations_containing_single_and_double_quotes,
+            // and ask the user for confirmation before export.
+            if (str.indexOf("'") >= 0 && str.indexOf('"') >= 0) {
+              annotations_containing_single_and_double_quotes.push(str);
+            }
+
+            // Replace double-quotes with a single quote.
+            return '"' + str.replaceAll('"', "'") + '"';
+          };
+
+          if (
+            this.$store.getters
+              .getResolvedNodesForPhylogeny(this.phylogeny, this.phyloref)
+              .includes(data["@id"])
+          ) {
+            if (has(this.phyloref, "@id")) {
+              annotations.push(
+                "phyloref:actual=" +
+                  convertToNexusAnnotationValue(this.phyloref["@id"])
+              );
+            }
+
+            if (has(this.phyloref, "label")) {
+              annotations.push(
+                "phyloref:actualLabel=" +
+                  convertToNexusAnnotationValue(this.phyloref["label"])
+              );
+            }
+
+            // We don't know what to call this phyloref, but nevertheless we label it minimally.
+            if (!has(this.phyloref, "@id") && !has(this.phyloref, "label"))
+              annotations.push("phyloref:actual=");
+          }
+
+          if (
+            this.selectedNodeLabel &&
+            this.selectedNodeLabel.toLowerCase() === data.name.toLowerCase()
+          ) {
+            if (has(this.phyloref, "@id")) {
+              annotations.push(
+                "phyloref:expected=" +
+                  convertToNexusAnnotationValue(this.phyloref["@id"])
+              );
+            }
+
+            if (has(this.phyloref, "label")) {
+              annotations.push(
+                "phyloref:expectedLabel=" +
+                  convertToNexusAnnotationValue(this.phyloref["label"])
+              );
+            }
+
+            // We don't know what to call this phyloref, but nevertheless we label it minimally.
+            if (!has(this.phyloref, "@id") && !has(this.phyloref, "label"))
+              annotations.push("phyloref:expected=");
+          }
+          console.log("Annotations: ", annotations);
+
+          if (annotations.length === 0) return undefined;
+          else return `[&${annotations.join(",")}]`;
+        }
+
+        return undefined;
+      });
+
+      // Create a Nexus file to store this `klados_tree` in.
+      const nexusStr = `#NEXUS\n\nBEGIN TREES;\n  TREE klados_tree = ${newickStr}\nEND;\n`;
+
+      // If there are annotations containing both single and double quotes, we report them here and
+      // request confirmation from the user before exporting data that can't be exported.
+      if (annotations_containing_single_and_double_quotes.length > 0) {
+        const example_annotations = annotations_containing_single_and_double_quotes.slice(0, 3);
+        if (
+          !window.confirm(
+            `Some annotations (such as ${example_annotations.join(
+              "; "
+            )}) contain both single quotes and double quotes. To comply with NEXUS format, the double quotes need ` +
+              "to be converted to single quotes, but this will be non-reversible because the string already contains " +
+              "single quotes. Do you still want to export this NEXUS file?"
+          )
+        ) {
+          // User doesn't want to do this export. Cancel this operation.
+          return;
+        }
+      }
+
+      // Write Nexus file to a location chosen by the user.
+      const filename = `${this.$store.getters.getDownloadFilenameForPhyx}.nex`;
+      // Save to local hard drive.
+      const newickFile = new File([nexusStr], filename, {
+        type: "text/plain;charset=utf-8",
+      });
+      // With charset=utf-8, saveAs defaults to adding a Unicode BOM.
+      // This will confuse downstream files, so we force it off here.
+      saveAs(newickFile, filename, { autoBom: false });
+    },
     recurseNodes(node, func, nodeCount = 0, parentCount = undefined) {
       // Recurse through PhyloTree nodes, executing function on each node.
       //  - node: The node to recurse from. The function will be called on node
@@ -245,20 +375,17 @@ export default {
               const newName = window.prompt(
                 `Rename node named '${existingName}' to:`
               );
-              // Apparently IE7 and IE8 will return the string 'undefined' if the user doesn't
-              // enter anything.
-              if (!newName || newName === "undefined") {
+              if (newName === null) {
+                // This means the user clicked "Cancel", so don't do anything.
+              } else if (!newName || newName === "undefined") {
+                // Apparently IE7 and IE8 will return the string 'undefined' if the user doesn't
+                // enter anything.
+                //
                 // Remove the current label.
                 node.name = "";
               } else {
                 // Set the new label.
-                const escapedName = newName.replace("'", "''");
-                // If the name contains whitespace, escape it.
-                if (/\w/.test(escapedName)) {
-                  node.name = "'" + escapedName + "'";
-                } else {
-                  node.name = escapedName;
-                }
+                node.name = newName;
               }
 
               // Export the entire phylogeny as a Newick string, and store that
@@ -385,9 +512,17 @@ export default {
               pinningNodeChildrenIRIs.add(source_id);
               this.recurseNodes(source, (node) => {
                 pinningNodeChildrenIRIs.add(node["@id"]);
-                console.log("Found child", node["@id"], "for source", source_id);
+                console.log(
+                  "Found child",
+                  node["@id"],
+                  "for source",
+                  source_id
+                );
               });
-              console.log("Set pinningNodeChildrenIRIs to ", pinningNodeChildrenIRIs);
+              console.log(
+                "Set pinningNodeChildrenIRIs to ",
+                pinningNodeChildrenIRIs
+              );
 
               element.classed("descendant-of-pinning-node-branch", true);
             } else if (pinningNodeChildrenIRIs.has(source_id)) {

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

@@ -403,14 +403,22 @@ export default {
     },
     getPhylorefExpectedNodeLabel(phyloref, phylogeny) {
       // Return a list of nodes that a phyloreference is expected to resolve to.
-      return this.$store.getters.getExpectedNodeLabel(phyloref, phylogeny);
+      return this.$store.getters.getExpectedNodeLabel(
+          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) {