@abi-software/map-side-bar 2.19.0 → 2.19.1-demo.0

package/src/components/ConnectivityCard.vue

@@ -33,6 +33,7 @@
 
 <script>
 import EventBus from './EventBus';
+import { capitalise as capitaliseText } from '../utils/common.js';
 
 export default {
   name: 'ConnectivityCard',
@@ -81,8 +82,7 @@ export default {
   },
   methods: {
     capitalise: function (text) {
-      if (text) return text.charAt(0).toUpperCase() + text.slice(1);
-      return '';
+      return capitaliseText(text);
     },
     cardClicked: function (data) {
       if (!this.loading) {

package/src/components/ConnectivityInfo.vue

@@ -343,6 +343,11 @@ import {
   ExternalResourceCard,
 } from '@abi-software/map-utilities';
 import '@abi-software/map-utilities/dist/style.css';
+import {
+  capitalise,
+  formatAlertText as formatAlertTextUtil,
+  scrollToRef,
+} from '../utils/common.js';
 
 const titleCase = (str) => {
   return str.replace(/\w\S*/g, (t) => {
@@ -350,11 +355,6 @@ const titleCase = (str) => {
   });
 };
 
-const capitalise = function (str) {
-  if (str) return str.charAt(0).toUpperCase() + str.slice(1);
-  return '';
-};
-
 export default {
   name: 'ConnectivityInfo',
   components: {
@@ -935,6 +935,9 @@ export default {
         return null;
       }
 
+      //A scicrunch entry typically looks like  https://scicrunch.org/resolver/RRID:XXXXXX
+      //but due to CORS issue, we need to replace it with sparc-api interface,
+      //Replacing the domain while leaving the subpath the same.
       const APIURL = isScicrunchURL
         ? url.replace(scicrunchBase, `${apiLocationBase}scicrunch`)
         : url.replace(orcidBase, orcidAPIBase);
@@ -1159,40 +1162,10 @@ export default {
       EventBus.emit('trackEvent', data);
     },
     showAlertMessage: function () {
-      // scroll to alert message
-      this.$nextTick(() => {
-        const alertElement = this.$refs.alertElement;
-        if (alertElement) {
-          alertElement.scrollIntoView({
-            behavior: 'smooth',
-            block: 'start',
-            inline: 'nearest',
-          });
-        }
-      });
+      scrollToRef(this, 'alertElement');
     },
     formatAlertText: function (text) {
-      if (!text) return '';
-      const escaped = text.replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;');
-      const linkified = escaped.replace(/(https?:\/\/[^\s"<>[]+)/g, (url) => {
-        const parts = url.match(/^(.*?)([\].,;:!?]*)$/);
-        const cleanUrl = parts ? parts[1] : url;
-        const suffix = parts ? parts[2] : '';
-        return `<a href="${cleanUrl}" target="_blank" rel="noopener noreferrer">${cleanUrl}</a>${suffix}`;
-      });
-
-      const normalised = linkified
-        .replace(/\\n/g, '\n')
-        .replace(/\r\n/g, '\n')
-        .replace(/\r/g, '\n');
-
-      return normalised
-        .split('\n')
-        .map((line) => {
-          const withBoldLabel = line.replace(/^\s*([A-Za-z][^:<]{0,120}:)/, '<strong>$1</strong>');
-          return `<div class="alert-line">${withBoldLabel}</div>`;
-        })
-        .join('\n');
+      return formatAlertTextUtil(text, { formatLines: true });
     },
   },
   mounted: function () {

package/src/components/SearchFilters.vue

@@ -143,10 +143,7 @@ import '@abi-software/svg-sprite/dist/style.css';
 import { AlgoliaClient } from '../algolia/algolia.js';
 import { facetPropPathMapping } from '../algolia/utils.js';
 import EventBus from './EventBus.js';
-
-const capitalise = function (txt) {
-  return txt.charAt(0).toUpperCase() + txt.slice(1);
-};
+import { capitalise } from '../utils/common.js';
 
 const convertReadableLabel = function (original) {
   const name = original.toLowerCase();
@@ -273,16 +270,22 @@ export default {
       return value;
     },
     createChildrenCascaderValue: function (children, facet, facets) {
+      const parentKey = facet.key;
+
       if (children?.length) {
         for (let i = 0; i < children.length; i++) {
           const facetItem = children[i];
           //copy the facets into
           if (children[i].facetPropPath !== 'supportingAwards.consortium.name') {
-            children[i].label = convertReadableLabel(facetItem.label);
+            // `sourceNomenclatureLabel` is from cell card explorer filters
+            if (parentKey === 'sourceNomenclatureLabel') {
+              children[i].label = facetItem.label;
+            } else {
+              children[i].label = convertReadableLabel(facetItem.label);
+            }
           }
-          if (facetItem.key && facet.key.includes('flatmap.connectivity.source.')) {
+          if (facetItem.key && parentKey.includes('flatmap.connectivity.source.')) {
             const childKey = facetItem.key;
-            const parentKey = facet.key;
             const key = childKey.replace(`${parentKey}.`, '');
             children[i].value = this.createCascaderItemValue([facet.label, key]);
           } else {

package/src/components/SearchHistory.vue

@@ -125,23 +125,10 @@
 
 <script>
 import EventBus from './EventBus.js';
+import { generateUUID } from '../utils/common.js';
 
 const MAX_SEARCH_HISTORY = 12;
 
-function generateUUID() {
-  const arr = new Uint8Array(16);
-  window.crypto.getRandomValues(arr);
-
-  arr[6] = (arr[6] & 0x0f) | 0x40;
-  arr[8] = (arr[8] & 0x3f) | 0x80;
-
-  const hex = Array.from(arr)
-    .map((byte) => byte.toString(16).padStart(2, '0'))
-    .join('');
-
-  return `${hex.slice(0, 8)}-${hex.slice(8, 12)}-${hex.slice(12, 16)}-${hex.slice(16, 20)}-${hex.slice(20)}`;
-}
-
 export default {
   name: 'SearchHistory',
   props: {
@@ -317,7 +304,14 @@ export default {
     getParentComponentName: function () {
       const isConnectivity = this.localStorageKey?.indexOf('connectivity') !== -1;
       const isDataset = this.localStorageKey?.indexOf('dataset') !== -1;
-      const location = isConnectivity ? 'connectivity' : isDataset ? 'dataset' : '';
+      const isCellCard = this.localStorageKey?.indexOf('cell-card') !== -1;
+      const location = isConnectivity
+        ? 'connectivity'
+        : isDataset
+          ? 'dataset'
+          : isCellCard
+            ? 'cell_card'
+            : '';
       return location;
     },
     search: function (item) {

package/src/components/SideBar.vue

@@ -65,6 +65,20 @@
                 @connectivity-item-close="onConnectivityItemClose"
               />
             </template>
+            <template v-else-if="tab.type === 'cellCardExplorer' && showCellCards">
+              <CellCardExplorer
+                :ref="'cellCardExplorerTab_' + tab.id"
+                class="sidebar-content-container"
+                v-show="tab.id === activeTabId"
+                :envVars="envVars"
+                :activeSpecies="activeSpeciesForEntries"
+                @search-changed="searchChanged(tab.id, $event)"
+                @dataset-search="openDatasetSearchFromCellCard($event)"
+                @connectivity-search="openConnectivitySearch($event.facets, $event.query)"
+                @soma-location-hovered="showSomaLocation"
+                @soma-locations-ready="onSomaLocationsReady"
+              />
+            </template>
             <template v-else>
               <DatasetExplorer
                 class="sidebar-content-container"
@@ -93,6 +107,7 @@ import EventBus from './EventBus.js';
 import Tabs from './Tabs.vue';
 import AnnotationTool from './AnnotationTool.vue';
 import ConnectivityExplorer from './ConnectivityExplorer.vue';
+import CellCardExplorer from './CellCardExplorer.vue';
 import { removeShowAllFacets } from '../algolia/utils.js';
 
 /**
@@ -106,6 +121,7 @@ export default {
     ElIconArrowRight,
     AnnotationTool,
     ConnectivityExplorer,
+    CellCardExplorer,
   },
   name: 'SideBar',
   props: {
@@ -115,6 +131,7 @@ export default {
         { title: 'Dataset Explorer', id: 1, type: 'datasetExplorer', closable: false },
         { title: 'Connectivity Explorer', id: 2, type: 'connectivityExplorer', closable: false },
         { title: 'Annotation', id: 3, type: 'annotation', closable: true },
+        { title: 'Cell Card Explorer', id: 4, type: 'cellCardExplorer', closable: false },
       ],
     },
     /**
@@ -180,6 +197,10 @@ export default {
       type: Boolean,
       default: false,
     },
+    showCellCards: {
+      type: Boolean,
+      default: false,
+    },
   },
   data: function () {
     return {
@@ -188,6 +209,7 @@ export default {
       activeTabId: 1,
       activeAnnotationData: { tabType: 'annotation' },
       activeConnectivityData: { tabType: 'connectivity' },
+      activeSpeciesForEntries: [],
       state: {
         dataset: {
           search: '',
@@ -197,6 +219,10 @@ export default {
           search: '',
           filters: [],
         },
+        cellCards: {
+          search: '',
+          filters: [],
+        },
         connectivityEntries: [],
         annotationEntries: [],
         activeTabId: this.activeTabId,
@@ -231,6 +257,16 @@ export default {
         this.activeAnnotationData = data;
       }
     },
+    /**
+     * This event is emitted when the mouse hover on or off a soma location in cell card explorer.
+     * @param name Soma location
+     */
+    showSomaLocation: function (name) {
+      this.$emit('soma-location-hovered', name);
+    },
+    onSomaLocationsReady: function (somaLocations) {
+      this.$emit('soma-locations-ready', somaLocations);
+    },
     /**
      * This event is emitted when the show connectivity button is clicked.
      * @arg featureIds
@@ -295,6 +331,42 @@ export default {
         datasetExplorerTabRef.openSearch(facets, query);
       });
     },
+    openCellCardExplorerSearch: function (filters, query) {
+      this.drawerOpen = true;
+      // Because refs are in v-for, nextTick is needed here
+      this.$nextTick(() => {
+        const cellCardExplorerTabRef = this.getTabRef(undefined, 'cellCardExplorer', true);
+        if (cellCardExplorerTabRef && typeof cellCardExplorerTabRef.openSearch === 'function') {
+          cellCardExplorerTabRef.openSearch(filters, query);
+        }
+      });
+    },
+    openDatasetSearchFromCellCard: function (payload) {
+      if (!payload || typeof payload !== 'object') {
+        this.openSearch([], payload);
+        return;
+      }
+
+      const facets = [];
+      if (payload.species) {
+        facets.push({
+          facet: payload.species,
+          term: 'Species',
+          facetPropPath: 'organisms.primary.species.name',
+        });
+      }
+
+      if (payload.location) {
+        facets.push({
+          facet: payload.location,
+          term: 'Anatomical structure',
+          facetPropPath: 'anatomy.organ.category.name',
+          AND: true,
+        });
+      }
+
+      this.openSearch(facets, '');
+    },
     /**
      * Get the ref id of the tab by id and type.
      */
@@ -432,6 +504,13 @@ export default {
         this.state.connectivity.filters = connectivityExplorerTabRef.getFilters();
       }
 
+      // Update cell card explorer state if available
+      const cellCardExplorerTabRef = this.getTabRef(undefined, 'cellCardExplorer');
+      if (cellCardExplorerTabRef) {
+        this.state.cellCards.search = cellCardExplorerTabRef.getSearch();
+        this.state.cellCards.filters = cellCardExplorerTabRef.getFilters();
+      }
+
       // Update connectivity entries if available
       if (this.connectivityEntry && this.connectivityEntry.length > 0) {
         this.state.connectivityEntries = this.connectivityEntry.map((entry) => entry.id);
@@ -461,11 +540,15 @@ export default {
     setState: function (state) {
       // if state is not provided or formatted incorrectly, do nothing
       if (!state || !state.dataset || !state.connectivity) return;
-      this.state = JSON.parse(JSON.stringify(state)); // deep copy to avoid reference issues
-      const datasetFilters = state.dataset.filters;
-      const connectivityFilters = state.connectivity.filters;
-      const datasetSearch = state.dataset.search;
-      const connectivitySearch = state.connectivity.search;
+      // Create a deep copy while preserving the original state structure for future extensibility
+      const newState = JSON.parse(JSON.stringify(state));
+      this.state = { ...this.state, ...newState };
+      const datasetFilters = this.state.dataset.filters;
+      const connectivityFilters = this.state.connectivity.filters;
+      const datasetSearch = this.state.dataset.search;
+      const connectivitySearch = this.state.connectivity.search;
+      const cellCardFilters = this.state.cellCards.filters || [];
+      const cellCardSearch = this.state.cellCards.search || '';
 
       if (datasetFilters.length || datasetSearch) {
         this.openSearch(datasetFilters, datasetSearch);
@@ -475,6 +558,10 @@ export default {
         this.openConnectivitySearch(connectivityFilters, connectivitySearch);
       }
 
+      if (cellCardFilters.length || cellCardSearch) {
+        this.openCellCardExplorerSearch(cellCardFilters, cellCardSearch);
+      }
+
       if (state.activeTabId) {
         this.$nextTick(() => {
           const hasTab = this.tabEntries.find((t) => t.id === state.activeTabId);
@@ -497,6 +584,16 @@ export default {
       };
       this.$emit('trackEvent', taggingData);
     },
+    /**
+     * @public
+     * Update the active species to use in filters.
+     * Used by SplitFlow component.
+     * @param activeSpecies
+     */
+    updateActiveSpeciesForEntries: function (activeSpecies) {
+      const speciesEntries = Array.isArray(activeSpecies) ? activeSpecies : [activeSpecies];
+      this.activeSpeciesForEntries = [...new Set(speciesEntries.filter(Boolean))];
+    },
   },
   computed: {
     // This should respect the information provided by the property
@@ -505,7 +602,8 @@ export default {
         (tab) =>
           tab.type === 'datasetExplorer' ||
           tab.type === 'connectivityExplorer' ||
-          (tab.type === 'annotation' && this.annotationEntry && this.annotationEntry.length > 0),
+          (tab.type === 'annotation' && this.annotationEntry && this.annotationEntry.length > 0) ||
+          (tab.type === 'cellCardExplorer' && this.showCellCards),
       );
     },
   },

package/src/components/Tabs.vue

@@ -4,7 +4,7 @@
       class="tab"
       v-for="tab in tabs"
       :key="tab.id"
-      :class="{ 'active-tab': tab.id == activeId }"
+      :class="{ 'active-tab': tab.id == activeId, 'closable-tab': tab.closable }"
       @click="tabClicked(tab)"
     >
       <span class="tab-title">{{ tab.title }}</span>
@@ -98,14 +98,23 @@ export default {
 .tab-title {
   text-align: center;
   font-size: 14px;
-  padding: 0 1rem;
+  padding: 0 0.75rem;
+
+  .closable-tab & {
+    padding-right: 0.25rem;
+  }
 }
 
 .tab-close-icon {
-  width: 20px !important;
-  height: 20px !important;
-  font-size: 20px !important;
-  padding-right: 4px !important;
+  width: 18px !important;
+  height: 18px !important;
+  font-size: 18px !important;
+  margin-right: 4px !important;
   color: $app-primary-color !important;
+  border-radius: 2px;
+
+  &:hover {
+    background-color: rgba($app-primary-color, 0.15) !important;
+  }
 }
 </style>

package/src/components/icons/IconOpenExternal.vue

@@ -0,0 +1,23 @@
+<template>
+  <svg viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" focusable="false">
+    <g stroke="none" stroke-width="1" fill="none" fill-rule="evenodd">
+      <polygon
+        fill="currentColor"
+        fill-rule="nonzero"
+        transform="translate(15.500000, 8.878680) rotate(225.000000) translate(-15.500000, -8.878680)"
+        points="16.25 4.12867966 16.25 13.6286797 14.75 13.6286797 14.75 4.12867966"
+      />
+      <polygon
+        fill="currentColor"
+        fill-rule="nonzero"
+        transform="translate(17.500000, 6.918996) rotate(225.000000) translate(-17.500000, -6.918996)"
+        points="20.9294459 3.82036868 22.058311 4.80812559 17.5 10.0176239 12.941689 4.80812559 14.0705541 3.82036868 17.5 7.739"
+      />
+      <polygon
+        fill="currentColor"
+        fill-rule="nonzero"
+        points="11.6570511 7.25 11.6570511 8.75 5.75 8.75 5.75 16.25 15.25 16.25 15.25 11.2267933 16.75 11.2267933 16.75 17.75 4.25 17.75 4.25 7.25"
+      />
+    </g>
+  </svg>
+</template>

package/src/components.d.ts

@@ -13,6 +13,8 @@ declare module 'vue' {
   export interface GlobalComponents {
     AnnotationTool: typeof import('./components/AnnotationTool.vue')['default']
     BadgesGroup: typeof import('./components/BadgesGroup.vue')['default']
+    CellCard: typeof import('./components/CellCard.vue')['default']
+    CellCardExplorer: typeof import('./components/CellCardExplorer.vue')['default']
     ConnectivityCard: typeof import('./components/ConnectivityCard.vue')['default']
     ConnectivityExplorer: typeof import('./components/ConnectivityExplorer.vue')['default']
     ConnectivityInfo: typeof import('./components/ConnectivityInfo.vue')['default']
@@ -48,6 +50,7 @@ declare module 'vue' {
     ElRow: typeof import('element-plus/es')['ElRow']
     ElSelect: typeof import('element-plus/es')['ElSelect']
     ElTag: typeof import('element-plus/es')['ElTag']
+    IconOpenExternal: typeof import('./components/icons/IconOpenExternal.vue')['default']
     ImageGallery: typeof import('./components/ImageGallery.vue')['default']
     SearchFilters: typeof import('./components/SearchFilters.vue')['default']
     SearchHistory: typeof import('./components/SearchHistory.vue')['default']

package/src/utils/common.js

@@ -0,0 +1,59 @@
+export function generateUUID() {
+  const arr = new Uint8Array(16);
+  window.crypto.getRandomValues(arr);
+
+  arr[6] = (arr[6] & 0x0f) | 0x40;
+  arr[8] = (arr[8] & 0x3f) | 0x80;
+
+  const hex = Array.from(arr)
+    .map((byte) => byte.toString(16).padStart(2, '0'))
+    .join('');
+
+  return `${hex.slice(0, 8)}-${hex.slice(8, 12)}-${hex.slice(12, 16)}-${hex.slice(16, 20)}-${hex.slice(20)}`;
+}
+
+export function capitalise(text) {
+  if (!text) return '';
+  const value = String(text);
+  return value.charAt(0).toUpperCase() + value.slice(1);
+}
+
+export function formatAlertText(text, { formatLines = false } = {}) {
+  if (!text) return '';
+
+  const escaped = String(text).replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;');
+
+  const linkified = escaped.replace(/(https?:\/\/[^\s"<>[]+)/g, (url) => {
+    const parts = url.match(/^(.*?)([\].,;:!?]*)$/);
+    const cleanUrl = parts ? parts[1] : url;
+    const suffix = parts ? parts[2] : '';
+    return `<a href="${cleanUrl}" target="_blank" rel="noopener noreferrer">${cleanUrl}</a>${suffix}`;
+  });
+
+  const normalised = linkified.replace(/\\n/g, '\n').replace(/\r\n/g, '\n').replace(/\r/g, '\n');
+
+  if (!formatLines) {
+    return normalised;
+  }
+
+  return normalised
+    .split('\n')
+    .map((line) => {
+      const withBoldLabel = line.replace(/^\s*([A-Za-z][^:<]{0,120}:)/, '<strong>$1</strong>');
+      return `<div class="alert-line">${withBoldLabel}</div>`;
+    })
+    .join('\n');
+}
+
+export function scrollToRef(vm, refName) {
+  vm?.$nextTick(() => {
+    const element = vm?.$refs?.[refName];
+    if (element) {
+      element.scrollIntoView({
+        behavior: 'smooth',
+        block: 'start',
+        inline: 'nearest',
+      });
+    }
+  });
+}