@abi-software/flatmapvuer 0.2.5-upstream-downstream → 0.2.5

package/src/components/Tooltip.vue

@@ -1,434 +1,267 @@
-<template>
-  <div class="tooltip-container">
-     <el-main v-if="content" class="main" v-loading="loading">
-      <div class="block" v-if="content.title">
-        <span class="title">{{capitalise(content.title)}}</span>
-      </div>
-      <div class="block" v-else>
-        <span class="title">{{content.featureId}}</span>
-      </div>
-      <!-- Currently we don't show the pubmed viewer, will remove once we are certain it won't be used -->
-      <pubmed-viewer v-if="content.featureIds" v-show="false" class="block" :flatmapAPI="flatmapAPI" :entry="content" @pubmedSearchUrl="pubmedSearchUrlUpdate"/>
-      {{content.paths}}
-      <div v-if="this.components" class="block">
-        <div class="attribute-title">Components</div>
-        <div v-for="component in components" class="attribute-content"  :key="component">
-          {{ capitalise(component) }}
-        </div>
-      </div>
-      <div v-if="this.dendrites" class="block">
-        <div class="attribute-title">Dendrites</div>
-        <div v-for="dendrite in dendrites" class="attribute-content"  :key="dendrite">
-          {{ capitalise(dendrite) }}
-        </div>
-        <el-button v-show="dendritesWithDatasets.length > 0" class="button" @click="openDendrites">
-          Explore dendrite data
-        </el-button>
-      </div>
-      <div v-if="this.axons" class="block">
-        <div class="attribute-title">Axons</div>
-        <div v-for="axon in axons" class="attribute-content"  :key="axon">
-          {{ capitalise(axon) }}
-        </div>
-        <el-button v-show="axonsWithDatasets.length > 0" class="button" @click="openAxons">
-          Explore axon data
-        </el-button>
-      </div>
-      <div v-if="content.uberon" class="block">
-        <div class="attribute-title">Feature Id</div>
-        <span class="attribute-content">{{content.uberon}}</span>
-      </div>
-      <el-button v-for="action in content.actions" round :key="action.title"
-        class="button" @click="resourceSelected(action)">
-        <i v-if="action.title === 'Search for dataset' || action.title === 'View Dataset' " class="el-icon-coin"></i>
-        {{action.title}}
-      </el-button>
-      <el-button  v-if="pubmedSearchUrl" class="button" icon="el-icon-notebook-2" @click="openUrl(pubmedSearchUrl)">
-        Open publications in pubmed
-      </el-button>
-    </el-main>
-  </div>
-</template>
-
-
-<script>
-/* eslint-disable no-alert, no-console */
-import Vue from "vue";
-import {
-  Button,
-  Container,
-  Header,
-  Icon,
-  Main
-} from "element-ui";
-import lang from "element-ui/lib/locale/lang/en";
-import locale from "element-ui/lib/locale";
-locale.use(lang);
-Vue.use(Button);
-Vue.use(Container);
-Vue.use(Header);
-Vue.use(Icon);
-Vue.use(Main);
-
-// pubmedviewer is currently not in use, but still under review so not ready to delete yet
-import PubmedViewer from './PubmedViewer.vue'
-import EventBus from './EventBus'
-
-const titleCase = (str) => {
-  return str.replace(/\w\S*/g, (t) => { return t.charAt(0).toUpperCase() + t.substr(1).toLowerCase() });
-}
-
-const capitalise = function(str){
-  return str.charAt(0).toUpperCase() + str.slice(1)
-}
-
-export default {
-  components: { PubmedViewer },
-  name: "Tooltip",
-  props: { 
-    flatmapAPI: {
-      type: String,
-      default: 'https://mapcore-demo.org/current/flatmap/v2/'
-    },
-    visible: {
-      type: Boolean,
-      default: false
-    },
-    content: {
-      type: Object,
-      default: undefined
-    },
-  },
-  data: function() {
-    return {
-      activeSpecies: undefined,
-      appendToBody: false,
-      pubmedSearchUrl: '',
-      loading: false,
-      axons: [],
-      dendrites: [],
-      components: [],
-      axonsWithDatasets: [],
-      dendritesWithDatasets: [],
-      uberons: [{id: undefined, name: undefined}]
-    };
-  },
-  watch: {
-    'content.featureIds': {
-      handler: function(){
-        this.pathwayQuery(this.content.featureIds)
-      }
-    }
-  },
-  mounted: function(){
-    this.getOrganCuries()
-  },
-  methods: {
-    resourceSelected: function(action) {
-      this.$emit("resource-selected", action); 
-    },
-    titleCase: function(title){
-      return titleCase(title)
-    },
-    capitalise: function(text){
-      return capitalise(text)
-    },
-    onClose: function() {
-      this.$emit("onClose");
-    },
-    openUrl: function(url){
-      window.open(url, '_blank')
-    },
-    openAxons: function(){
-      EventBus.$emit('onActionClick', {type:'Facets', labels: this.axonsWithDatasets.map(a=>a.name)})
-    },
-    openDendrites: function(){
-      EventBus.$emit('onActionClick', {type:'Facets', labels: this.dendritesWithDatasets.map(a=>a.name)})
-    },
-    pubmedSearchUrlUpdate: function (val){
-      this.pubmedSearchUrl = val
-    },
-    findComponents: function(connectivity){
-      let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
-      let nodes = [...new Set(dnodes)]; // remove duplicates
-
-      let found = []
-      let terminal = false
-      nodes.forEach(node=>{
-          let n = node.flat() // Find all terms on the node
-          terminal = false
-
-          // Check if the node is an axon or dendrite
-          n.forEach(s=>{
-              if(connectivity.axons.includes(s)){
-                  terminal = true
-              }
-              if(connectivity.dendrites.includes(s)){
-                  terminal = true
-              }
-          })
-          if (!terminal){
-            found.push(node)
-          }
-      })
-
-      // remove duplicates
-      let foundUnique = [...new Set(found.map(n=>n[0]))]
-      return foundUnique
-    },
-    getOrganCuries: function(){
-      fetch('https://api.sparc.science/get-organ-curies/')
-        .then(response=>response.json())
-        .then(data=>{
-          this.uberons = data.uberon.array
-        })
-    },
-    buildConnectivitySqlStatement: function(keastIds) {
-      let sql = 'select knowledge from knowledge where entity in ('
-      if (keastIds.length === 1) {
-        sql += `'${keastIds[0]}')`
-      } else if (keastIds.length > 1) {
-        for (let i in keastIds) {
-          sql += `'${keastIds[i]}'${i >= keastIds.length - 1 ? ')' : ','} `
-        }
-      }
-      return sql
-    },
-    buildLabelSqlStatement: function(uberons) {
-      let sql = 'select label from labels where entity in ('
-      if (uberons.length === 1) {
-        sql += `'${uberons[0]}')`
-      } else if (uberons.length > 1) {
-        for (let i in uberons) {
-          sql += `'${uberons[i]}'${i >= uberons.length - 1 ? ')' : ','} `
-        }
-      }
-      return sql
-    },
-    createLabelLookup: function(uberons) {
-      return new Promise(resolve=> {
-        let uberonMap = {}
-        const data = { sql: this.buildLabelSqlStatement(uberons)}
-        fetch(`${this.flatmapAPI}knowledge/query/`, {
-            method: 'POST',
-            headers: {
-              'Content-Type': 'application/json',
-            },
-            body: JSON.stringify(data),
-          })
-          .then(response => response.json())
-          .then(data => {
-            uberons.forEach((el,i)=>{
-              uberonMap[el] = data.values[i][0]
-            })
-            resolve(uberonMap)
-          })
-      })
-    },
-    pathwayQuery: function(keastIds){
-      this.axons = []
-      this.dendrites = []
-      this.components = []
-      this.loading = true
-      if (!keastIds || keastIds.length == 0) return
-      const data = { sql: this.buildConnectivitySqlStatement(keastIds)};
-      fetch(`${this.flatmapAPI}knowledge/query/`, {
-        method: 'POST',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-        body: JSON.stringify(data),
-      })
-      .then(response => response.json())
-      .then(data => {
-        let connectivity = JSON.parse(data.values[0][0])
-        let components = this.findComponents(connectivity)
-
-        // Create list of ids to get labels for
-        let conIds = connectivity.axons.concat(connectivity.dendrites.concat(components))
-        this.createLabelLookup(conIds).then(lookUp=>{
-          this.axons = connectivity.axons.map(a=>lookUp[a])
-          this.dendrites = connectivity.dendrites.map(d=>lookUp[d])
-          this.components = components.map(c=>lookUp[c])
-        })
-
-        // Filter for the anatomy which is annotated on datasets
-        this.axonsWithDatasets = this.uberons.filter(ub => connectivity.axons.indexOf(ub.id) !== -1)
-        this.dendritesWithDatasets = this.uberons.filter(ub => connectivity.dendrites.indexOf(ub.id) !== -1)
-        this.loading = false
-      })
-      .catch((error) => {
-        console.error('Error:', error);
-      })
-    }
-  }
-};
-</script>
-
-<style scoped lang="scss">
-@import "~element-ui/packages/theme-chalk/src/button";
-@import "~element-ui/packages/theme-chalk/src/container";
-@import "~element-ui/packages/theme-chalk/src/header";
-@import "~element-ui/packages/theme-chalk/src/main";
-
-.tooltip-container {
-  text-align:justify;
-  border-radius: 4px;
-  box-shadow: 0 1px 2px rgba(0,0,0,.1);
-  pointer-events: auto;
-  background: #fff;
-  border: 1px solid $app-primary-color;
-  display: flex;
-  justify-content: center;
-  align-items: center;
-}
-
-.display {
-  width: 44px;
-  word-break: normal;
-}
-
-.title {
-  text-align: left;
-  width: 16em;
-  line-height: 1.5em !important;
-  font-size: 1em;
-  font-family: Helvetica;
-  font-weight: 500;
-  /* font-weight: bold; */
-  padding-bottom: 8px;
-}
-
-.block {
-  margin-bottom: 1.5em;
-}
-
-.pub {
-  width: 16rem;
-}
-
-.icon {
-  right: 0px;
-  position: absolute;
-  top: 10px;
-}
-
-.icon:hover {
-  cursor: pointer;
-}
-
-.main {
-  font-size: 14px;
-  text-align: left;
-  line-height: 1.5em;
-  font-family: Helvetica;
-  font-weight: 400;
-  /* outline: thin red solid; */
-  padding: 1em !important;
-  overflow: hidden;
-  min-width: 16rem;
-}
-
-.title{
-  font-size: 18px;
-  font-weight: 500;
-  font-weight: bold;
-  padding-bottom: 8px;
-  color: rgb(131, 0, 191);
-
-}
-
-.attribute-title{
-  font-size: 16px;
-  font-weight: 600;
-  /* font-weight: bold; */
-  text-transform: uppercase;
-}
-
-.attribute-content{
-  font-size: 14px;
-  font-weight: 500;
-}
-
-.popover-container {
-  height: 100%;
-  width: 100%;
-}
-
-.main {
-  .el-button.is-round{
-    border-radius: 4px;
-    padding: 9px 20px 10px 20px;
-    display: flex;
-    height: 36px;
-  }
-}
-
-.button {
-  margin-left: 0px !important;
-  margin-top: 0px !important;
-  font-size: 14px !important;
-  background-color: $app-primary-color;
-  color: #fff;
-  &+.button {
-    margin-top: 10px !important;
-  }
-  &:hover {
-    color: #fff !important;
-    background: #ac76c5 !important;
-    border: 1px solid #ac76c5 !important;
-  }
-}
-
-.tooltip-container{
-  &::after, &::before {
-    content: '';
-    display: block;
-    position: absolute;
-    width: 0;
-    height: 0;
-    border-style: solid;
-    flex-shrink: 0;
-  }
-}
-
-.mapboxgl-popup-anchor-bottom {
-  .tooltip-container {
-    &::after, &::before {
-      top: 100%;
-      border-width: 12px;
-    }
-    &::after {
-      margin-top:-1px;
-      border-color: rgb(255, 255, 255) transparent transparent  transparent ;
-    }
-    &::before {
-      margin: 0 auto;
-      border-color: $app-primary-color  transparent  transparent transparent ;
-    }
-  }
-}
-
-.mapboxgl-popup-anchor-top {
-  .tooltip-container {
-    &::after, &::before {
-      top: -24px;
-      border-width: 12px;
-    }
-    &::after {
-      margin-top: 1px;
-      border-color: transparent transparent rgb(255, 255, 255) transparent ;
-    }
-    &::before {
-      margin: 0 auto;
-      border-color: transparent transparent $app-primary-color transparent ;
-    }
-  }
-}
-
-
-/* Fix for chrome bug where under triangle pops up above one on top of it  */
-.selector:not(*:root), .tooltip-container::after{
-  top: 99.4%;
-}
-</style>
+<template>
+  <div class="tooltip-container">
+     <el-main v-if="content" class="main">
+      <div class="block" v-if="content.title">
+        <span class="title">{{titleCase(content.title)}}</span>
+      </div>
+      <div class="block" v-else>
+        <span class="title">{{content.featureId}}</span>
+      </div>
+      
+
+      <pubmed-viewer v-if="content.featureId" class="block" :flatmapAPI=flatmapAPI :featureId="content.featureId" @pubmedSearchUrl="pubmedSearchUrlUpdate"/>
+      <div v-if="content.components" class="block">
+        <div class="attribute-title">Components</div>
+        <span class="attribute-content">{{content.components}}</span>
+      </div>
+      <div v-if="content.start" class="block">
+        <div class="attribute-title">Origin</div>
+        <span class="attribute-content">{{content.start}}</span>
+      </div>
+      <div v-if="content.distribution" class="block">
+        <div class="attribute-title">Distribution</div>
+        <span class="attribute-content">{{content.distribution}}</span>
+      </div>
+      <el-button v-for="action in content.actions" round :key="action.title"
+        class="button" @click="resourceSelected(action)">
+        <i v-if="action.title === 'Search for dataset' || action.title === 'View Dataset' " class="el-icon-coin"></i>
+        {{action.title}}
+      </el-button>
+      <el-button  v-if="pubmedSearchUrl" class="button" icon="el-icon-notebook-2" @click="openUrl(pubmedSearchUrl)">
+        Open publications in pubmed
+      </el-button>
+    </el-main>
+  </div>
+</template>
+
+
+<script>
+/* eslint-disable no-alert, no-console */
+import Vue from "vue";
+import {
+  Button,
+  Container,
+  Header,
+  Icon,
+  Main
+} from "element-ui";
+import lang from "element-ui/lib/locale/lang/en";
+import locale from "element-ui/lib/locale";
+locale.use(lang);
+Vue.use(Button);
+Vue.use(Container);
+Vue.use(Header);
+Vue.use(Icon);
+Vue.use(Main);
+
+import PubmedViewer from './PubmedViewer.vue'
+
+const titleCase = (str) => {
+  return str.replace(/\w\S*/g, (t) => { return t.charAt(0).toUpperCase() + t.substr(1).toLowerCase() });
+}
+
+export default {
+  components: { PubmedViewer },
+  name: "Tooltip",
+  props: { 
+    visible: {
+      type: Boolean,
+      default: false
+    },
+    content: {
+      type: Object,
+      default: undefined
+    },
+        /**
+     * Specify the endpoint of the flatmap server.
+     */
+    flatmapAPI: {
+      type: String,
+      default: "https://mapcore-demo.org/flatmaps/"
+    }
+  },
+  data: function() {
+    return {
+      activeSpecies: undefined,
+      appendToBody: false,
+      pubmedSearchUrl: ''
+    };
+  },
+  methods: {
+    resourceSelected: function(action) {
+      this.$emit("resource-selected", action); 
+    },
+    titleCase: function(title){
+      return titleCase(title)
+    },
+    onClose: function() {
+      this.$emit("onClose");
+    },
+    openUrl: function(url){
+      window.open(url, '_blank')
+    },
+    pubmedSearchUrlUpdate: function (val){
+      this.pubmedSearchUrl = val
+    }
+  }
+};
+</script>
+
+<style scoped lang="scss">
+@import "~element-ui/packages/theme-chalk/src/button";
+@import "~element-ui/packages/theme-chalk/src/container";
+@import "~element-ui/packages/theme-chalk/src/header";
+@import "~element-ui/packages/theme-chalk/src/main";
+
+.tooltip-container {
+  text-align:justify;
+  border-radius: 4px;
+  box-shadow: 0 1px 2px rgba(0,0,0,.1);
+  pointer-events: auto;
+  background: #fff;
+  border: 1px solid $app-primary-color;
+  display: flex;
+  justify-content: center;
+  align-items: center;
+}
+
+.display {
+  width: 44px;
+  word-break: normal;
+}
+
+.title {
+  text-align: left;
+  width: 16em;
+  line-height: 1.5em !important;
+  font-size: 1em;
+  font-family: Helvetica;
+  font-weight: 500;
+  /* font-weight: bold; */
+  padding-bottom: 8px;
+}
+
+.block {
+  margin-bottom: 1.5em;
+}
+
+.pub {
+  width: 16rem;
+}
+
+.icon {
+  right: 0px;
+  position: absolute;
+  top: 10px;
+}
+
+.icon:hover {
+  cursor: pointer;
+}
+
+.main {
+  font-size: 14px;
+  text-align: left;
+  line-height: 1.5em;
+  font-family: Helvetica;
+  font-weight: 400;
+  /* outline: thin red solid; */
+  padding: 1em !important;
+  overflow: hidden;
+  min-width: 16rem;
+}
+
+.attribute-title{
+  font-size: 16px;
+  font-weight: 600;
+  /* font-weight: bold; */
+  text-transform: uppercase;
+}
+
+.attribute-content{
+  font-size: 14px;
+  font-weight: 400;
+}
+
+.popover-container {
+  height: 100%;
+  width: 100%;
+}
+
+.main {
+  .el-button.is-round{
+    border-radius: 4px;
+    padding: 9px 20px 10px 20px;
+    display: flex;
+    height: 36px;
+  }
+}
+
+.button {
+  margin-left: 0px !important;
+  margin-top: 0px !important;
+  font-size: 14px !important;
+  background-color: $app-primary-color;
+  color: #fff;
+  &+.button {
+    margin-top: 10px !important;
+  }
+  &:hover {
+    color: #fff !important;
+    background: #ac76c5 !important;
+    border: 1px solid #ac76c5 !important;
+  }
+}
+
+.tooltip-container{
+  &::after, &::before {
+    content: '';
+    display: block;
+    position: absolute;
+    width: 0;
+    height: 0;
+    border-style: solid;
+    flex-shrink: 0;
+  }
+}
+
+.mapboxgl-popup-anchor-bottom {
+  .tooltip-container {
+    &::after, &::before {
+      top: 100%;
+      border-width: 12px;
+    }
+    &::after {
+      margin-top:-1px;
+      border-color: rgb(255, 255, 255) transparent transparent  transparent ;
+    }
+    &::before {
+      margin: 0 auto;
+      border-color: $app-primary-color  transparent  transparent transparent ;
+    }
+  }
+}
+
+.mapboxgl-popup-anchor-top {
+  .tooltip-container {
+    &::after, &::before {
+      top: -24px;
+      border-width: 12px;
+    }
+    &::after {
+      margin-top: 1px;
+      border-color: transparent transparent rgb(255, 255, 255) transparent ;
+    }
+    &::before {
+      margin: 0 auto;
+      border-color: transparent transparent $app-primary-color transparent ;
+    }
+  }
+}
+
+
+/* Fix for chrome bug where under triangle pops up above one on top of it  */
+.selector:not(*:root), .tooltip-container::after{
+  top: 99.4%;
+}
+</style>