@abi-software/flatmapvuer 0.4.0 → 0.4.1-beta.0

package/src/services/flatmapQueries.js

@@ -0,0 +1,381 @@
+/* eslint-disable no-alert, no-console */
+// remove duplicates by stringifying the objects
+const removeDuplicates = function(arrayOfAnything){
+  return [...new Set(arrayOfAnything.map(e => JSON.stringify(e)))].map(e => JSON.parse(e)) 
+}
+
+const inArray = function(ar1, ar2){
+  let as1 = JSON.stringify(ar1)
+  let as2 = JSON.stringify(ar2)
+  return as1.indexOf(as2) !== -1
+}
+
+export class FlatmapQueries {
+  constructor(sparcApi, flatmapApi) {
+    this.sparcApi = sparcApi
+    this.flatmapApi = flatmapApi
+    this.destinations = []
+    this.origins = []
+    this.components = []
+    this.uberons = []
+    this.urls = []
+    this.controller = undefined
+    this.getOrganCuries().then(uberons=>{
+      this.uberons = uberons
+      this.createLabelLookup(uberons).then(lookUp=>{
+        this.lookUp = lookUp
+      })
+    })
+  }
+
+  createTooltipData = function (eventData) {
+    let tooltipData = {
+      destinations: this.destinations, 
+      origins: this.origins,
+      components: this.components,
+      destinationsWithDatasets: this.destinationsWithDatasets,
+      originsWithDatasets: this.originsWithDatasets,
+      componentsWithDatasets: this.componentsWithDatasets,
+      title: eventData.label,
+      featureId: eventData.resource,
+      hyperlinks: eventData.feature.hyperlinks ? eventData.feature.hyperlinks : this.urls.map(url=>({url: url, id: "pubmed"})),
+    }
+    return tooltipData
+  }
+
+  getOrganCuries = function(){
+    return new Promise(resolve=> {
+    fetch(`${this.sparcAPI}get-organ-curies/`)
+      .then(response=>response.json())
+      .then(data=>{
+        resolve(data.uberon.array)
+      })
+    })
+  }
+
+  createComponentsLabelList = function(components, lookUp){
+    let labelList = []
+    components.forEach(n=>{
+      labelList.push(this.createLabelFromNeuralNode(n[0]), lookUp)
+      if (n.length === 2){
+        labelList.push(this.createLabelFromNeuralNode(n[1]), lookUp)
+      }
+    })
+    return labelList
+  }
+
+  createLabelLookup = function(uberons) {
+    return new Promise(resolve=> {
+      let uberonMap = {}
+      const data = { sql: this.buildLabelSqlStatement(uberons)}
+      fetch(`${this.flatmapApi}knowledge/query/`, {
+          method: 'POST',
+          headers: {
+            'Content-Type': 'application/json',
+          },
+          body: JSON.stringify(data),
+        })
+        .then(response => response.json())
+        .then(payload => {
+          const entity = payload.keys.indexOf("entity");
+          const label = payload.keys.indexOf("label");
+          if (entity > -1 && label > -1) {
+            payload.values.forEach(pair => {
+              uberonMap[pair[entity]] = pair[label];
+            });
+          }
+        resolve(uberonMap)
+        })
+    })
+  }
+
+  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]}'${i >= keastIds.length - 1 ? ')' : ','} `
+      }
+    }
+    return sql
+  }
+  buildLabelSqlStatement = function (uberons) {
+    let sql = 'select entity, label from labels where entity in ('
+    if (uberons.length === 1) {
+      sql += `'${uberons[0]}')`
+    } else if (uberons.length > 1) {
+      for (let i in uberons) {
+        sql += `'${uberons[i]}'${i >= uberons.length - 1 ? ')' : ','} `
+      }
+    }
+    return sql
+  }
+
+  findAllIdsFromConnectivity = function (connectivity) {
+    let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
+    let nodes = [...new Set(dnodes)] // remove duplicates
+    let found = []
+    nodes.forEach(n => {
+      if (Array.isArray(n)) {
+        found.push(n.flat())
+      } else {
+        found.push(n)
+      }
+    })
+    return [... new Set(found.flat())]
+  }
+
+  flattenConntectivity = function (connectivity) {
+    let dnodes = connectivity.flat() // get nodes from edgelist
+    let nodes = [...new Set(dnodes)] // remove duplicates
+    let found = []
+    nodes.forEach(n => {
+      if (Array.isArray(n)) {
+        found.push(n.flat())
+      } else {
+        found.push(n)
+      }
+    })
+    return found.flat()
+  }
+
+  findComponents = function (connectivity) {
+    let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
+    let nodes = removeDuplicates(dnodes)
+
+    let found = []
+    let terminal = false
+    nodes.forEach(node => {
+      terminal = false
+      // Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
+      if (inArray(connectivity.axons, node)) {
+        terminal = true
+      }
+      if (inArray(connectivity.dendrites, node)) {
+        terminal = true
+      }
+      if (!terminal) {
+        found.push(node)
+      }
+    })
+
+    return found
+  }
+
+  retrieveFlatmapKnowledgeForEvent = async function(eventData){
+      // check if there is an existing query
+      if (this.controller) this.controller.abort();
+
+      // set up the abort controller
+      this.controller = new AbortController();
+      const signal = this.controller.signal;
+
+      const keastIds = eventData.resource
+      this.destinations = []
+      this.origins = []
+      this.components = []
+      if (!keastIds || keastIds.length == 0) return
+      const data = { sql: this.buildConnectivitySqlStatement(keastIds)};
+      let prom1 = new Promise(resolve=>{
+        fetch(`${this.flatmapApi}knowledge/query/`, {
+          method: 'POST',
+          headers: {
+            'Content-Type': 'application/json',
+          },
+          body: JSON.stringify(data),
+          signal: signal
+        })
+        .then(response => response.json())
+        .then(data => {
+          if(this.connectivityExists(data)){
+            let connectivity = JSON.parse(data.values[0][0])
+            this.processConnectivity(connectivity).then(()=>{
+              resolve(true)
+            })
+          } else {
+            console.log('No connectivity data found')
+            resolve(true)
+          }
+        })
+        .catch((error) => {
+          console.error('Error:', error);
+          resolve(false)
+        })
+      })
+      let prom2 = this.pubmedQueryOnIds(eventData)
+      return await Promise.all([prom1, prom2])
+    
+  }
+
+  connectivityExists = function(data){
+    if (data.values && data.values.length > 0 && JSON.parse(data.values[0][0]).connectivity && JSON.parse(data.values[0][0]).connectivity.length > 0) {
+      return true
+    } else {
+      return false
+    }
+  }
+
+  createLabelFromNeuralNode = function(node, lookUp){
+    let label = lookUp[node[0]]
+    if (node.length === 2 && node[1].length > 0){
+      node[1].forEach(n=>{
+        if (lookUp[n] == undefined){
+          label += `, ${n}` 
+        } else {
+          label += `, ${lookUp[n]}`
+        }
+      })
+    }
+    return label
+  }
+
+  flattenAndFindDatasets(components, axons, dendrites){
+      
+    // process the nodes for finding datasets (Note this is not critical to the tooltip, only for the 'search on components' button)
+    let componentsFlat = this.flattenConntectivity(components)
+    let axonsFlat = this.flattenConntectivity(axons)
+    let dendritesFlat = this.flattenConntectivity(dendrites)
+
+    // Filter for the anatomy which is annotated on datasets
+    this.destinationsWithDatasets = this.uberons.filter(ub => axonsFlat.indexOf(ub.id) !== -1)
+    this.originsWithDatasets = this.uberons.filter(ub => dendritesFlat.indexOf(ub.id) !== -1)
+    this.componentsWithDatasets = this.uberons.filter(ub => componentsFlat.indexOf(ub.id) !== -1)
+  }
+
+  processConnectivity(connectivity){
+    return new Promise (resolve=>{
+
+      // Filter the origin and destinations from components
+      let components = this.findComponents(connectivity)
+
+      // Remove duplicates
+      let axons = removeDuplicates(connectivity.axons)
+      let dendrites = removeDuplicates(connectivity.dendrites)
+
+      // Create list of ids to get labels for
+      let conIds = this.findAllIdsFromConnectivity(connectivity)  
+
+      // Create readable labels from the nodes. Setting this to 'this.origins' updates the display
+      this.createLabelLookup(conIds).then(lookUp=>{
+        this.destinations = axons.map(a=>this.createLabelFromNeuralNode(a,lookUp))
+        this.origins = dendrites.map(d=>this.createLabelFromNeuralNode(d,lookUp))
+        this.components = components.map(c=>this.createLabelFromNeuralNode(c, lookUp))
+        this.flattenAndFindDatasets(components, axons, dendrites)
+        resolve(true)
+      })
+    })
+  }
+
+  flattenConntectivity(connectivity){
+    let dnodes = connectivity.flat() // get nodes from edgelist
+    let nodes = [...new Set(dnodes)] // remove duplicates
+    let found = []
+    nodes.forEach(n=>{
+      if (Array.isArray(n)){
+        found.push(n.flat())
+      } else {
+        found.push(n)
+      }
+    })
+    return found.flat()
+  }
+
+  findComponents = function(connectivity){
+    let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
+    let nodes = removeDuplicates(dnodes)
+
+    let found = []
+    let terminal = false
+    nodes.forEach(node=>{
+      terminal = false
+      // Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
+      if(inArray(connectivity.axons,node)){
+        terminal = true
+      }
+      if(inArray(connectivity.dendrites, node)){
+        terminal = true
+      }
+      if (!terminal){
+        found.push(node)
+      }
+    })
+
+    return found
+  }
+
+  stripPMIDPrefix = function (pubmedId){
+    return pubmedId.split(':')[1]
+  }
+
+  buildPubmedSqlStatement = function(keastIds) {
+    let sql = 'select distinct publication from publications 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
+  }
+
+  buildPubmedSqlStatementForModels = function(model) {
+    return `select distinct publication from publications where entity = '${model}'`
+  }
+
+  flatmapQuery = function(sql){
+    const data = { sql: sql}
+    return fetch(`${this.flatmapApi}knowledge/query/`, {
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+      },
+      body: JSON.stringify(data),
+    })
+    .then(response => response.json())
+    .catch((error) => {
+      console.error('Error:', error)
+    })
+  }
+
+  pubmedQueryOnIds = function(eventData){
+    const keastIds = eventData.resource
+    const source = eventData.feature.source
+    if(!keastIds || keastIds.length === 0) return
+    const sql = this.buildPubmedSqlStatement(keastIds)
+    return this.flatmapQuery(sql).then(data=>{
+      // Create pubmed url on paths if we have them
+      if (data.values.length > 0){
+        this.urls = [this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0])))]
+        return true
+      } else { // Create pubmed url on models
+        this.pubmedQueryOnModels(source).then(()=>{return true})
+      }
+    })
+  }
+
+  pubmedQueryOnModels = function(source){
+    return this.flatmapQuery(this.buildPubmedSqlStatementForModels(source)).then(data=>{
+      if (Array.isArray(data.values) && data.values.length > 0){
+        this.urls = [this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0])))]
+      } else {
+        this.urls = [] // Clears the pubmed search button 
+      } 
+      return
+    })
+  }
+
+  pubmedSearchUrl = function(ids) {
+    let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
+    let params = new URLSearchParams()
+    params.append('term', ids)
+    return url + params.toString()
+  }
+}
+
+
+
+
+
+export default FlatmapQueries

package/src/components/PubmedViewer.vue

@@ -1,150 +0,0 @@
-<template>
-  <div class="pubmed-container">
-    <!-- To view old pubmed display go to: https://github.com/Tehsurfer/flatmapvuer/commit/eca131f8d32cdcac4d136d1722d7fe4df25f6c3a -->
-  </div>
-</template>
-
-
-<script>
-/* eslint-disable no-alert, no-console */
-
-export default {
-  name: "Tooltip",
-  props: {
-    entry: {
-      type: Object,
-      default: () => {}
-    },
-  },
-  watch: {
-    'entry.featureIds': {
-      handler: function(ids) {
-        this.pubmedQueryOnIds(ids)
-      }
-    }
-  },
-  inject: ['flatmapAPI'],
-  data: function() {
-    return {
-      pubmeds: [],
-      pubmedIds: [],
-    };
-  },
-  mounted: function() {
-    if (this.entry.featureIds)
-      this.pubmedQueryOnIds(this.entry.featureIds)
-  },
-  methods: {
-    stripPMIDPrefix: function (pubmedId){
-      return pubmedId.split(':')[1]
-    },
-    buildPubmedSqlStatement: function(keastIds) {
-      let sql = 'select distinct publication from publications where entity in ('
-      if (keastIds.length === 1) {
-        sql += `'${keastIds[0]}')`
-      } else if (keastIds.length > 1) {
-        for (let i in keastIds) {
-          sql += `'${keastIds[i]}'${i >= keastIds.length - 1 ? ')' : ','} `
-        }
-      }
-      return sql
-    },
-    buildPubmedSqlStatementForModels: function(model) {
-      return `select distinct publication from publications where entity = '${model}'`
-    },
-    flatmapQuery: function(sql){
-      const data = { sql: sql}
-      return fetch(`${this.flatmapAPI}knowledge/query/`, {
-        method: 'POST',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-        body: JSON.stringify(data),
-      })
-      .then(response => response.json())
-      .catch((error) => {
-        console.error('Error:', error)
-      })
-    },
-    pubmedQueryOnIds: function(keastIds){
-      if(!keastIds || keastIds.length === 0) return
-      const sql = this.buildPubmedSqlStatement(keastIds)
-      this.flatmapQuery(sql).then(data=>{
-        this.responseData = data
-        // Create pubmed url on paths if we have them
-        if (data.values.length > 0){
-          this.$emit('pubmedSearchUrl', this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0]))))
-        } else { // Create pubmed url on models
-          this.pubmedQueryOnModels(this.entry.source)
-        }
-      })
-    },
-    pubmedQueryOnModels(source){
-      this.flatmapQuery(this.buildPubmedSqlStatementForModels(source)).then(data=>{
-        if (Array.isArray(data.values) && data.values.length > 0){
-          this.$emit('pubmedSearchUrl', this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0]))))
-        } else {
-          this.$emit('pubmedSearchUrl', '') // Clears the pubmed search button 
-        } 
-      })
-    },
-    pubmedSearchUrl: function(ids) {
-      let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
-      let params = new URLSearchParams()
-      params.append('term', ids)
-      return url + params.toString()
-    }
-  }
-};
-</script>
-
-<style scoped lang="scss">
-@import "~element-ui/packages/theme-chalk/src/link";
-@import "~element-ui/packages/theme-chalk/src/carousel";
-@import "~element-ui/packages/theme-chalk/src/carousel-item";
-
-.attribute-title{
-  font-size: 16px;
-  font-weight: 600;
-  /* font-weight: bold; */
-  text-transform: uppercase;
-}
-
-.attribute-content{
-  font-size: 14px;
-  font-weight: 400;
-}
-
-.el-link {
-  color: $app-primary-color;
-  text-decoration: none;
-  word-wrap: break-word;
-  &:hover, &:focus{
-    color: $app-primary-color;
-    text-decoration: underline;
-  }
-}
-
-::v-deep .el-carousel__button {
-  background-color: $app-primary-color;  
-}
-
-.button {
-  margin-left: 0px !important;
-  margin-top: 0px !important;
-  font-size: 14px !important;
-  background-color: $app-primary-color;
-  color: #fff;
-  &:hover{
-    color: #fff !important;
-    background: #ac76c5 !important;
-    border: 1px solid #ac76c5 !important;
-  }
-  &+.button {
-    margin-top: 10px !important;
-    background-color: $app-primary-color;
-    color: #fff; 
-  }
-}
-
-</style>