From f77534939e7bec20346958158b3ee30eda4dfe7b Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Wed, 11 Sep 2019 16:56:20 -0400
Subject: [PATCH 01/10] Assocation Table and Taxon Filtering WIP

---
 src/api/BioLink.js                   |  71 ++----
 src/components/AssocTable.vue        | 366 ++++++++++++---------------
 src/components/NodeSidebar.vue       |  23 +-
 src/components/NodeSidebarFacets.vue | 102 --------
 src/components/TaxonFilter.vue       | 150 +++++++++++
 src/lib/TaxonMap.js                  |   5 +
 src/views/Node.vue                   |  54 +---
 7 files changed, 354 insertions(+), 417 deletions(-)
 delete mode 100644 src/components/NodeSidebarFacets.vue
 create mode 100644 src/components/TaxonFilter.vue

diff --git a/src/api/BioLink.js b/src/api/BioLink.js
index a71646a3..a3fb28d1 100644
--- a/src/api/BioLink.js
+++ b/src/api/BioLink.js
@@ -1,5 +1,5 @@
 import axios from 'axios';
-import { labelToId, isTaxonCardType } from '../lib/TaxonMap';
+import {labelToId, isTaxonCardType, isSubjectCardType} from '../lib/TaxonMap';
 
 // TIP: Example of a domain-specific (as opposed to a generic loadJSON)
 // service function. This set of domain-specific services will pretty much
@@ -23,20 +23,6 @@ const servers = {
     'owlsim_services_url': 'https://beta.monarchinitiative.org/owlsim',
     'analytics_id': '',
     'biolink_url': 'https://api-dev.monarchinitiative.org/api/',
-    // 'biolink_url': 'https://api.monarchinitiative.org/api/',
-  },
-
-  production: {
-    'type': 'production',
-    'app_base': 'https://monarchinitiative.org',
-    'scigraph_url': 'https://scigraph-ontology.monarchinitiative.org/scigraph/',
-    'scigraph_data_url': 'https://scigraph-data.monarchinitiative.org/scigraph/',
-    'golr_url': 'https://solr.monarchinitiative.org/solr/golr/',
-    'search_url': 'https://solr.monarchinitiative.org/solr/search/',
-    'owlsim_services_url': 'https://monarchinitiative.org/owlsim',
-    'analytics_id': '',
-    // 'biolink_url': 'https://api.monarchinitiative.org/api/',
-    'biolink_url': 'https://api.monarchinitiative.org/api/',
   },
 
   beta: {
@@ -51,11 +37,22 @@ const servers = {
     'biolink_url': 'https://api-dev.monarchinitiative.org/api/'
   },
 
+  production: {
+    'type': 'production',
+    'app_base': 'https://monarchinitiative.org',
+    'scigraph_url': 'https://scigraph-ontology.monarchinitiative.org/scigraph/',
+    'scigraph_data_url': 'https://scigraph-data.monarchinitiative.org/scigraph/',
+    'golr_url': 'https://solr.monarchinitiative.org/solr/golr/',
+    'search_url': 'https://solr.monarchinitiative.org/solr/search/',
+    'owlsim_services_url': 'https://monarchinitiative.org/owlsim',
+    'analytics_id': '',
+    'biolink_url': 'https://api.monarchinitiative.org/api/',
+  }
+
 };
 
 const productionServers = [
-  // 'localhost',
-  'monarchinitiative.org',
+  'monarchinitiative.org'
 ];
 
 const defaultApiServer =
@@ -69,7 +66,7 @@ const biolink = serverConfiguration.biolink_url;
 const scigraph = serverConfiguration.scigraph_url;
 
 /**
-  Lighter-weight BL node info. Used by LocalNav.vue
+  Lighter-weight BioLink node info. Used by LocalNav.vue
  */
 
 export async function getNodeSummary(nodeId, nodeType) {
@@ -138,8 +135,6 @@ export async function getNode(nodeId, nodeType) {
     [
       axios.get(bioentityUrl, { params }),
       axios.get(getIdentifierUrl),
-      // axios.get(golrUrl1, {}),
-      // axios.get(golrUrl2, {}),
     ]
   ).then(
     axios.spread(
@@ -423,33 +418,21 @@ export async function getNodeAssociations(nodeType, nodeId, cardType, taxons, pa
   const biolinkMappedCardType = getBiolinkAnnotation(cardType);
   const urlExtension = `${nodeType}/${nodeId}/${biolinkMappedCardType}`;
   const url = `${baseUrl}${urlExtension}`;
-  const useTaxonRestriction = taxons && taxons.length > 0 && isTaxonCardType(cardType);
-
-  if (useTaxonRestriction) {
-    // console.log('getNodeAssociations', nodeType, nodeId, cardType);
-    // console.log(JSON.stringify(params, null, 2));
-    // console.log(JSON.stringify(taxons, null, 2));
-    params.start = 0;
-    params.rows = 10000;
-  }
-  const response = await axios.get(url, { params });
 
-  if (useTaxonRestriction) {
-    response.data.associations = response.data.associations.filter((d) => {
-      const subjTaxon = d.subject.taxon;
-      const objTaxon = d.object.taxon;
-      let result = false;
-      if (subjTaxon.id !== null && taxons.indexOf(subjTaxon.id) >= 0) {
-        result = true;
-      }
-      if (objTaxon.id !== null && taxons.indexOf(objTaxon.id) >= 0) {
-        result = true;
-      }
-      return result;
-    });
-    response.data.numFound = response.data.associations.length;
+
+  if (isTaxonCardType(cardType)) {
+    params.facet = true;
+    params.facet_fields = "object_taxon";
+    if(isSubjectCardType(cardType)){
+      params.facet_fields = "subject_taxon";
+    }
+
+    if(taxons != null && taxons !== -1){
+      params.taxon = taxons.length > 1 ? taxons.join(","): taxons[0];
+    }
   }
 
+  const response = await axios.get(url, { params });
   return response;
 }
 
diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index c492be09..6e1a8b20 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -6,22 +6,24 @@
         {{ dataError }}
       </div>
     </div>
-
-    <div v-show="!dataFetched && !dataError" class="loading-div">
-
-      <b-spinner class="loading-spinner" type="grow" label="Spinning"/>
-    </div>
-
-    <div v-show="dataFetched && !dataError">
-
-      <h5>
-        &nbsp;<strong>{{ totalAssociations }}</strong>&nbsp;
-        <strong>{{ cardType }}</strong> associations.
-      </h5>
-
+    <div v-show="!dataError && initialLoad">
+      <taxon-filter @toggle-filter="toggleTaxonFilter($event)"  :is-visible="isFacetsShowing" v-model="taxonFilter"></taxon-filter>
+      <div>
+        <h5>
+          &nbsp;<strong>{{ totalAssociations }}</strong>&nbsp;
+          <strong>{{ cardType }}</strong> associations.
+        </h5>
+
+        <b-button class="taxon-filter" size="sm" v-if="nodeType === 'gene' && hasTaxon"
+                  @click="toggleTaxonFilter()"
+                  variant="primary">
+        <i class="fa fa-filter" aria-hidden="true"></i> Taxon Filter</b-button>
+        <br>
+      </div>
       <b-table
         ref="tableRef"
         :items="rowsProvider"
+        :busy="tableBusy"
         :fields="fields"
         :current-page="currentPage"
         :per-page="rowsPerPage"
@@ -36,6 +38,12 @@
           <i>{{ data.item.taxonLabel }}</i>
         </template>
 
+        <template slot="table-busy">
+          <div class="text-center text-danger my-2">
+            <b-spinner class="loading-spinner" label="Spinning"></b-spinner>
+          </div>
+        </template>
+
         <template slot="assocObject" slot-scope="data">
           <template v-if="data.item.objectLink">
             <strong>
@@ -125,14 +133,8 @@
               &blacktriangleright;&nbsp;
             </span>
 
-            <span
-              v-for="(icon, index) in data.item.supportIcons"
-              :key="index"
-            >
-              <i
-                :class="icon"
-                class="fa fa-fw"
-              />
+            <span v-for="(icon, index) in data.item.supportIcons" :key="index">
+              <i :class="icon" class="fa fa-fw"></i>
             </span>
             <small>{{ data.item.supportLength }}</small>
           </b-button>
@@ -146,8 +148,7 @@
               class="row"
             >
               <div class="col-9 px-1">
-                <template
-                  v-if="support.useRouter">
+                <template v-if="support.useRouter">
                   <router-link :to="support.url">
                     {{ support.label }}
                   </router-link>
@@ -170,43 +171,32 @@
                 <small>{{ support.type }}</small>
               </div>
               <div class="col-1 px-1" style="text-align: center;">
-                <i
-                  :class="support.typeIcon"
-                  class="fa fa-fw text-info"
-                />
+                <i :class="support.typeIcon" class="fa fa-fw text-info"></i>
               </div>
             </div>
           </div>
         </template>
       </b-table>
-      <div
-        v-if="totalAssociations > rowsPerPage">
         <b-pagination
           v-model="currentPage"
           :per-page="rowsPerPage"
-          :total-rows="totalAssociations"
+          :total-rows="paginationTotals"
           class="pag-width my-1"
           align="center"
-          size="md"
-        />
-      </div>
+          size="md"></b-pagination>
     </div>
   </div>
 </template>
 
 <script>
-import * as BL from '@/api/BioLink';
+import * as bioLinkService from '@/api/BioLink';
 import sourceToImage from '../lib/sources';
 import { isTaxonCardType } from '../lib/TaxonMap';
-
-function isFrequencyOnsetType(nodeType, cardType) {
-  return (nodeType === 'disease' && cardType === 'phenotype') ||
-         (nodeType === 'phenotype' && cardType === 'disease');
-}
-
+import TaxonFilter from '@/components/TaxonFilter.vue';
 
 export default {
   components: {
+    'taxon-filter': TaxonFilter,
   },
   props: {
     nodeId: {
@@ -221,69 +211,74 @@ export default {
       type: String,
       required: true
     },
-    cardCounts: {
+    taxonCounts: {
       type: Object,
+      required: true,
+    },
+    isFacetsShowing: {
+      type: Boolean,
       required: false,
-      default: null,
     },
-    facets: {
-      type: Object,
-      default: null,
-      required: false
-    }
   },
   data() {
     return {
       currentPage: 1,
-      rowsPerPage: 25,
+      rowsPerPage: 10,
       totalAssociations: 0,
+      paginationTotals: 0,
       hasTaxon: false,
+      taxonLoaded : false,
       hasFrequencyOnset: false,
       associationData: '',
-      dataFetched: false,
+      tableBusy: false,
       dataError: false,
-      dataFetchedPage: 0,
-      dataFetchedRowsPerPage: 0,
+      initialLoad: false,
       fields: [],
       rows: [],
       lastSelection: [],
+      taxonFilter: {
+        counts: {},
+        taxons: {}
+      },
+      filterActive: null
     };
   },
   watch: {
     cardType() {
-      this.dataFetched = false;
       this.dataError = false;
       window.scroll(0, 0);
       this.currentPage = 1;
       this.generateFields();
 
       this.$refs.tableRef.refresh();
-    },
-    facets: {
-      handler() {
-        this.currentPage = 1;
-        this.$refs.tableRef.refresh();
-      },
-      deep: true
     }
   },
   mounted() {
     this.generateFields();
   },
   methods: {
-    hasFalseFacets() {
-      let foundFalseFacets = false;
-      Object.entries(this.facets.selectedTaxons)
+    filterTable(row, filter){
+      return this.taxonFilter.taxons[row.taxonId];
+    },
+    toggleTaxonFilter(shouldApply) {
+      if(this.isFacetsShowing && shouldApply){
+        this.$refs.tableRef.refresh();
+      }
+      this.$emit('toggle-facets');
+    },
+    hasFalseFilter() {
+      let foundFalseTaxons = false;
+      Object.entries(this.taxonFilter.taxons)
         .forEach((elem) => {
           if (!elem[1]) {
-            foundFalseFacets = true;
+            foundFalseTaxons = true;
           }
         });
-      return foundFalseFacets;
+      return foundFalseTaxons;
     },
-    trueFacets() {
+    trueTaxonFilters() {
       const truth = [];
-      Object.entries(this.facets.selectedTaxons)
+      Object.entries(this.taxonFilter.taxons)
         .forEach((elem) => {
           if (elem[1]) {
             truth.push(elem[0]);
@@ -292,9 +287,8 @@ export default {
       return truth;
     },
     allFacets() {
-      return Object.entries(this.facets.selectedTaxons).map(elem => elem[0]);
+      return Object.entries(this.taxonFilter.taxons).map(elem => elem[0]);
     },
-
     async rowsProvider(ctx, callback) {
       this.fetchData().then(() => {
         callback(this.rows);
@@ -302,93 +296,46 @@ export default {
         callback([]);
       });
     },
-
-    keyMap(key) {
-      const keyMappings = {
-        'Skeletal system': 'HP:0000924',
-        'Limbs': 'HP:0040064',
-        'Nervous system': 'HP:0000707',
-        'Head or neck': 'HP:0000152',
-        'Metabolism/homeostasis': 'HP:0001939',
-        'Cardiovascular system': 'HP:0001626',
-        'Integument': 'HP:0001574',
-        'Genitourinary system': 'HP:0000119',
-        'Eye': 'HP:0000478',
-        'Musculature': 'HP:0003011',
-        'Neoplasm': 'HP:0002664',
-        'Digestive system': 'HP:0025031',
-        'Immune System': 'HP:0002715',
-        'Blood and blood-forming tissues': 'HP:0001871',
-        'Endocrine': 'HP:0000818',
-        'Respiratory system': 'HP:0002086',
-        'Ear': 'HP:0000598',
-        'Connective tissue': 'HP:0003549',
-        'Prenatal development or birth': 'HP:0001197',
-        'Growth': 'HP:0001507',
-        'Constitutional': 'HP:0025142',
-        'Thoracic cavity': 'HP:0045027',
-        'Breast': 'HP:0000769',
-        'Voice': 'HP:0001608',
-        'Cellular': 'HP:0025354',
-      };
-      return keyMappings[key];
-    },
-
-    async fetchData() {
+    async fetchData(reset) {
       const that = this;
-      if (that.dataFetchedPage === that.currentPage
-           && that.dataFetchedRowsPerPage === that.rowsPerPage) {
-        console.log('####fetchData inhibited due to cached values.');
-      }
-      else {
-        this.dataFetched = false;
-        this.dataError = false;
-        try {
-          const params = {
-            fetch_objects: true,
-            start: ((this.currentPage - 1) * this.rowsPerPage),
-            rows: this.rowsPerPage
-          };
-
-          const taxons = this.hasFalseFacets() ? this.trueFacets() : null;
-          const associationsResponse = await BL.getNodeAssociations(
-            this.nodeType,
-            this.nodeId,
-            this.cardType,
-            taxons,
-            params
-          );
-          // console.log('associationsResponse');
-          // console.log(JSON.stringify(associationsResponse, null, 2));
-
-          if (!associationsResponse.data
-              || !associationsResponse.data.associations) {
-            that.associationData = null;
-            throw new Error('BL.getNodeAssociations() returned no data');
-          }
-          that.associationData = associationsResponse.data;
-          that.dataFetched = true;
-          that.dataFetchedPage = this.currentPage;
-          that.dataFetchedRowsPerPage = this.currentPage;
-
-          // associationData.associations.forEach(a => {
-          //   console.log(a.subject.label, a.subject.taxon.label);
-          // });
-          // that.currentPage = 1;
-          that.populateRows();
+      this.tableBusy = true;
+      this.dataError = false;
+      this.initialLoad = true;
+      try {
+        const params = {
+          fetch_objects: true,
+          start: ((this.currentPage - 1) * this.rowsPerPage),
+          rows: this.rowsPerPage
+        };
+
+        const taxons = this.hasFalseFilter() ? this.trueTaxonFilters() : null;
+        const associationsResponse = await bioLinkService.getNodeAssociations(
+          this.nodeType,
+          this.nodeId,
+          this.cardType,
+          taxons,
+          params
+        );
+        if (!associationsResponse.data || !associationsResponse.data.associations) {
+          that.associationData = null;
+          throw new Error('BioLink returned no data');
         }
-        catch (e) {
-          that.dataError = e;
-          console.log('BioLink Error', e);
+        that.associationData = associationsResponse.data;
+        if(reset){
+          this.currentPage = 1;
         }
+        that.tableBusy = false;
+        that.populateRows();
+      }
+      catch (e) {
+        that.dataError = e;
+        console.log('BioLink Error', e);
       }
     },
-
     fixupRelation(elem, nodeType, cardType) {
       const relation = elem.relation;
 
       if (!relation) {
-        console.log('fixupRelation NO RELATION');
         console.log(JSON.stringify(elem, null, 2));
         elem.relation = {
           label: 'Unknown',
@@ -549,62 +496,70 @@ export default {
         }
 
         const supportLength = support.length;
-        if (objectTaxon.id && this.allFacets().includes(objectTaxon.id) && !this.trueFacets().includes(objectTaxon.id)) {
-          // console.log('skipping', objectTaxon.id, elem);
+        let simplifiedCardType = this.cardType;
+        if (simplifiedCardType === 'interaction' || simplifiedCardType === 'ortholog-phenotype' || simplifiedCardType === 'ortholog-disease') {
+          simplifiedCardType = 'gene';
+          objectTaxon = this.parseTaxon(subjectElem);
         }
-        else {
-          let simplifiedCardType = this.cardType.replace(/ortholog-/g, '');
-          if (simplifiedCardType === 'interaction' || simplifiedCardType === 'homolog' ||
-                  simplifiedCardType === 'phenotype' || simplifiedCardType === 'disease') {
-            simplifiedCardType = 'gene';
-            objectTaxon = this.parseTaxon(subjectElem);
-          }
 
-          let objectLink = `/${simplifiedCardType}/${objectElem.id}`;
-          if (objectElem.id.indexOf(':.well-known') === 0) {
-            objectLink = null;
-          }
-          const subjectLink = `/${this.nodeType}/${subjectElem.id}`;
-
-          this.fixupRelation(elem, this.nodeType, this.cardType);
-
-          this.rows.push({
-            publications: pubs,
-            publicationsLength: pubsLength,
-            annotationType: this.cardType,
-            evidence,
-            evidenceLength,
-            support,
-            supportLength,
-            supportIcons,
-            objectCurie: objectElem.id,
-            sources: elem.provided_by,
-            sourcesLength: elem.provided_by.length,
-            assocObject: objectElem.label,
-            objectLink,
-            assocSubject: subjectElem.label,
-            subjectLink,
-            taxonLabel: objectTaxon.label,
-            taxonId: objectTaxon.id,
-            relation: elem.relation,
-            frequency: elem.frequency,
-            onset: elem.onset,
-            _showDetails: false,
-          });
+        let objectLink = `/${simplifiedCardType}/${objectElem.id}`;
+        if (objectElem.id.indexOf(':.well-known') === 0) {
+          objectLink = null;
+        }
+        const subjectLink = `/${this.nodeType}/${subjectElem.id}`;
+
+        this.fixupRelation(elem, this.nodeType, this.cardType);
+        this.rows.push({
+          publications: pubs,
+          publicationsLength: pubsLength,
+          annotationType: this.cardType,
+          evidence,
+          evidenceLength,
+          support,
+          supportLength,
+          supportIcons,
+          objectCurie: objectElem.id,
+          sources: elem.provided_by,
+          sourcesLength: elem.provided_by.length,
+          assocObject: objectElem.label,
+          objectLink,
+          assocSubject: subjectElem.label,
+          subjectLink,
+          taxonLabel: objectTaxon.label,
+          taxonId: objectTaxon.id,
+          relation: elem.relation,
+          frequency: elem.frequency,
+          onset: elem.onset,
+          _showDetails: false,
+        });
 
-          elem.relation.url = this.relationHref(elem.relation);
-          if (elem.frequency) {
-            elem.frequency.url = this.frequencyHref(elem.frequency);
-          }
-          if (elem.onset) {
-            elem.onset.url = this.onsetHref(elem.onset);
-          }
+        elem.relation.url = this.relationHref(elem.relation);
+        if (elem.frequency) {
+          elem.frequency.url = this.frequencyHref(elem.frequency);
+        }
+        if (elem.onset) {
+          elem.onset.url = this.onsetHref(elem.onset);
         }
       });
 
-      // console.log('this.associationData', this.associationData.numFound, this.rows.length);
-      // console.log(JSON.stringify(this.associationData.associations, null, 2));
-      this.totalAssociations = this.associationData.numFound;
+      if(isTaxonCardType(this.cardType) && !this.taxonLoaded){
+        const taxonFacetTarget = Object.keys(this.associationData.facet_counts)[0];
+        Object.keys(this.associationData.facet_counts[taxonFacetTarget]).forEach(key => {
+          this.taxonFilter.taxons[key] = true;
+        });
+        this.taxonFilter.counts = this.associationData.facet_counts[taxonFacetTarget];
+        this.taxonLoaded = true;
+      }
+      this.paginationTotals = this.getTotalRowCounts();
+      console.log(this.paginationTotals);
+      this.totalAssociations = this.associationData.numFound
+    },
+    getTotalRowCounts(){
+      let count = 0;
+      for(let taxon of this.trueTaxonFilters()){
+        count += this.taxonFilter.counts[taxon];
+      }
+      return count;
     },
     generateFields() {
       this.hasTaxon = false;
@@ -636,7 +591,7 @@ export default {
         },
       ];
 
-      if (isFrequencyOnsetType(this.nodeType, this.cardType)) {
+      if (this.isFrequencyOnsetType(this.nodeType, this.cardType)) {
         this.hasFrequencyOnset = true;
         fields.splice(3, 0, {
           key: 'frequency',
@@ -690,7 +645,6 @@ export default {
       return val.charAt(0)
         .toUpperCase() + val.slice(1);
     },
-
     pubHref(curie) {
       return `/publication/${curie}`;
       // const identifier = curie.split(/[:]+/).pop();
@@ -722,6 +676,10 @@ export default {
         .split(/[.]+/)[0]
         .toUpperCase();
       return result;
+    },
+    isFrequencyOnsetType(nodeType, cardType) {
+      return (nodeType === 'disease' && cardType === 'phenotype') ||
+              (nodeType === 'phenotype' && cardType === 'disease');
     }
   }
 };
@@ -731,13 +689,17 @@ export default {
 @import "~@/style/variables";
 .assoc-table {
   width: 100%;
-  .loading-div {
-      margin: 15% calc(50% - 14%);
-      text-align: center;
+  .loading-spinner {
+    color: $monarch-bg-color;
+  }
+
+  .taxon-filter {
+    background-color: $monarch-bg-color;
+    margin-bottom: 15px;
   }
 
   .table {
-    width:inherit;
+    width: 100%;
   }
   .table.b-table tr {
     outline: 1px solid lightgray;
diff --git a/src/components/NodeSidebar.vue b/src/components/NodeSidebar.vue
index c6bc67a3..4291506f 100644
--- a/src/components/NodeSidebar.vue
+++ b/src/components/NodeSidebar.vue
@@ -27,13 +27,6 @@
             <span class="list-group-item-value">Neighbors</span>
           </b-link>
         </li>
-
-        <li class="list-group-item list-group-item-squat">
-          <b-link :disabled="facetsDisabled" @click="toggleFacets()">
-            <i class="fa fa-fw fa-cubes"/>
-            <span class="list-group-item-value">Facets</span>
-          </b-link>
-        </li>
         <li
           v-for="cardType in cardsToDisplay"
           :class="{ active: expandedCard === cardType }"
@@ -42,7 +35,7 @@
           <a :href="'#' + cardType" @click="expandCard(cardType)">
             <img :src="$parent.icons[cardType]" class="entity-type-icon">
             <span class="list-group-item-value">
-              {{ $parent.labels[cardType] }} <span class="count">{{ cardCounts[cardType] }}</span>
+              {{ $parent.labels[cardType] }} <!--<span class="count">{{ cardCounts[cardType] }}</span>-->
             </span>
           </a>
         </li>
@@ -50,10 +43,6 @@
       </ul>
     </div>
 
-    <node-sidebar-facets
-      :is-visible="isFacetsShowing"
-      v-model="facetObject"
-    />
 
   </div>
 
@@ -64,7 +53,6 @@
 import * as biolinkService from '@/api/BioLink';
 
 import NodeSidebarNeighborhood from '@/components/NodeSidebarNeighborhood.vue';
-import NodeSidebarFacets from '@/components/NodeSidebarFacets.vue';
 import vClickOutside from 'v-click-outside';
 
 export default {
@@ -72,7 +60,6 @@ export default {
 
   components: {
     'node-sidebar-neighborhood': NodeSidebarNeighborhood,
-    'node-sidebar-facets': NodeSidebarFacets,
   },
   directives: {
     clickOutside: vClickOutside.directive
@@ -113,11 +100,6 @@ export default {
       required: false,
       default: null,
     },
-    facetObject: {
-      type: Object,
-      required: false,
-      default: null,
-    },
     isNeighborhoodShowing: {
       type: Boolean,
       required: false,
@@ -138,9 +120,6 @@ export default {
     neighborhoodDisabled() {
       return (!this.superclasses || this.superclasses.length === 0) && (!this.subclasses || this.subclasses.length === 0);
     },
-    facetsDisabled() {
-      return false; // this.nodeType === 'publication';
-    },
     debugServerURL() {
       const debugHash = (this.$route.hash.length > 1)
         ? (this.$route.hash + 's')
diff --git a/src/components/NodeSidebarFacets.vue b/src/components/NodeSidebarFacets.vue
deleted file mode 100644
index e0f356be..00000000
--- a/src/components/NodeSidebarFacets.vue
+++ /dev/null
@@ -1,102 +0,0 @@
-<template>
-  <div
-    id="facets"
-    :class="{ active: isVisible }"
-    class="container-fluid">
-
-    <div
-      v-for="(value, key) in model.selectedTaxons"
-      :key="key"
-      class="facet-item row">
-
-      <div
-        class="col-10">
-        <b-form-checkbox
-          v-model="model.selectedTaxons[key]"
-        >
-          <i>{{ idToLabel(key) }}</i>&nbsp;({{ key }})
-        </b-form-checkbox>
-      </div>
-
-      <div
-        class="col-2">
-        {{ idToCount(key) }}
-      </div>
-
-    </div>
-  </div>
-</template>
-
-
-<script>
-import { idToLabel } from '../lib/TaxonMap';
-
-export default {
-  name: 'NodeSidebarFacets',
-
-  model: {
-    prop: 'model',
-  },
-
-  props: {
-    model: {
-      type: Object,
-      required: false,
-      default: null,
-    },
-    isVisible: {
-      type: Boolean,
-      required: false,
-      default: false,
-    },
-  },
-
-  methods: {
-    idToLabel(id) {
-      return idToLabel(id);
-    },
-
-    idToCount(id) {
-      return this.model.taxons[id];
-    },
-  },
-};
-
-</script>
-
-<style lang="scss">
-@import "~@/style/variables";
-
-$facets-width: 500px;
-
-#facets {
-  width: $facets-width;
-  position: fixed;
-  top: ($navbar-height + 95);
-  left: (-$facets-width);
-  min-height: 40px;
-  z-index: $monarch-node-sidebar-flyout-z;
-  transition: all 0.3s;
-  overflow-y: auto;
-  overflow-x: hidden;
-  background: ghostwhite;
-  border:2px solid gray;
-  border-radius: 5px;
-  font-size: 0.95rem;
-  padding: 5px;
-}
-
-#facets.active {
-  left: 0;
-  box-shadow: 3px 3px 3px rgba(0, 0, 0, 0.2);
-}
-
-#facets .facet-item {
-  background: white;
-
-  .custom-control.custom-checkbox label {
-    padding-top: 2px;
-  }
-}
-
-</style>
diff --git a/src/components/TaxonFilter.vue b/src/components/TaxonFilter.vue
new file mode 100644
index 00000000..0b3ee416
--- /dev/null
+++ b/src/components/TaxonFilter.vue
@@ -0,0 +1,150 @@
+<template>
+  <div
+    id="filter"
+    :class="{ active: isVisible }"
+    class="container-fluid"
+  >
+    <div class="top-row">
+      <b-button class=""  size="sm" @click="toggleSelectedFilter">
+        Select All
+      </b-button>
+
+      <b-button class="exit" size="sm" @click="hideFilter">
+        Apply & Close
+      </b-button>
+    </div>
+    <div
+      v-for="(value, key) in taxonFilter.taxons"
+      :key="key"
+      class="facet-item row">
+
+      <div class="col-lg-10">
+        <b-form-checkbox v-on:input="updateTaxonFilter" v-model="taxonFilter.taxons[key]">
+          <i>{{ idToLabel(key) }}</i>&nbsp;({{ key }})
+        </b-form-checkbox>
+      </div>
+
+      <div class="col-lg-2">
+        {{ idToCount(key) }}
+      </div>
+
+    </div>
+  </div>
+</template>
+
+
+<script>
+import { idToLabel } from '../lib/TaxonMap';
+export default {
+  name: 'TaxonFilter',
+  model: {
+    prop: 'taxonFilter'
+  },
+  props: {
+    taxonFilter: {
+      type: Object,
+      required: false,
+      default: null,
+    },
+    isVisible: {
+      type: Boolean,
+      required: false,
+      default: false,
+    },
+  },
+  data() {
+    return {
+      selectedAll: true,
+      localCopy: {}
+    }
+  },
+  mounted() {
+    this.localCopy = JSON.parse(JSON.stringify(this.taxonFilter));
+  },
+  watch: {
+  },
+  methods: {
+    updateTaxonFilter: function(){
+      this.$forceUpdate();
+    },
+    idToLabel(id) {
+      return idToLabel(id);
+    },
+
+    idToCount(id) {
+      return this.taxonFilter.counts[id];
+    },
+    hideFilter() {
+      if(this.taxonFilter !== this.localCopy){
+        this.$emit('toggle-filter', true);
+      }else {
+        this.$emit('toggle-filter', false);
+      }
+    },
+    toggleSelectedFilter(){
+      this.selectedAll = !this.selectedAll;
+      for (var key in this.taxonFilter.taxons) {
+        this.taxonFilter.taxons[key] = this.selectedAll;
+      }
+      this.updateTaxonFilter();
+    },
+  },
+};
+
+</script>
+
+<style lang="scss">
+@import "~@/style/variables";
+
+$filter-width: 600px;
+
+#filter {
+  width: $filter-width;
+  display: none;
+  position: fixed;
+  top: 20%;
+  left: 35%;
+  min-height: 40px;
+  z-index: $monarch-node-sidebar-flyout-z;
+  transition: all 0.3s;
+  overflow-y: auto;
+  overflow-x: hidden;
+  background: ghostwhite;
+  border:2px solid gray;
+  border-radius: 5px;
+  font-size: 0.95rem;
+  padding: 20px;
+}
+
+#filter.active {
+  display: unset;
+  box-shadow: 3px 3px 3px rgba(0, 0, 0, 0.2);
+}
+
+#filter .facet-item {
+  background: white;
+
+  .custom-control.custom-checkbox label {
+    padding-top: 2px;
+  }
+}
+
+#filter .exit {
+  float:right;
+  cursor: pointer;
+
+  &:hover {
+    opacity: 0.8;
+  }
+}
+
+#filter .top-row {
+  padding: 5px 15px 0 5px;
+  margin-bottom: 15px;
+
+  .btn {
+    background-color: $monarch-bg-color;
+  }
+}
+
+</style>
diff --git a/src/lib/TaxonMap.js b/src/lib/TaxonMap.js
index 5805b6d8..6019e881 100644
--- a/src/lib/TaxonMap.js
+++ b/src/lib/TaxonMap.js
@@ -91,6 +91,11 @@ export function isTaxonCardType(cardType) {
   return cardTypesSupportingTaxon.indexOf(cardType) >= 0;
 }
 
+export function isSubjectCardType(cardType) {
+  const subjectCardTypes = ['ortholog-phenotype', 'variant'];
+  return subjectCardTypes.includes(cardType);
+}
+
 
 const apolloAGRTaxons = [
   6239, // 'Caenorhabditis elegans'
diff --git a/src/views/Node.vue b/src/views/Node.vue
index af0567e2..bc9badb2 100644
--- a/src/views/Node.vue
+++ b/src/views/Node.vue
@@ -11,13 +11,11 @@
       :card-counts="counts"
       :parent-node="node"
       :parent-node-id="nodeId"
-      :facet-object="facetObject"
       :is-facets-showing="isFacetsShowing"
       :is-neighborhood-showing="isNeighborhoodShowing"
       :subclasses="subclasses"
       :superclasses="superclasses"
       @expand-card="expandCard"
-      @toggle-facets="toggleFacets"
       @toggle-neighborhood="toggleNeighborhood"
     />
 
@@ -165,11 +163,12 @@
 
           <div v-if="expandedCard" class="expanded-card-view">
             <assoc-table
-              :facets="facetObject"
-              :card-counts="counts"
+              :taxon-counts="taxonCounts"
               :node-type="nodeType"
               :card-type="expandedCard"
               :node-id="nodeId"
+              :is-facets-showing="isFacetsShowing"
+              @toggle-facets="toggleFacets"
             />
           </div>
           <div v-if="!expandedCard && nodeType === 'variant'">
@@ -299,8 +298,6 @@ export default {
       isFacetsShowing: false,
       isNeighborhoodShowing: false,
       facetObject: {
-        selectedTaxons: {
-        },
         evidence: {
           IEA: true
         },
@@ -338,6 +335,7 @@ export default {
         models: false,
         diseases: false
       },
+      taxonCounts: {},
       node: null,
       nodeError: null,
       equivalentClasses: null,
@@ -403,8 +401,6 @@ export default {
   watch: {
     facetObject: {
       handler(val, oldVal) {
-        // console.log('facetObject');
-        // console.log(JSON.stringify(val.selectedTaxons, null, 2));
         this.updateCounts();
       },
       deep: true
@@ -412,7 +408,6 @@ export default {
 
     $route(to, _from) {
       // Only fetchData if the path is different.
-
       if (to.path !== this.path) {
         this.fetchData();
       }
@@ -461,31 +456,11 @@ export default {
       this.isNeighborhoodShowing = !this.isNeighborhoodShowing;
     },
 
-    buildFacets() {
+    buildCounts() {
       if (!this.node.association_counts) {
         console.log('Missing association_counts', this.node);
       }
       else {
-        const associationCountsByCardType = this.node.association_counts;
-
-        const taxonTotals = {};
-        const selectedTaxons = {};
-        Object.keys(associationCountsByCardType).forEach((cardType) => {
-          const associationCounts = associationCountsByCardType[cardType];
-          const count = (associationCounts && associationCounts.counts) || 0;
-          const countsByTaxon = (associationCounts && associationCounts.counts_by_taxon) || {};
-
-          if (countsByTaxon) {
-            Object.keys(countsByTaxon).forEach((taxon) => {
-              selectedTaxons[taxon] = true;
-              const taxonCount = taxonTotals[taxon] || 0;
-              taxonTotals[taxon] = taxonCount + countsByTaxon[taxon];
-            });
-          }
-        });
-
-        this.facetObject.taxons = taxonTotals;
-        this.facetObject.selectedTaxons = selectedTaxons;
         this.updateCounts();
       }
     },
@@ -497,25 +472,10 @@ export default {
       }
       else {
         const associationCountsByCardType = this.node.association_counts;
-        // console.log(JSON.stringify(Object.keys(associationCountsByCardType), null, 2));
-
         this.availableCards.forEach((cardType) => {
-
           const associationCounts = associationCountsByCardType[cardType];
           const count = (associationCounts && associationCounts.counts) || 0;
-          const countsByTaxon = (associationCounts && associationCounts.counts_by_taxon) || {};
-          const taxonTotal = count;
-          let taxonFiltered = count;
-
-          if (countsByTaxon) {
-            Object.keys(countsByTaxon).forEach((t) => {
-              if (!this.facetObject.selectedTaxons[t]) {
-                taxonFiltered -= countsByTaxon[t];
-              }
-            });
-          }
-
-          this.counts[cardType] = taxonFiltered;
+          this.counts[cardType] = count;
           if (count > 0) {
             nonEmptyCards.push(cardType);
           }
@@ -682,7 +642,7 @@ export default {
       this.modelIcon = this.icons.model;
       this.hasGeneExac = (this.nodeType === 'gene' || this.nodeType === 'variant');
 
-      this.buildFacets();
+      this.buildCounts();
 
       //
       // If we got here via someone specifying a cardType in the

From 149ad14e6a9591386645c3ee5670cf2ac9da4acf Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Thu, 12 Sep 2019 11:26:30 -0400
Subject: [PATCH 02/10] updating packages

---
 package-lock.json | 67 +++++++++++++++++++++++++----------------------
 package.json      |  4 +--
 2 files changed, 37 insertions(+), 34 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 26a93b00..a447e76f 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1092,13 +1092,13 @@
       "dev": true
     },
     "@nuxt/opencollective": {
-      "version": "0.2.2",
-      "resolved": "https://registry.npmjs.org/@nuxt/opencollective/-/opencollective-0.2.2.tgz",
-      "integrity": "sha512-ie50SpS47L+0gLsW4yP23zI/PtjsDRglyozX2G09jeiUazC1AJlGPZo0JUs9iuCDUoIgsDEf66y7/bSfig0BpA==",
+      "version": "0.3.0",
+      "resolved": "https://registry.npmjs.org/@nuxt/opencollective/-/opencollective-0.3.0.tgz",
+      "integrity": "sha512-Vf09BxCdj1iT2IRqVwX5snaY2WCTkvM0O4cWWSO1ThCFuc4if0Q/nNwAgCxRU0FeYHJ7DdyMUNSdswCLKlVqeg==",
       "requires": {
-        "chalk": "^2.4.1",
-        "consola": "^2.3.0",
-        "node-fetch": "^2.3.0"
+        "chalk": "^2.4.2",
+        "consola": "^2.10.1",
+        "node-fetch": "^2.6.0"
       }
     },
     "@protobufjs/aspromise": {
@@ -1656,12 +1656,12 @@
       }
     },
     "@vue/cli-plugin-e2e-nightwatch": {
-      "version": "3.9.2",
-      "resolved": "https://registry.npmjs.org/@vue/cli-plugin-e2e-nightwatch/-/cli-plugin-e2e-nightwatch-3.9.2.tgz",
-      "integrity": "sha512-olDeE3C5Fmd8ZG2SxNIjWKyhLzi8RXaDNKIFw7ZNrdoJKe8Av0OAweSjP6y5iRApgOQOX2JfS1vum47LC/Dh8g==",
+      "version": "3.11.0",
+      "resolved": "https://registry.npmjs.org/@vue/cli-plugin-e2e-nightwatch/-/cli-plugin-e2e-nightwatch-3.11.0.tgz",
+      "integrity": "sha512-18R/DohTNquODMVce0uZ/NQayB/fpNvtr7TRINtQe/d9kIpHzRgbNJ7NPHvCWBQDAgLKIWcXDwT2ADhbRPJAhw==",
       "dev": true,
       "requires": {
-        "@vue/cli-shared-utils": "^3.9.0",
+        "@vue/cli-shared-utils": "^3.11.0",
         "chromedriver": "^2.46.0",
         "deepmerge": "^3.2.0",
         "execa": "^1.0.0",
@@ -1670,9 +1670,9 @@
       },
       "dependencies": {
         "@vue/cli-shared-utils": {
-          "version": "3.9.0",
-          "resolved": "https://registry.npmjs.org/@vue/cli-shared-utils/-/cli-shared-utils-3.9.0.tgz",
-          "integrity": "sha512-wumeMZTz5aQ+1Y6uxTKegIsgOXEWT3hT8f9sW2mj5SwNDVyQ+AHZTgSynYExTUJg3dH81uKgFDUpPdAvGxzh8g==",
+          "version": "3.11.0",
+          "resolved": "https://registry.npmjs.org/@vue/cli-shared-utils/-/cli-shared-utils-3.11.0.tgz",
+          "integrity": "sha512-D7pst/4v9H1DD66fLxlZOwRR09R03MV0ROdKxBHmh3FmnApCA/RiaolFA/8w+B3CnevYMlV3SJ5fOAgedbswbA==",
           "dev": true,
           "requires": {
             "@hapi/joi": "^15.0.1",
@@ -3507,14 +3507,14 @@
       "integrity": "sha512-rXqOmH1VilAt2DyPzluTi2blhk17bO7ef+zLLPlWvG494pDxcM234pJ8wTc/6R40UWizAIIMgxjvxZg5kmsbag=="
     },
     "bootstrap-vue": {
-      "version": "2.0.0-rc.26",
-      "resolved": "https://registry.npmjs.org/bootstrap-vue/-/bootstrap-vue-2.0.0-rc.26.tgz",
-      "integrity": "sha512-AzN+IRTmfR9rLFWNGt+v2XPmQjZiAlH4x5z2kStA3UoJ5LR91K34iZ8apaa6isDo+DfWDcwH4q7OwHM+VNxWwg==",
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/bootstrap-vue/-/bootstrap-vue-2.0.0.tgz",
+      "integrity": "sha512-lBqkMtkXMqdIwMSDnWydVb38sOIQ0v+RRn/H0PEcLNd2OFarh81mHzGR+ARofGnO9Ubt0o1WJDRWk8RsNK2JfA==",
       "requires": {
-        "@nuxt/opencollective": "^0.2.2",
-        "bootstrap": "^4.3.1",
+        "@nuxt/opencollective": "^0.3.0",
+        "bootstrap": ">=4.3.1 <5.0.0",
         "popper.js": "^1.15.0",
-        "portal-vue": "^2.1.5",
+        "portal-vue": "^2.1.6",
         "vue-functional-data-merge": "^3.1.0"
       }
     },
@@ -4759,9 +4759,9 @@
       "dev": true
     },
     "consola": {
-      "version": "2.9.0",
-      "resolved": "https://registry.npmjs.org/consola/-/consola-2.9.0.tgz",
-      "integrity": "sha512-34Iue+LRcWbndFIfZc5boNizWlsrRjqIBJZTe591vImgbnq7nx2EzlrLtANj9TH2Fxm7puFJBJAOk5BhvZOddQ=="
+      "version": "2.10.1",
+      "resolved": "https://registry.npmjs.org/consola/-/consola-2.10.1.tgz",
+      "integrity": "sha512-4sxpH6SGFYLADfUip4vuY65f/gEogrzJoniVhNUYkJHtng0l8ZjnDCqxxrSVRHOHwKxsy8Vm5ONZh1wOR3/l/w=="
     },
     "console-browserify": {
       "version": "1.1.0",
@@ -5805,9 +5805,9 @@
       },
       "dependencies": {
         "@types/node": {
-          "version": "8.10.50",
-          "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.50.tgz",
-          "integrity": "sha512-+ZbcUwJdaBgOZpwXeT0v+gHC/jQbEfzoc9s4d0rN0JIKeQbuTrT+A2n1aQY6LpZjrLXJT7avVUqiCecCJeeZxA==",
+          "version": "8.10.54",
+          "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.54.tgz",
+          "integrity": "sha512-kaYyLYf6ICn6/isAyD4K1MyWWd5Q3JgH6bnMN089LUx88+s4W8GvK9Q6JMBVu5vsFFp7pMdSxdKmlBXwH/VFRg==",
           "dev": true
         }
       }
@@ -7219,10 +7219,13 @@
       }
     },
     "eslint-utils": {
-      "version": "1.3.1",
-      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-1.3.1.tgz",
-      "integrity": "sha512-Z7YjnIldX+2XMcjr7ZkgEsOj/bREONV60qYeB/bjMAqqqZ4zxKyWX+BOUkdmRmA9riiIPVvo5x86m5elviOk0Q==",
-      "dev": true
+      "version": "1.4.2",
+      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-1.4.2.tgz",
+      "integrity": "sha512-eAZS2sEUMlIeCjBeubdj45dmBHQwPHWyBcT1VSYB7o9x9WRRqKxyUoiXlRjyAwzN7YEzHJlYg0NmzDRWx6GP4Q==",
+      "dev": true,
+      "requires": {
+        "eslint-visitor-keys": "^1.0.0"
+      }
     },
     "eslint-visitor-keys": {
       "version": "1.0.0",
@@ -13536,9 +13539,9 @@
       "integrity": "sha512-w010cY1oCUmI+9KwwlWki+r5jxKfTFDVoadl7MSrIujHU5MJ5OR6HTDj6Xo8aoR/QsA56x8jKjA59qGH4ELtrA=="
     },
     "portal-vue": {
-      "version": "2.1.5",
-      "resolved": "https://registry.npmjs.org/portal-vue/-/portal-vue-2.1.5.tgz",
-      "integrity": "sha512-vZmdMn0mOo7puvxoMQ5zju6S29aFD+9yygJxyWQtPaMXS9xunAeoYdnx6yzfL9J8HD8pMZYgSieEIbioAKhrSQ=="
+      "version": "2.1.6",
+      "resolved": "https://registry.npmjs.org/portal-vue/-/portal-vue-2.1.6.tgz",
+      "integrity": "sha512-lvCF85D4e8whd0nN32D8FqKwwkk7nYUI3Ku8UAEx4Z1reomu75dv5evRUTZNaj1EalxxWNXiNl0EHRq36fG8WA=="
     },
     "portfinder": {
       "version": "1.0.20",
diff --git a/package.json b/package.json
index 62f79899..68528254 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,7 @@
     "axios": "^0.19.0",
     "babel-polyfill": "^6.26.0",
     "bootstrap": "4.3.1",
-    "bootstrap-vue": "^2.0.0-rc.26",
+    "bootstrap-vue": "^2.0.0",
     "d3": "^5.9.2",
     "d3-axis": "^1.0.12",
     "d3-scale": "^3.0.0",
@@ -49,7 +49,7 @@
   "devDependencies": {
     "@vue/cli": "^3.8.2",
     "@vue/cli-plugin-babel": "^3.8.0",
-    "@vue/cli-plugin-e2e-nightwatch": "^3.9.2",
+    "@vue/cli-plugin-e2e-nightwatch": "^3.11.0",
     "@vue/cli-plugin-eslint": "^3.8.0",
     "@vue/cli-plugin-unit-mocha": "^3.8.0",
     "@vue/cli-service": "^3.8.0",

From 350009f09c64013839878ed3e41611abd1f0c8fa Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Thu, 12 Sep 2019 12:51:43 -0400
Subject: [PATCH 03/10] reverting package upgrades due to breaking changes

---
 package-lock.json | 67 ++++++++++++++++++++++-------------------------
 package.json      |  4 +--
 2 files changed, 34 insertions(+), 37 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index a447e76f..26a93b00 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1092,13 +1092,13 @@
       "dev": true
     },
     "@nuxt/opencollective": {
-      "version": "0.3.0",
-      "resolved": "https://registry.npmjs.org/@nuxt/opencollective/-/opencollective-0.3.0.tgz",
-      "integrity": "sha512-Vf09BxCdj1iT2IRqVwX5snaY2WCTkvM0O4cWWSO1ThCFuc4if0Q/nNwAgCxRU0FeYHJ7DdyMUNSdswCLKlVqeg==",
+      "version": "0.2.2",
+      "resolved": "https://registry.npmjs.org/@nuxt/opencollective/-/opencollective-0.2.2.tgz",
+      "integrity": "sha512-ie50SpS47L+0gLsW4yP23zI/PtjsDRglyozX2G09jeiUazC1AJlGPZo0JUs9iuCDUoIgsDEf66y7/bSfig0BpA==",
       "requires": {
-        "chalk": "^2.4.2",
-        "consola": "^2.10.1",
-        "node-fetch": "^2.6.0"
+        "chalk": "^2.4.1",
+        "consola": "^2.3.0",
+        "node-fetch": "^2.3.0"
       }
     },
     "@protobufjs/aspromise": {
@@ -1656,12 +1656,12 @@
       }
     },
     "@vue/cli-plugin-e2e-nightwatch": {
-      "version": "3.11.0",
-      "resolved": "https://registry.npmjs.org/@vue/cli-plugin-e2e-nightwatch/-/cli-plugin-e2e-nightwatch-3.11.0.tgz",
-      "integrity": "sha512-18R/DohTNquODMVce0uZ/NQayB/fpNvtr7TRINtQe/d9kIpHzRgbNJ7NPHvCWBQDAgLKIWcXDwT2ADhbRPJAhw==",
+      "version": "3.9.2",
+      "resolved": "https://registry.npmjs.org/@vue/cli-plugin-e2e-nightwatch/-/cli-plugin-e2e-nightwatch-3.9.2.tgz",
+      "integrity": "sha512-olDeE3C5Fmd8ZG2SxNIjWKyhLzi8RXaDNKIFw7ZNrdoJKe8Av0OAweSjP6y5iRApgOQOX2JfS1vum47LC/Dh8g==",
       "dev": true,
       "requires": {
-        "@vue/cli-shared-utils": "^3.11.0",
+        "@vue/cli-shared-utils": "^3.9.0",
         "chromedriver": "^2.46.0",
         "deepmerge": "^3.2.0",
         "execa": "^1.0.0",
@@ -1670,9 +1670,9 @@
       },
       "dependencies": {
         "@vue/cli-shared-utils": {
-          "version": "3.11.0",
-          "resolved": "https://registry.npmjs.org/@vue/cli-shared-utils/-/cli-shared-utils-3.11.0.tgz",
-          "integrity": "sha512-D7pst/4v9H1DD66fLxlZOwRR09R03MV0ROdKxBHmh3FmnApCA/RiaolFA/8w+B3CnevYMlV3SJ5fOAgedbswbA==",
+          "version": "3.9.0",
+          "resolved": "https://registry.npmjs.org/@vue/cli-shared-utils/-/cli-shared-utils-3.9.0.tgz",
+          "integrity": "sha512-wumeMZTz5aQ+1Y6uxTKegIsgOXEWT3hT8f9sW2mj5SwNDVyQ+AHZTgSynYExTUJg3dH81uKgFDUpPdAvGxzh8g==",
           "dev": true,
           "requires": {
             "@hapi/joi": "^15.0.1",
@@ -3507,14 +3507,14 @@
       "integrity": "sha512-rXqOmH1VilAt2DyPzluTi2blhk17bO7ef+zLLPlWvG494pDxcM234pJ8wTc/6R40UWizAIIMgxjvxZg5kmsbag=="
     },
     "bootstrap-vue": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/bootstrap-vue/-/bootstrap-vue-2.0.0.tgz",
-      "integrity": "sha512-lBqkMtkXMqdIwMSDnWydVb38sOIQ0v+RRn/H0PEcLNd2OFarh81mHzGR+ARofGnO9Ubt0o1WJDRWk8RsNK2JfA==",
+      "version": "2.0.0-rc.26",
+      "resolved": "https://registry.npmjs.org/bootstrap-vue/-/bootstrap-vue-2.0.0-rc.26.tgz",
+      "integrity": "sha512-AzN+IRTmfR9rLFWNGt+v2XPmQjZiAlH4x5z2kStA3UoJ5LR91K34iZ8apaa6isDo+DfWDcwH4q7OwHM+VNxWwg==",
       "requires": {
-        "@nuxt/opencollective": "^0.3.0",
-        "bootstrap": ">=4.3.1 <5.0.0",
+        "@nuxt/opencollective": "^0.2.2",
+        "bootstrap": "^4.3.1",
         "popper.js": "^1.15.0",
-        "portal-vue": "^2.1.6",
+        "portal-vue": "^2.1.5",
         "vue-functional-data-merge": "^3.1.0"
       }
     },
@@ -4759,9 +4759,9 @@
       "dev": true
     },
     "consola": {
-      "version": "2.10.1",
-      "resolved": "https://registry.npmjs.org/consola/-/consola-2.10.1.tgz",
-      "integrity": "sha512-4sxpH6SGFYLADfUip4vuY65f/gEogrzJoniVhNUYkJHtng0l8ZjnDCqxxrSVRHOHwKxsy8Vm5ONZh1wOR3/l/w=="
+      "version": "2.9.0",
+      "resolved": "https://registry.npmjs.org/consola/-/consola-2.9.0.tgz",
+      "integrity": "sha512-34Iue+LRcWbndFIfZc5boNizWlsrRjqIBJZTe591vImgbnq7nx2EzlrLtANj9TH2Fxm7puFJBJAOk5BhvZOddQ=="
     },
     "console-browserify": {
       "version": "1.1.0",
@@ -5805,9 +5805,9 @@
       },
       "dependencies": {
         "@types/node": {
-          "version": "8.10.54",
-          "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.54.tgz",
-          "integrity": "sha512-kaYyLYf6ICn6/isAyD4K1MyWWd5Q3JgH6bnMN089LUx88+s4W8GvK9Q6JMBVu5vsFFp7pMdSxdKmlBXwH/VFRg==",
+          "version": "8.10.50",
+          "resolved": "https://registry.npmjs.org/@types/node/-/node-8.10.50.tgz",
+          "integrity": "sha512-+ZbcUwJdaBgOZpwXeT0v+gHC/jQbEfzoc9s4d0rN0JIKeQbuTrT+A2n1aQY6LpZjrLXJT7avVUqiCecCJeeZxA==",
           "dev": true
         }
       }
@@ -7219,13 +7219,10 @@
       }
     },
     "eslint-utils": {
-      "version": "1.4.2",
-      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-1.4.2.tgz",
-      "integrity": "sha512-eAZS2sEUMlIeCjBeubdj45dmBHQwPHWyBcT1VSYB7o9x9WRRqKxyUoiXlRjyAwzN7YEzHJlYg0NmzDRWx6GP4Q==",
-      "dev": true,
-      "requires": {
-        "eslint-visitor-keys": "^1.0.0"
-      }
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-1.3.1.tgz",
+      "integrity": "sha512-Z7YjnIldX+2XMcjr7ZkgEsOj/bREONV60qYeB/bjMAqqqZ4zxKyWX+BOUkdmRmA9riiIPVvo5x86m5elviOk0Q==",
+      "dev": true
     },
     "eslint-visitor-keys": {
       "version": "1.0.0",
@@ -13539,9 +13536,9 @@
       "integrity": "sha512-w010cY1oCUmI+9KwwlWki+r5jxKfTFDVoadl7MSrIujHU5MJ5OR6HTDj6Xo8aoR/QsA56x8jKjA59qGH4ELtrA=="
     },
     "portal-vue": {
-      "version": "2.1.6",
-      "resolved": "https://registry.npmjs.org/portal-vue/-/portal-vue-2.1.6.tgz",
-      "integrity": "sha512-lvCF85D4e8whd0nN32D8FqKwwkk7nYUI3Ku8UAEx4Z1reomu75dv5evRUTZNaj1EalxxWNXiNl0EHRq36fG8WA=="
+      "version": "2.1.5",
+      "resolved": "https://registry.npmjs.org/portal-vue/-/portal-vue-2.1.5.tgz",
+      "integrity": "sha512-vZmdMn0mOo7puvxoMQ5zju6S29aFD+9yygJxyWQtPaMXS9xunAeoYdnx6yzfL9J8HD8pMZYgSieEIbioAKhrSQ=="
     },
     "portfinder": {
       "version": "1.0.20",
diff --git a/package.json b/package.json
index 68528254..62f79899 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,7 @@
     "axios": "^0.19.0",
     "babel-polyfill": "^6.26.0",
     "bootstrap": "4.3.1",
-    "bootstrap-vue": "^2.0.0",
+    "bootstrap-vue": "^2.0.0-rc.26",
     "d3": "^5.9.2",
     "d3-axis": "^1.0.12",
     "d3-scale": "^3.0.0",
@@ -49,7 +49,7 @@
   "devDependencies": {
     "@vue/cli": "^3.8.2",
     "@vue/cli-plugin-babel": "^3.8.0",
-    "@vue/cli-plugin-e2e-nightwatch": "^3.11.0",
+    "@vue/cli-plugin-e2e-nightwatch": "^3.9.2",
     "@vue/cli-plugin-eslint": "^3.8.0",
     "@vue/cli-plugin-unit-mocha": "^3.8.0",
     "@vue/cli-service": "^3.8.0",

From 6364c0c6c1db2f2e354291c8a760670ea1921aa7 Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Thu, 12 Sep 2019 17:32:42 -0400
Subject: [PATCH 04/10] Continued refactoring for taxon filtering

---
 src/api/BioLink.js             | 10 ++++--
 src/components/AssocTable.vue  | 56 ++++++++++++++++------------------
 src/components/TaxonFilter.vue | 36 +++++++++++++++++-----
 src/lib/TaxonMap.js            |  2 +-
 src/views/Node.vue             | 13 +-------
 5 files changed, 65 insertions(+), 52 deletions(-)

diff --git a/src/api/BioLink.js b/src/api/BioLink.js
index 4bba07f9..3e9a80a3 100644
--- a/src/api/BioLink.js
+++ b/src/api/BioLink.js
@@ -693,11 +693,15 @@ export async function getNodeAssociations(nodeType, nodeId, cardType, taxons, pa
     }
 
     if(taxons != null && taxons !== -1){
-      params.taxon = taxons.length > 1 ? taxons.join(","): taxons[0];
+      params.taxon = taxons.length > 1 ? taxons: taxons[0];
     }
-  }
 
-  const response = await axios.get(url, { params });
+  }
+  const qs = require('qs');
+  const response = await axios.get(url, { params,
+    paramsSerializer: function(params) {
+      return qs.stringify(params, {arrayFormat: 'repeat'})
+    }});
   return response;
 }
 
diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index 6e1a8b20..c40f6695 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -10,14 +10,14 @@
       <taxon-filter @toggle-filter="toggleTaxonFilter($event)"  :is-visible="isFacetsShowing" v-model="taxonFilter"></taxon-filter>
       <div>
         <h5>
-          &nbsp;<strong>{{ totalAssociations }}</strong>&nbsp;
-          <strong>{{ cardType }}</strong> associations.
+          <strong v-if="totalAssociations > 0">{{ totalAssociations }}</strong>
+          {{ cardType }} associations.
         </h5>
 
         <b-button class="taxon-filter" size="sm" v-if="nodeType === 'gene' && hasTaxon"
                   @click="toggleTaxonFilter()"
                   variant="primary">
-        <i class="fa fa-filter" aria-hidden="true"></i> Taxon Filter</b-button>
+        <i class="fa fa-filter" v-bind:class="{ 'filter-active': hasFalseFilter() }" aria-hidden="true"></i> Taxon Filter</b-button>
         <br>
       </div>
       <b-table
@@ -214,11 +214,7 @@ export default {
     taxonCounts: {
       type: Object,
       required: true,
-    },
-    isFacetsShowing: {
-      type: Boolean,
-      required: false,
-    },
+    }
   },
   data() {
     return {
@@ -227,7 +223,6 @@ export default {
       totalAssociations: 0,
       paginationTotals: 0,
       hasTaxon: false,
-      taxonLoaded : false,
       hasFrequencyOnset: false,
       associationData: '',
       tableBusy: false,
@@ -236,6 +231,7 @@ export default {
       fields: [],
       rows: [],
       lastSelection: [],
+      isFacetsShowing: false,
       taxonFilter: {
         counts: {},
         taxons: {}
@@ -245,7 +241,12 @@ export default {
   },
   watch: {
     cardType() {
+      this.taxonFilter = {counts: {}, taxons: {}};
+      this.initialLoad = false;
       this.dataError = false;
+      this.isFacetsShowing = false;
+
+
       window.scroll(0, 0);
       this.currentPage = 1;
       this.generateFields();
@@ -257,14 +258,12 @@ export default {
     this.generateFields();
   },
   methods: {
-    filterTable(row, filter){
-      return this.taxonFilter.taxons[row.taxonId];
-    },
     toggleTaxonFilter(shouldApply) {
+      console.log(shouldApply);
       if(this.isFacetsShowing && shouldApply){
         this.$refs.tableRef.refresh();
       }
-      this.$emit('toggle-facets');
+      this.isFacetsShowing = !this.isFacetsShowing;
     },
     hasFalseFilter() {
       let foundFalseTaxons = false;
@@ -286,9 +285,6 @@ export default {
         });
       return truth;
     },
-    allFacets() {
-      return Object.entries(this.taxonFilter.taxons).map(elem => elem[0]);
-    },
     async rowsProvider(ctx, callback) {
       this.fetchData().then(() => {
         callback(this.rows);
@@ -300,7 +296,6 @@ export default {
       const that = this;
       this.tableBusy = true;
       this.dataError = false;
-      this.initialLoad = true;
       try {
         const params = {
           fetch_objects: true,
@@ -310,12 +305,12 @@ export default {
 
         const taxons = this.hasFalseFilter() ? this.trueTaxonFilters() : null;
         const associationsResponse = await bioLinkService.getNodeAssociations(
-          this.nodeType,
-          this.nodeId,
-          this.cardType,
-          taxons,
-          params
-        );
+                this.nodeType,
+                this.nodeId,
+                this.cardType,
+                taxons,
+                params);
+
         if (!associationsResponse.data || !associationsResponse.data.associations) {
           that.associationData = null;
           throw new Error('BioLink returned no data');
@@ -324,8 +319,9 @@ export default {
         if(reset){
           this.currentPage = 1;
         }
-        that.tableBusy = false;
         that.populateRows();
+        that.tableBusy = false;
+        this.initialLoad = true;
       }
       catch (e) {
         that.dataError = e;
@@ -497,7 +493,8 @@ export default {
 
         const supportLength = support.length;
         let simplifiedCardType = this.cardType;
-        if (simplifiedCardType === 'interaction' || simplifiedCardType === 'ortholog-phenotype' || simplifiedCardType === 'ortholog-disease') {
+        if (simplifiedCardType === 'interaction' || simplifiedCardType === 'ortholog-phenotype'
+                || simplifiedCardType === 'ortholog-disease') {
           simplifiedCardType = 'gene';
           objectTaxon = this.parseTaxon(subjectElem);
         }
@@ -541,17 +538,14 @@ export default {
           elem.onset.url = this.onsetHref(elem.onset);
         }
       });
-
-      if(isTaxonCardType(this.cardType) && !this.taxonLoaded){
+      if(isTaxonCardType(this.cardType)){
         const taxonFacetTarget = Object.keys(this.associationData.facet_counts)[0];
         Object.keys(this.associationData.facet_counts[taxonFacetTarget]).forEach(key => {
           this.taxonFilter.taxons[key] = true;
         });
         this.taxonFilter.counts = this.associationData.facet_counts[taxonFacetTarget];
-        this.taxonLoaded = true;
       }
       this.paginationTotals = this.getTotalRowCounts();
-      console.log(this.paginationTotals);
       this.totalAssociations = this.associationData.numFound
     },
     getTotalRowCounts(){
@@ -689,6 +683,10 @@ export default {
 @import "~@/style/variables";
 .assoc-table {
   width: 100%;
+
+  .filter-active {
+    color: #cce34c;
+  }
   .loading-spinner {
     color: $monarch-bg-color;
   }
diff --git a/src/components/TaxonFilter.vue b/src/components/TaxonFilter.vue
index 0b3ee416..cc53ccf2 100644
--- a/src/components/TaxonFilter.vue
+++ b/src/components/TaxonFilter.vue
@@ -8,10 +8,10 @@
       <b-button class=""  size="sm" @click="toggleSelectedFilter">
         Select All
       </b-button>
-
       <b-button class="exit" size="sm" @click="hideFilter">
         Apply & Close
       </b-button>
+      <p class="warning" v-if="showMessage">You must select at least 1 taxon.</p>
     </div>
     <div
       v-for="(value, key) in taxonFilter.taxons"
@@ -55,13 +55,23 @@ export default {
   data() {
     return {
       selectedAll: true,
-      localCopy: {}
+      localCopy: {},
+      showMessage: false,
+      initialDataFlag: false,
     }
   },
   mounted() {
-    this.localCopy = JSON.parse(JSON.stringify(this.taxonFilter));
+
+  },
+  beforeUpdate(){
+    if(!this.initialDataFlag){
+      this.initialDataFlag = true;
+    }
   },
   watch: {
+    isVisible(newval) {
+      this.localCopy = JSON.parse(JSON.stringify(this.taxonFilter))
+    }
   },
   methods: {
     updateTaxonFilter: function(){
@@ -75,15 +85,22 @@ export default {
       return this.taxonFilter.counts[id];
     },
     hideFilter() {
-      if(this.taxonFilter !== this.localCopy){
-        this.$emit('toggle-filter', true);
+      if(!Object.values(this.taxonFilter.taxons).includes(true)){
+        this.showMessage = true;
       }else {
-        this.$emit('toggle-filter', false);
+        this.showMessage = false;
+        const newTaxons = Object.values(this.taxonFilter.taxons);
+        const originalTaxons = Object.values(this.localCopy.taxons);
+        if(!newTaxons.sort().every(function(value, index) { return value === originalTaxons.sort()[index]})){
+          this.$emit('toggle-filter', true);
+        }else {
+          this.$emit('toggle-filter', false);
+        }
       }
     },
     toggleSelectedFilter(){
       this.selectedAll = !this.selectedAll;
-      for (var key in this.taxonFilter.taxons) {
+      for (let key in this.taxonFilter.taxons) {
         this.taxonFilter.taxons[key] = this.selectedAll;
       }
       this.updateTaxonFilter();
@@ -116,6 +133,11 @@ $filter-width: 600px;
   padding: 20px;
 }
 
+#filter .warning {
+  color: #ba121d;
+  text-align: center;
+}
+
 #filter.active {
   display: unset;
   box-shadow: 3px 3px 3px rgba(0, 0, 0, 0.2);
diff --git a/src/lib/TaxonMap.js b/src/lib/TaxonMap.js
index 6019e881..71d15f23 100644
--- a/src/lib/TaxonMap.js
+++ b/src/lib/TaxonMap.js
@@ -92,7 +92,7 @@ export function isTaxonCardType(cardType) {
 }
 
 export function isSubjectCardType(cardType) {
-  const subjectCardTypes = ['ortholog-phenotype', 'variant'];
+  const subjectCardTypes = ['ortholog-phenotype', 'ortholog-disease', 'variant'];
   return subjectCardTypes.includes(cardType);
 }
 
diff --git a/src/views/Node.vue b/src/views/Node.vue
index bc9badb2..d0f34b54 100644
--- a/src/views/Node.vue
+++ b/src/views/Node.vue
@@ -11,7 +11,6 @@
       :card-counts="counts"
       :parent-node="node"
       :parent-node-id="nodeId"
-      :is-facets-showing="isFacetsShowing"
       :is-neighborhood-showing="isNeighborhoodShowing"
       :subclasses="subclasses"
       :superclasses="superclasses"
@@ -21,7 +20,7 @@
 
     <div class="container-cards">
       <div class="wrapper">
-        <div :class="{ active: isNeighborhoodShowing || isFacetsShowing }" class="overlay"/>
+        <div :class="{ active: isNeighborhoodShowing }" class="overlay"></div>
 
         <div v-if="!node" class="loading">
           <div v-if="nodeError">
@@ -167,8 +166,6 @@
               :node-type="nodeType"
               :card-type="expandedCard"
               :node-id="nodeId"
-              :is-facets-showing="isFacetsShowing"
-              @toggle-facets="toggleFacets"
             />
           </div>
           <div v-if="!expandedCard && nodeType === 'variant'">
@@ -442,17 +439,10 @@ export default {
     },
 
     hideOverlay() {
-      this.isFacetsShowing = false;
       this.isNeighborhoodShowing = false;
     },
 
-    toggleFacets() {
-      this.isNeighborhoodShowing = false;
-      this.isFacetsShowing = !this.isFacetsShowing;
-    },
-
     toggleNeighborhood() {
-      this.isFacetsShowing = false;
       this.isNeighborhoodShowing = !this.isNeighborhoodShowing;
     },
 
@@ -497,7 +487,6 @@ export default {
       this.entrezResult = null;
       this.expandedCard = null;
       this.nonEmptyCards = [];
-      this.isFacetsShowing = false;
       this.isNeighborhoodShowing = false;
       this.inheritance = null;
       this.modifiers = null;

From 190f176d89a61bd99b62b46d6232970f5caba9c3 Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Fri, 13 Sep 2019 09:24:00 -0400
Subject: [PATCH 05/10] removing facets from sidebar

---
 src/components/NodeSidebar.vue | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

diff --git a/src/components/NodeSidebar.vue b/src/components/NodeSidebar.vue
index 4291506f..8dff446d 100644
--- a/src/components/NodeSidebar.vue
+++ b/src/components/NodeSidebar.vue
@@ -35,7 +35,7 @@
           <a :href="'#' + cardType" @click="expandCard(cardType)">
             <img :src="$parent.icons[cardType]" class="entity-type-icon">
             <span class="list-group-item-value">
-              {{ $parent.labels[cardType] }} <!--<span class="count">{{ cardCounts[cardType] }}</span>-->
+              {{ $parent.labels[cardType] }} <span class="count">{{ cardCounts[cardType] }}</span>
             </span>
           </a>
         </li>
@@ -104,12 +104,7 @@ export default {
       type: Boolean,
       required: false,
       default: false,
-    },
-    isFacetsShowing: {
-      type: Boolean,
-      required: false,
-      default: false,
-    },
+    }
   },
 
   data() {
@@ -147,11 +142,6 @@ export default {
     expandCard(cardType) {
       this.$emit('expand-card', cardType);
     },
-
-    toggleFacets() {
-      this.$emit('toggle-facets');
-    },
-
     toggleNeighborhood() {
       this.$emit('toggle-neighborhood');
     },
@@ -159,9 +149,6 @@ export default {
       if (this.isNeighborhoodShowing) {
         this.toggleNeighborhood();
       }
-      else if (this.isFacetsShowing) {
-        this.toggleFacets();
-      }
     }
   }
 };

From 3e18efb6f8ee697ed4eb88cde6b337cd8f5274ad Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Thu, 24 Oct 2019 11:16:48 -0400
Subject: [PATCH 06/10] minor updates

---
 src/components/AssocTable.vue |  1 -
 src/views/Node.vue            | 10 ----------
 2 files changed, 11 deletions(-)

diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index c40f6695..96bf2770 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -259,7 +259,6 @@ export default {
   },
   methods: {
     toggleTaxonFilter(shouldApply) {
-      console.log(shouldApply);
       if(this.isFacetsShowing && shouldApply){
         this.$refs.tableRef.refresh();
       }
diff --git a/src/views/Node.vue b/src/views/Node.vue
index 112be20e..7351af90 100644
--- a/src/views/Node.vue
+++ b/src/views/Node.vue
@@ -44,17 +44,7 @@
               (Redirected from {{ originalId }})
             </span>
           </h4>
-          <span v-if="node.taxon && node.taxon.id" class="node-label-taxon">
-            <a
-              :href="node.taxon.uri"
-              target="_blank"
-              rel="noopener noreferrer"
-              class="node-label-id">
-              <em>{{ node.taxon.label }}</em>
-            </a>
-          </span>
           &nbsp;
-
           <!--
               <a
                 v-if="entrezResult && entrezResult.abstractURL"

From 7308e36d9a29c4909b95e70cffb59f69512d1d9b Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Sun, 2 Feb 2020 20:44:28 -0500
Subject: [PATCH 07/10] small changes for taxon filter api

---
 src/api/BioLink.js             |  70 ++++------------
 src/components/AssocTable.vue  | 149 ++++++++++++++++++---------------
 src/components/NodeSidebar.vue |  14 ----
 src/views/Node.vue             |  24 ------
 4 files changed, 100 insertions(+), 157 deletions(-)

diff --git a/src/api/BioLink.js b/src/api/BioLink.js
index 52de71a7..323942b1 100644
--- a/src/api/BioLink.js
+++ b/src/api/BioLink.js
@@ -1,7 +1,6 @@
 import axios from 'axios';
 import us from 'underscore';
 import * as bbopgraph from 'bbop-graph';
-import { labelToId, isTaxonCardType } from '../lib/TaxonMap';
 import getStaticSourceData from './StaticSourceData';
 import * as bbopgraphUtil from './BBOPGraphUtil';
 import {labelToId, isTaxonCardType, isSubjectCardType} from '../lib/TaxonMap';
@@ -128,43 +127,9 @@ export async function getNode(nodeId, nodeType) {
     rows: 1
   };
 
-<<<<<<< HEAD
   const nodeSummary = axios.get(bioentityUrl, { params })
     .then((bioentityResp) => {
       const bioentityResponseData = bioentityResp.data;
-=======
-  //
-  // There should be no need for a separate API call to get the uri field.
-  // the /bioentity/ endpoints should return uri when appropriate.
-  // Until then, we parallelize a call to identifier/prefixes/expand to get a uri,
-  // which is really stupid.
-  // Once BL's bioentity/ endpoint returns uri, we can delete this hack.
-  //
-
-  const getIdentifierUrl = `${biolink}identifier/prefixes/expand/${nodeId}`;
-
-  //
-  // Temporary hack until BL gets taxon-faceted association counts built in.
-  //
-  const useAssociationTypeKey = false;
-  const subjectKey = useAssociationTypeKey ? 'association_type' : 'subject_category';
-  const objectKey = useAssociationTypeKey ? 'association_type' : 'object_category';
-
-  const nodeSummary = axios.all(
-    [
-      axios.get(bioentityUrl, { params }),
-      axios.get(getIdentifierUrl),
-    ]
-  ).then(
-    axios.spread(
-      function response(bioentityResp, getIdentifierResp) {
-        const bioentityResponseData = bioentityResp.data;
-
-        if (!bioentityResponseData.xrefs) {
-          bioentityResponseData.xrefs = [
-          ];
-        }
->>>>>>> 3e18efb6f8ee697ed4eb88cde6b337cd8f5274ad
 
       if (!bioentityResponseData.xrefs) {
         bioentityResponseData.xrefs = [];
@@ -522,24 +487,6 @@ export async function getNodeAssociations(nodeType, nodeId, cardType, taxons, pa
     params.start = 0;
     params.rows = 10000;
   }
-  const response = await axios.get(url, { params });
-
-  if (useTaxonRestriction) {
-    response.data.associations = response.data.associations.filter((d) => {
-      const subjTaxon = d.subject.taxon;
-      const objTaxon = d.object.taxon;
-      let result = false;
-      if (subjTaxon.id !== null && taxons.indexOf(subjTaxon.id) >= 0) {
-        result = true;
-      }
-      if (objTaxon.id !== null && taxons.indexOf(objTaxon.id) >= 0) {
-        result = true;
-      }
-      return result;
-    });
-    response.data.numFound = response.data.associations.length;
-  }
-
 
   if (isTaxonCardType(cardType)) {
     params.facet = true;
@@ -550,6 +497,7 @@ export async function getNodeAssociations(nodeType, nodeId, cardType, taxons, pa
 
     if(taxons != null && taxons !== -1){
       params.taxon = taxons.length > 1 ? taxons: taxons[0];
+      params.direct_taxon = true;
     }
 
   }
@@ -558,6 +506,22 @@ export async function getNodeAssociations(nodeType, nodeId, cardType, taxons, pa
     paramsSerializer: function(params) {
       return qs.stringify(params, {arrayFormat: 'repeat'})
     }});
+
+    if (useTaxonRestriction) {
+      response.data.associations = response.data.associations.filter((d) => {
+        const subjTaxon = d.subject.taxon;
+        const objTaxon = d.object.taxon;
+        let result = false;
+        if (subjTaxon.id !== null && taxons.indexOf(subjTaxon.id) >= 0) {
+          result = true;
+        }
+        if (objTaxon.id !== null && taxons.indexOf(objTaxon.id) >= 0) {
+          result = true;
+        }
+        return result;
+      });
+      response.data.numFound = response.data.associations.length;
+    }
   return response;
 }
 
diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index 72d6b478..f9bfdf77 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -7,7 +7,7 @@
       </div>
     </div>
     <div v-show="!dataError && initialLoad">
-      <taxon-filter @toggle-filter="toggleTaxonFilter($event)"  :is-visible="isFacetsShowing" v-model="taxonFilter"></taxon-filter>
+      <taxon-filter @toggle-filter="toggleTaxonFilter($event)"  :is-visible="isTaxonShowing" v-model="taxonFilter"></taxon-filter>
       <div>
         <h5>
           <strong v-if="totalAssociations > 0">{{ totalAssociations }}</strong>
@@ -176,7 +176,17 @@ export default {
     },
     taxonCounts: {
       type: Object,
-      required: true,
+      required: true
+    },
+    isFacetsShowing: {
+      type: Boolean,
+      required: false,
+      default: false
+    },
+    isGroup: {
+      type: Boolean,
+      required: false,
+      default: false
     }
   },
   data() {
@@ -199,7 +209,8 @@ export default {
         counts: {},
         taxons: {}
       },
-      filterActive: null
+      filterActive: null,
+      isTaxonShowing: this.isFacetsShowing
     };
   },
   watch: {
@@ -207,7 +218,7 @@ export default {
       this.taxonFilter = {counts: {}, taxons: {}};
       this.initialLoad = false;
       this.dataError = false;
-      this.isFacetsShowing = false;
+      this.isTaxonShowing = false;
 
 
       window.scroll(0, 0);
@@ -222,10 +233,10 @@ export default {
   },
   methods: {
     toggleTaxonFilter(shouldApply) {
-      if(this.isFacetsShowing && shouldApply){
+      if(this.isTaxonShowing && shouldApply){
         this.$refs.tableRef.refresh();
       }
-      this.isFacetsShowing = !this.isFacetsShowing;
+      this.isTaxonShowing = !this.isTaxonShowing;
     },
     hasFalseFilter() {
       let foundFalseTaxons = false;
@@ -357,98 +368,105 @@ export default {
       }
       }
     },
-
     populateRows() {
       this.rows = [];
       let count = 0;
       this.associationData.associations.forEach((elem) => {
         count += 1;
-
         const objectElem = elem.object;
         const subjectElem = elem.subject;
         let objectTaxon = this.parseTaxon(objectElem);
-
         const evidence = us.pick(
           elem, ['id', 'provided_by', 'publications', 'evidence_types']
         );
-
         evidence.publications = processPublications(evidence.publications);
-
         evidence.provided_by = processSources(evidence.provided_by);
-
         // Provide icon and label for database (provided_by)
         evidence.provided_by = evidence.provided_by.map(db => sourceToLabel(db));
-
         // add href for ECO code
         evidence.evidence_types = evidence.evidence_types.map(eco => ({
           id: eco.id,
           label: eco.label,
           url: this.eviHref(eco.id)
         }));
-
         const supportIcons = [];
-
         if (evidence.evidence_types.length > 0) {
           const eviIcon = 'fa-flask'; // 'fa-legal' 'fa-chain';
           supportIcons.push(eviIcon);
         }
-
         if (evidence.publications.length > 0) {
           const pubIcon = 'fa-book';
           supportIcons.push(pubIcon);
         }
-
         if (evidence.provided_by.length > 0) {
           const sourceIcon = 'fa-database';
           supportIcons.push(sourceIcon);
         }
-
-        const supportLength = support.length;
-        let simplifiedCardType = this.cardType;
-        if (simplifiedCardType === 'interaction' || simplifiedCardType === 'ortholog-phenotype'
-                || simplifiedCardType === 'ortholog-disease') {
-          simplifiedCardType = 'gene';
-          objectTaxon = this.parseTaxon(subjectElem);
-        }
-
-        let objectLink = `/${simplifiedCardType}/${objectElem.id}`;
-        if (objectElem.id.indexOf(':.well-known') === 0) {
-          objectLink = null;
-        }
-        const subjectLink = `/${this.nodeType}/${subjectElem.id}`;
-
-        this.fixupRelation(elem, this.nodeType, this.cardType);
-        this.rows.push({
-          publications: pubs,
-          publicationsLength: pubsLength,
-          annotationType: this.cardType,
-          evidence,
-          evidenceLength,
-          support,
-          supportLength,
-          supportIcons,
-          objectCurie: objectElem.id,
-          sources: elem.provided_by,
-          sourcesLength: elem.provided_by.length,
-          assocObject: objectElem.label,
-          objectLink,
-          assocSubject: subjectElem.label,
-          subjectLink,
-          taxonLabel: objectTaxon.label,
-          taxonId: objectTaxon.id,
-          relation: elem.relation,
-          frequency: elem.frequency,
-          onset: elem.onset,
-          _showDetails: false,
-        });
-
-        elem.relation.url = this.relationHref(elem.relation);
-        if (elem.frequency) {
-          elem.frequency.url = this.frequencyHref(elem.frequency);
-        }
-        if (elem.onset) {
-          elem.onset.url = this.onsetHref(elem.onset);
-        }
+        const supportLength = [
+          evidence.provided_by.length,
+          evidence.publications.length,
+          evidence.evidence_types.length,
+        ].reduce((accum, item) => accum + item);
+          let modifiedCardType = this.cardType;
+          if (modifiedCardType === 'interaction') {
+            modifiedCardType = 'gene';
+            objectTaxon = this.parseTaxon(subjectElem);
+          } else if (modifiedCardType === 'ortholog-phenotype') {
+            modifiedCardType = 'phenotype';
+            objectTaxon = this.parseTaxon(subjectElem);
+          } else if (modifiedCardType === 'ortholog-disease') {
+            modifiedCardType = 'disease';
+            objectTaxon = this.parseTaxon(subjectElem);
+          } else if (modifiedCardType === 'homolog') {
+            modifiedCardType = 'gene';
+            objectTaxon = this.parseTaxon(objectElem);
+          } else if (
+            modifiedCardType === 'causal-disease'
+            || modifiedCardType === 'noncausal-disease'
+          ) {
+            modifiedCardType = 'disease';
+          } else if (
+            modifiedCardType === 'causal-gene'
+            || modifiedCardType === 'noncausal-gene'
+          ) {
+            modifiedCardType = 'gene';
+          }
+          let objectLink = `/${modifiedCardType}/${objectElem.id}`;
+          if (modifiedCardType === 'model') {
+            // Models are an index level type (not in our db)
+            // see if the resolver can better type this node
+            objectLink = `/${objectElem.id}`;
+          }
+          if (objectElem.id.startsWith('BNODE')
+              && modifiedCardType !== 'publication') {
+            objectLink = null;
+          }
+          const subjectLink = `/${this.nodeType}/${subjectElem.id}`;
+          this.fixupRelation(elem, this.nodeType, this.cardType);
+          this.rows.push({
+            annotationType: this.cardType,
+            evidence,
+            supportLength,
+            supportIcons,
+            objectCurie: objectElem.id,
+            assocObject: objectElem.label,
+            objectLink,
+            assocSubject: subjectElem.label,
+            subjectLink,
+            taxonLabel: objectTaxon.label,
+            taxonId: objectTaxon.id,
+            relation: elem.relation,
+            frequency: elem.frequency,
+            onset: elem.onset,
+            _showDetails: false,
+          });
+          elem.relation.url = this.relationHref(elem.relation);
+          if (elem.frequency) {
+            elem.frequency.url = this.frequencyHref(elem.frequency);
+          }
+          if (elem.onset) {
+            elem.onset.url = this.onsetHref(elem.onset);
+          }
       });
       if(isTaxonCardType(this.cardType)){
         const taxonFacetTarget = Object.keys(this.associationData.facet_counts)[0];
@@ -457,8 +475,7 @@ export default {
         });
         this.taxonFilter.counts = this.associationData.facet_counts[taxonFacetTarget];
       }
-      this.paginationTotals = this.getTotalRowCounts();
-      this.totalAssociations = this.associationData.numFound
+      this.totalAssociations = this.associationData.numFound;
     },
     getTotalRowCounts(){
       let count = 0;
diff --git a/src/components/NodeSidebar.vue b/src/components/NodeSidebar.vue
index 218e9b2a..e72d643d 100644
--- a/src/components/NodeSidebar.vue
+++ b/src/components/NodeSidebar.vue
@@ -106,21 +106,12 @@ export default {
       type: Boolean,
       required: false,
       default: false,
-<<<<<<< HEAD
-    },
-    isFacetsShowing: {
-      type: Boolean,
-      required: false,
-      default: false,
     },
     isGroup: {
       type: Boolean,
       required: false,
       default: false
     },
-=======
-    }
->>>>>>> 3e18efb6f8ee697ed4eb88cde6b337cd8f5274ad
   },
 
   data() {
@@ -157,11 +148,6 @@ export default {
     hideNeighborhoodOrFacets() {
       if (this.isNeighborhoodShowing) {
         this.toggleNeighborhood();
-<<<<<<< HEAD
-      } else if (this.isFacetsShowing) {
-        this.toggleFacets();
-=======
->>>>>>> 3e18efb6f8ee697ed4eb88cde6b337cd8f5274ad
       }
     }
   }
diff --git a/src/views/Node.vue b/src/views/Node.vue
index 593fea17..6b23f44d 100644
--- a/src/views/Node.vue
+++ b/src/views/Node.vue
@@ -467,32 +467,8 @@ export default {
     buildCounts() {
       if (!this.node.association_counts) {
         console.log('Missing association_counts', this.node);
-<<<<<<< HEAD
-      } else {
-        const associationCountsByCardType = this.node.association_counts;
-
-        const taxonTotals = {};
-        const selectedTaxons = {};
-        Object.keys(associationCountsByCardType).forEach((cardType) => {
-          const associationCounts = associationCountsByCardType[cardType];
-          const count = (associationCounts && associationCounts.counts) || 0;
-          const countsByTaxon = (associationCounts && associationCounts.counts_by_taxon) || {};
-
-          if (countsByTaxon) {
-            Object.keys(countsByTaxon).forEach((taxon) => {
-              selectedTaxons[taxon] = true;
-              const taxonCount = taxonTotals[taxon] || 0;
-              taxonTotals[taxon] = taxonCount + countsByTaxon[taxon];
-            });
-          }
-        });
-
-        this.facetObject.taxons = taxonTotals;
-        this.facetObject.selectedTaxons = selectedTaxons;
-=======
       }
       else {
->>>>>>> 3e18efb6f8ee697ed4eb88cde6b337cd8f5274ad
         this.updateCounts();
       }
     },

From 7b266aa964e0975ed5bc3881a5bc85d672e79ccb Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Tue, 4 Feb 2020 11:49:23 -0500
Subject: [PATCH 08/10] changing rows per page

---
 src/components/AssocTable.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index f9bfdf77..edbcc19f 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -192,7 +192,7 @@ export default {
   data() {
     return {
       currentPage: 1,
-      rowsPerPage: 10,
+      rowsPerPage: 25,
       totalAssociations: 0,
       paginationTotals: 0,
       hasTaxon: false,

From 03f2911577615d16baf33c15c563c699fc5598c5 Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Tue, 4 Feb 2020 16:54:14 -0500
Subject: [PATCH 09/10] fixing pagination

---
 src/components/AssocTable.vue | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index edbcc19f..474c3c24 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -138,7 +138,7 @@
         <b-pagination
           v-model="currentPage"
           :per-page="rowsPerPage"
-          :total-rows="paginationTotals"
+          :total-rows="totalAssociations"
           class="pag-width my-1"
           align="center"
           size="md"></b-pagination>
@@ -192,9 +192,8 @@ export default {
   data() {
     return {
       currentPage: 1,
-      rowsPerPage: 25,
+      rowsPerPage: 20,
       totalAssociations: 0,
-      paginationTotals: 0,
       hasTaxon: false,
       hasFrequencyOnset: false,
       associationData: '',

From 41eff776a5a040d297d815fc1d27bada72c730ef Mon Sep 17 00:00:00 2001
From: Michael Gargano <Michael.Gargano@jax.org>
Date: Tue, 4 Feb 2020 17:29:50 -0500
Subject: [PATCH 10/10] adding back in changes

---
 src/components/AssocTable.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/AssocTable.vue b/src/components/AssocTable.vue
index 474c3c24..2b8795a2 100644
--- a/src/components/AssocTable.vue
+++ b/src/components/AssocTable.vue
@@ -136,6 +136,7 @@
         </template>
       </b-table>
         <b-pagination
+          v-if="totalAssociations > rowsPerPage"
           v-model="currentPage"
           :per-page="rowsPerPage"
           :total-rows="totalAssociations"