feat(R207): Update for R207.

BREAKING CHANGE: R207 taxonomy

assets/models/taxon-history.ts

@@ -7,6 +7,7 @@ export enum TaxonHistoryRelease {
   R89 = "89",
   R95 = "95",
   R202 = "202",
+  R207 = "207",
   NCBI = "NCBI"
 }
 
@@ -18,6 +19,7 @@ export const TaxonHistoryReleases = [
   TaxonHistoryRelease.R89,
   TaxonHistoryRelease.R95,
   TaxonHistoryRelease.R202,
+  TaxonHistoryRelease.R207,
   TaxonHistoryRelease.NCBI
 ]
 

components/genome/GenomeTaxonHistory.vue

@@ -177,7 +177,7 @@ export default Vue.extend({
   methods: {
     // Compute the taxon history URL for the current taxon
     getHistUrl(taxon: string) {
-      return `/taxon-history/?from=R80&to=R202&query=${encodeURIComponent(taxon)}`
+      return `/taxon-history?from=R80&to=R207&query=${encodeURIComponent(taxon)}`
     },
 
     // Retrieve the taxon history for this accession

components/index/NotifyBar.vue

@@ -1,13 +1,63 @@
 <template>
-  <div class="notifyBar body-2 text-center py-1">
-    <slot></slot>
+  <div v-if="isVisible" class="notifyBar py-1 d-flex">
+    <div class="d-flex ml-5" style="min-width: 30px;">
+    </div>
+    <div class="d-flex mx-auto my-auto body-2">
+      <slot></slot>
+    </div>
+    <div class="d-flex mr-5" style="min-width: 30px;">
+      <v-btn
+        color="#a0b8a0"
+        depressed
+        icon
+        small
+        @click="close"
+      >
+        <v-icon>
+          {{ mdiCloseCircleOutlineSvg }}
+        </v-icon>
+      </v-btn>
+    </div>
   </div>
 </template>
 
 <script lang="ts">
 import Vue from 'vue';
 
-export default Vue.extend({})
+import {mdiCloseCircleOutline} from '@mdi/js';
+
+export default Vue.extend({
+  props: {
+    uid: {
+      type: String,
+      required: true,
+    },
+  },
+  computed: {
+    cookieKey(): string {
+      return `gtdb-notify-bar-hidden-${this.uid}`;
+    }
+  },
+  data: () => ({
+    isVisible: true,
+    mdiCloseCircleOutlineSvg: mdiCloseCircleOutline,
+  }),
+  methods: {
+    close() {
+      this.$cookies.set(this.cookieKey, 'true', {
+        path: '/',
+        maxAge: 2147483647,
+        sameSite: true,
+      });
+      this.isVisible = false;
+    },
+  },
+  created() {
+    if (this.$cookies.get(this.cookieKey)) {
+      this.isVisible = false;
+    }
+  }
+})
 </script>
 
 <style scoped>

components/search/ResultsFromPreviousReleases.vue

@@ -44,7 +44,7 @@
 
             <!-- Rows -->
             <template v-slot:item.view="{ item }">
-              <nuxt-link :to="`/taxon-history?from=${item.firstSeen}&to=R202&query=${item.taxon}`">
+              <nuxt-link :to="`/taxon-history?from=${item.firstSeen}&to=R207&query=${item.taxon}`">
                 Taxon History ({{ item.firstSeen }} to {{ item.lastSeen }})
               </nuxt-link>
             </template>

components/stats/REDr207.vue

@@ -0,0 +1,32 @@
+<template>
+  <div class="mt-2">
+<!--    <h3>Bacteria</h3>-->
+<!--    <div id="fig_el730431405688597008165473308651"></div>-->
+
+<!--    <h3>Archaea</h3>-->
+<!--    <div id="fig_el729391400845065580326015787637"></div>-->
+
+  </div>
+</template>
+
+<script lang="ts">
+import Vue from 'vue';
+
+import * as d3 from 'd3v5';
+//@ts-ignore
+import mpld3 from 'mpld3';
+
+// const archaea = require('~/assets/data/stats/r202/red-archaea.json')
+// const bacteria = require('~/assets/data/stats/r202/red-bacteria.json')
+
+export default Vue.extend({
+  mounted() {
+    // mpld3.draw_figure("fig_el729391400845065580326015787637", archaea);
+    // mpld3.draw_figure("fig_el730431405688597008165473308651", bacteria);
+  }
+})
+</script>
+
+<style scoped>
+
+</style>

components/taxon-history/TaxonHistoryFullTaxonomy.vue

@@ -41,7 +41,7 @@
             <td v-if="currentTaxonIndex >= 0"
             >
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.d.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.d.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.d}`">
                   {{ item.taxonomy.d }}
                 </nuxt-link>
@@ -53,7 +53,7 @@
             </td>
             <td v-if="currentTaxonIndex >= 1">
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.p.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.p.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.p}`">
                   {{ item.taxonomy.p }}
                 </nuxt-link>
@@ -65,7 +65,7 @@
             </td>
             <td v-if="currentTaxonIndex >= 2">
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.c.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.c.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.c}`">
                   {{ item.taxonomy.c }}
                 </nuxt-link>
@@ -77,7 +77,7 @@
             </td>
             <td v-if="currentTaxonIndex >= 3">
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.o.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.o.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.o}`">
                   {{ item.taxonomy.o }}
                 </nuxt-link>
@@ -89,7 +89,7 @@
             </td>
             <td v-if="currentTaxonIndex >= 4">
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.f.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.f.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.f}`">
                   {{ item.taxonomy.f }}
                 </nuxt-link>
@@ -101,7 +101,7 @@
             </td>
             <td v-if="currentTaxonIndex >= 5">
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.g.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.g.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.g}`">
                   {{ item.taxonomy.g }}
                 </nuxt-link>
@@ -113,7 +113,7 @@
             </td>
             <td v-if="currentTaxonIndex >= 6">
               <!-- If this is the current release, link to the tree -->
-              <template v-if="item.release === 'R202' && item.taxonomy.s.length > 3">
+              <template v-if="item.release === 'R207' && item.taxonomy.s.length > 3">
                 <nuxt-link :to="`/tree?r=${item.taxonomy.s}`">
                   {{ item.taxonomy.s }}
                 </nuxt-link>

layouts/default.vue

@@ -216,6 +216,13 @@ export default {
         },
       ],
       navStatistics: [
+        {
+          icon: 'mdi-apps',
+          title: 'Release 207',
+          to: '/stats/r207',
+          nuxt: true,
+          external: false,
+        },
         {
           icon: 'mdi-apps',
           title: 'Release 202',

nuxt.config.js

@@ -48,7 +48,8 @@ export default {
   // Modules: https://go.nuxtjs.dev/config-modules
   modules: [// https://go.nuxtjs.dev/axios
     '@nuxtjs/axios', // https://go.nuxtjs.dev/pwa
-    '@nuxtjs/pwa' // https://pwa.nuxtjs.org/
+    '@nuxtjs/pwa', // https://pwa.nuxtjs.org/
+    'cookie-universal-nuxt' // https://www.npmjs.com/package/cookie-universal-nuxt
   ],
 
   // Axios module configuration: https://go.nuxtjs.dev/config-axios
@@ -120,7 +121,7 @@ export default {
     advancedMaxHistory: 50,  // Maximum number of history states to retain in advanced search
     captchaSiteKey: process.env.CAPTCHA_KEY,
     googleAnalyticsId: process.env.GA_TRACKING_ID,
-    latestStatsPageUrl: '/stats/r202',  // this is used to point to the latest stats page,
+    latestStatsPageUrl: '/stats/r207',  // this is used to point to the latest stats page,
     nuxtVersion: version
   },
 

package.json

@@ -13,6 +13,7 @@
   "dependencies": {
     "@nuxtjs/axios": "^5.13.6",
     "@nuxtjs/pwa": "^3.3.5",
+    "cookie-universal-nuxt": "^2.1.5",
     "core-js": "^3.21.1",
     "d3-sankey": "^0.12.3",
     "d3-scale-chromatic": "^3.0.0",
@@ -22,7 +23,7 @@
     "nuxt": "^2.15.8",
     "nuxt-typed-vuex": "^0.3.0",
     "vue-gtag": "^1.16.1",
-    "vuetify": "^2.6.3"
+    "vuetify": "^2.6.4"
   },
   "devDependencies": {
     "@babel/eslint-parser": "^7.17.0",