Store curation information and default nomenclatural code in cookies

package.json

@@ -27,6 +27,7 @@
     "newick-js": "^1.1.1",
     "popper.js": "^1.16.1",
     "vue": "^2.6.11",
+    "vue-cookies": "^1.8.1",
     "vue-resize": "^0.4.5",
     "vuex": "^3.5.1",
     "x-hub-signature": "^1.2.0"

src/App.vue

@@ -46,6 +46,14 @@ import PhyxView from './components/phyx/PhyxView.vue';
 import AboutCurationToolModal from './components/modals/AboutCurationToolModal.vue';
 import AdvancedOptionsModal from './components/modals/AdvancedOptionsModal.vue';
 
+// Load some configuration options.
+import {
+  COOKIE_EXPIRY,
+  COOKIE_CURATOR_NAME,
+  COOKIE_CURATOR_EMAIL,
+  COOKIE_CURATOR_ORCID,
+} from './config';
+
 export default {
   name: 'App',
   components: {
@@ -74,6 +82,24 @@ export default {
     },
   },
   created() {
+    // We store some information as browser cookies so that users don't need to re-enter them
+    // every time. One of these (the default nomenclatural code) is entirely handled in modules/phyx.js.
+    // Three of them need to be set on the default empty Phyx file here:
+    if (this.$cookies.get(COOKIE_CURATOR_NAME)) {
+      this.$store.commit('setCurator', { name: this.$cookies.get(COOKIE_CURATOR_NAME) });
+    }
+
+    if (this.$cookies.get(COOKIE_CURATOR_EMAIL)) {
+      this.$store.commit('setCurator', { email: this.$cookies.get(COOKIE_CURATOR_EMAIL) });
+    }
+
+    if (this.$cookies.get(COOKIE_CURATOR_ORCID)) {
+      this.$store.commit('setCurator', { orcid: this.$cookies.get(COOKIE_CURATOR_ORCID) });
+    }
+
+    // Reset the "changed" flags (in case the above code changed the Phyx file)
+    this.$store.commit('setLoadedPhyx');
+
     // If someone tries to navigate away from the window while the
     // PHYX has been modified, ask users to confirm before leaving.
     // Confirmation message to display to the user. Note that modern

src/components/phyx/PhyxView.vue

@@ -65,8 +65,8 @@
                 @change="$store.commit('setDefaultNomenCodeURI', { defaultNomenclaturalCodeURI: $event.target.value })"
               >
                 <option
-                  v-for="(nomenCode, nomenCodeIndex) of nomenCodes"
-                  :value="nomenCode.uri"
+                  v-for="nomenCode of nomenCodes"
+                  :value="nomenCode.iri"
                 >
                   {{ nomenCode.label }}
                 </option>

src/config.js

@@ -18,4 +18,17 @@ module.exports = {
   // Open Tree Taxonomy IDs
   // (https://github.com/OpenTreeOfLife/germinator/wiki/Synthetic-tree-API-v3#induced_subtree)
   OPEN_TREE_INDUCED_SUBTREE_URL: 'https://api.opentreeoflife.org/v3/tree_of_life/induced_subtree',
+
+  // The default cookie expiry setting (see https://www.npmjs.com/package/vue-cookies for formats)
+  COOKIE_EXPIRY: '30d', // Expire cookies in 30 days
+
+  // Cookie names to use for:
+  // - the default nomenclatural code
+  COOKIE_DEFAULT_NOMEN_CODE_URI: 'kladosDefaultNomenclaturalCodeURI',
+  // - curator name
+  COOKIE_CURATOR_NAME: 'kladosCuratorName',
+  // - curator e-mail address
+  COOKIE_CURATOR_EMAIL: 'kladosCuratorEmail',
+  // - curator ORCID
+  COOKIE_CURATOR_ORCID: 'kladosCuratorORCID',
 };

src/main.js

@@ -27,6 +27,7 @@ Vue.prototype.$config = require('./config.js');
 // Add additional features to Vue.
 Vue.use(BootstrapVue);
 Vue.use(VueResize);
+Vue.use(require('vue-cookies')); // Use https://www.npmjs.com/package/vue-cookies
 
 // Turn off the Vue production tip on the console on Vue startup.
 Vue.config.productionTip = false;

src/store/modules/phyx.js

@@ -17,8 +17,23 @@ import {
   OPEN_TREE_ABOUT_URL,
   OPEN_TREE_TNRS_MATCH_NAMES_URL,
   OPEN_TREE_INDUCED_SUBTREE_URL,
+
+  COOKIE_EXPIRY,
+  COOKIE_DEFAULT_NOMEN_CODE_URI, COOKIE_CURATOR_NAME, COOKIE_CURATOR_EMAIL, COOKIE_CURATOR_ORCID,
 } from '../../config';
 
+// Shared code for reading and writing cookies.
+
+/** Get a cookie from the browser. */
+function getKladosCookie($cookies, keyName, valueIfNotSet = undefined) {
+  return $cookies.get(keyName) || valueIfNotSet;
+}
+
+/** Set a cookie on the browser. */
+function setKladosCookie($cookies, keyName, value, expiry = COOKIE_EXPIRY) {
+  $cookies.set(keyName, value, expiry);
+}
+
 export default {
   state: {
     // The currently loaded Phyx file. All methods modify and change this variable.
@@ -39,8 +54,10 @@ export default {
       return !isEqual(state.currentPhyx, state.loadedPhyx);
     },
     getDefaultNomenCodeURI(state) {
+      // If no default nomenclatural code is set in the Phyx file, we will attempt to look up that information
+      // using a cookie.
       return state.currentPhyx.defaultNomenclaturalCodeURI
-        || TaxonNameWrapper.UNKNOWN_CODE;
+          || getKladosCookie(Vue.$cookies, COOKIE_DEFAULT_NOMEN_CODE_URI, TaxonNameWrapper.UNKNOWN_CODE);
     },
     getDownloadFilenameForPhyx(state) {
       // Return a filename to be used to name downloads of this Phyx document.
@@ -131,6 +148,9 @@ export default {
         throw new Error('No default nomenclatural code URI provided to setDefaultNomenCodeURI');
       }
 
+      // Overwrite the current default nomenclatural code cookie.
+      setKladosCookie(Vue.$cookies, COOKIE_DEFAULT_NOMEN_CODE_URI, payload.defaultNomenclaturalCodeURI);
+
       Vue.set(state.currentPhyx, 'defaultNomenclaturalCodeURI', payload.defaultNomenclaturalCodeURI);
     },
     duplicatePhyloref(state, payload) {
@@ -144,9 +164,18 @@ export default {
     },
     setCurator(state, payload) {
       // Set the curator name, e-mail address or (eventually) ORCID.
-      if (has(payload, 'name')) Vue.set(state.currentPhyx, 'curator', payload.name);
-      if (has(payload, 'email')) Vue.set(state.currentPhyx, 'curatorEmail', payload.email);
-      if (has(payload, 'orcid')) Vue.set(state.currentPhyx, 'curatorORCID', payload.orcid);
+      if (has(payload, 'name')) {
+        setKladosCookie(Vue.$cookies, COOKIE_CURATOR_NAME, payload.name);
+        Vue.set(state.currentPhyx, 'curator', payload.name);
+      }
+      if (has(payload, 'email')) {
+        setKladosCookie(Vue.$cookies, COOKIE_CURATOR_EMAIL, payload.email);
+        Vue.set(state.currentPhyx, 'curatorEmail', payload.email);
+      }
+      if (has(payload, 'orcid')) {
+        setKladosCookie(Vue.$cookies, COOKIE_CURATOR_ORCID, payload.orcid);
+        Vue.set(state.currentPhyx, 'curatorORCID', payload.orcid);
+      }
     },
   },
   actions: {