@abi-software/flatmapvuer 0.5.10 → 0.6.0-vue3-0

package/src/services/flatmapQueries.js

@@ -1,415 +1,451 @@
-/* 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 cachedLabels = {};
-
-const findTaxonomyLabel = async function(flatmapAPI, taxonomy){
-  if (cachedLabels && cachedLabels.hasOwnProperty(taxonomy)) {
-    return cachedLabels[taxonomy];
-  }
-
-  return new Promise(resolve=>{
-    fetch(`${flatmapAPI}knowledge/label/${taxonomy}`, {
-      method: 'GET',
-    })
-    .then(response => response.json())
-    .then(data => {
-      let label = data.label;
-      if (label === "Mammalia") {
-        label = "Mammalia not otherwise specified";
-      }
-      cachedLabels[taxonomy] = label;
-      resolve(label);
-    })
-    .catch((error) => {
-      console.error('Error:', error);
-      cachedLabels[taxonomy] = taxonomy;
-      resolve(taxonomy);
-    })
-  });
-}
-
-const inArray = function(ar1, ar2){
-  let as1 = JSON.stringify(ar1)
-  let as2 = JSON.stringify(ar2)
-  return as1.indexOf(as2) !== -1
-}
-
-let FlatmapQueries = function(){
-
-  this.initialise  = function(flatmapApi){
-    this.flatmapApi = flatmapApi
-    this.destinations = []
-    this.origins = []
-    this.components = []
-    this.urls = []
-    this.controller = undefined
-    this.uberons = []
-    this.lookUp = []
-  }
-
-  this.createTooltipData = async function (eventData) {
-    let hyperlinks = []
-    if (eventData.feature.hyperlinks && eventData.feature.hyperlinks.length > 0) {
-      hyperlinks = eventData.feature.hyperlinks
-    } else {
-      hyperlinks = this.urls.map(url=>({url: url, id: "pubmed"}))
-    }
-    let taxonomyLabel = undefined;
-    if (eventData.provenanceTaxonomy) {
-      taxonomyLabel = [];
-      for (let i = 0; eventData.provenanceTaxonomy.length > i; i++) {
-        taxonomyLabel.push(await findTaxonomyLabel(this.flatmapAPI, eventData.provenanceTaxonomy[i]))
-      }
-    }
-
-    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: hyperlinks,
-      provenanceTaxonomy: eventData.provenanceTaxonomy,
-      provenanceTaxonomyLabel: taxonomyLabel
-    }
-    return tooltipData
-  }
-
-  this.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
-  }
-
-  this.createLabelLookup = function(uberons) {
-    return new Promise(resolve=> {
-      let uberonMap = {}
-      this.uberons = []
-      const data = { sql: this.buildLabelSqlStatement(uberons)}
-      fetch(`${this.flatmapApi}knowledge/query/`, {
-          method: 'POST',
-          headers: {
-            'Content-Type': 'application/json',
-          },
-          body: JSON.stringify(data),
-        })
-        .then(response => response.json())
-        .then(payload => {
-          const entity = payload.keys.indexOf("entity");
-          const label = payload.keys.indexOf("label");
-          if (entity > -1 && label > -1) {
-            payload.values.forEach(pair => {
-              uberonMap[pair[entity]] = pair[label];
-              this.uberons.push({
-                id: pair[entity],
-                name: pair[label]
-              })
-            });
-          }
-        resolve(uberonMap)
-        })
-    })
-  }
-
-  this.buildConnectivitySqlStatement = function (keastIds) {
-    let sql = 'select knowledge from knowledge where entity in ('
-    if (keastIds.length === 1) {
-      sql += `'${keastIds[0]}')`
-    } else if (keastIds.length > 1) {
-      for (let i in keastIds) {
-        sql += `'${keastIds[i]}'${i >= keastIds.length - 1 ? ')' : ','} `
-      }
-    }
-    return sql
-  }
-
-  this.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
-  }
-
-  this.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())]
-  }
-
-  this.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()
-  }
-
-  this.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
-  }
-
-  this.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 {
-            resolve(false)
-          }
-        })
-        .catch((error) => {
-          console.error('Error:', error);
-          resolve(false)
-        })
-      })
-      let prom2 = await this.pubmedQueryOnIds(eventData)
-      let results = await Promise.all([prom1, prom2])
-      return results
-  }
-
-  this.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
-    }
-  }
-
-  this.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
-  }
-
-  this.flattenAndFindDatasets = function(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)
-  }
-
-  this.processConnectivity = function(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)
-      })
-    })
-  }
-
-  this.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()
-  }
-
-  this.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
-  }
-
-  this.stripPMIDPrefix = function (pubmedId){
-    return pubmedId.split(':')[1]
-  }
-
-  this.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
-  }
-
-  this.buildPubmedSqlStatementForModels = function(model) {
-    return `select distinct publication from publications where entity = '${model}'`
-  }
-
-  this.flatmapQuery = function(sql){
-    const data = { sql: sql}
-    return fetch(`${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)
-    })
-  }
-  // Note that this functin WILL run to the end, as it doesn not catch the second level of promises
-  this.pubmedQueryOnIds = function(eventData){
-    return new Promise(resolve=>{
-      const keastIds = eventData.resource
-      const source = eventData.feature.source
-      if(!keastIds || keastIds.length === 0) return
-      const sql = this.buildPubmedSqlStatement(keastIds)
-      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])))]
-          resolve(true)
-        } else { // Create pubmed url on models
-          this.pubmedQueryOnModels(source).then(result=>{
-            resolve(result)
-          })
-        }
-      })
-    })
-  }
-
-  this.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])))]
-        return true
-      } else {
-        this.urls = [] // Clears the pubmed search button 
-      } 
-      return false
-    })
-  }
-
-  this.pubmedSearchUrl = function(ids) {
-    let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
-    let params = new URLSearchParams()
-    params.append('term', ids)
-    return url + params.toString()
-  }
-}
-
-export {FlatmapQueries, findTaxonomyLabel}
+/* 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 cachedLabels = {}
+
+const findTaxonomyLabel = async function (flatmapAPI, taxonomy) {
+  if (cachedLabels && cachedLabels.hasOwnProperty(taxonomy)) {
+    return cachedLabels[taxonomy]
+  }
+
+  return new Promise((resolve) => {
+    fetch(`${flatmapAPI}knowledge/label/${taxonomy}`, {
+      method: 'GET',
+    })
+      .then((response) => response.json())
+      .then((data) => {
+        let label = data.label
+        if (label === 'Mammalia') {
+          label = 'Mammalia not otherwise specified'
+        }
+        cachedLabels[taxonomy] = label
+        resolve(label)
+      })
+      .catch((error) => {
+        console.error('Error:', error)
+        cachedLabels[taxonomy] = taxonomy
+        resolve(taxonomy)
+      })
+  })
+}
+
+const inArray = function (ar1, ar2) {
+  let as1 = JSON.stringify(ar1)
+  let as2 = JSON.stringify(ar2)
+  return as1.indexOf(as2) !== -1
+}
+
+let FlatmapQueries = function () {
+  this.initialise = function (flatmapApi) {
+    this.flatmapApi = flatmapApi
+    this.destinations = []
+    this.origins = []
+    this.components = []
+    this.urls = []
+    this.controller = undefined
+    this.uberons = []
+    this.lookUp = []
+  }
+
+  this.createTooltipData = async function (eventData) {
+    let hyperlinks = []
+    if (
+      eventData.feature.hyperlinks &&
+      eventData.feature.hyperlinks.length > 0
+    ) {
+      hyperlinks = eventData.feature.hyperlinks
+    } else {
+      hyperlinks = this.urls.map((url) => ({ url: url, id: 'pubmed' }))
+    }
+    let taxonomyLabel = undefined
+    if (eventData.provenanceTaxonomy) {
+      taxonomyLabel = []
+      for (let i = 0; eventData.provenanceTaxonomy.length > i; i++) {
+        taxonomyLabel.push(
+          await findTaxonomyLabel(
+            this.flatmapAPI,
+            eventData.provenanceTaxonomy[i]
+          )
+        )
+      }
+    }
+
+    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: hyperlinks,
+      provenanceTaxonomy: eventData.provenanceTaxonomy,
+      provenanceTaxonomyLabel: taxonomyLabel,
+    }
+    return tooltipData
+  }
+
+  this.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
+  }
+
+  this.createLabelLookup = function (uberons) {
+    return new Promise((resolve) => {
+      let uberonMap = {}
+      this.uberons = []
+      const data = { sql: this.buildLabelSqlStatement(uberons) }
+      fetch(`${this.flatmapApi}knowledge/query/`, {
+        method: 'POST',
+        headers: {
+          'Content-Type': 'application/json',
+        },
+        body: JSON.stringify(data),
+      })
+        .then((response) => response.json())
+        .then((payload) => {
+          const entity = payload.keys.indexOf('entity')
+          const label = payload.keys.indexOf('label')
+          if (entity > -1 && label > -1) {
+            payload.values.forEach((pair) => {
+              uberonMap[pair[entity]] = pair[label]
+              this.uberons.push({
+                id: pair[entity],
+                name: pair[label],
+              })
+            })
+          }
+          resolve(uberonMap)
+        })
+    })
+  }
+
+  this.buildConnectivitySqlStatement = function (keastIds) {
+    let sql = 'select knowledge from knowledge where entity in ('
+    if (keastIds.length === 1) {
+      sql += `'${keastIds[0]}')`
+    } else if (keastIds.length > 1) {
+      for (let i in keastIds) {
+        sql += `'${keastIds[i]}'${i >= keastIds.length - 1 ? ')' : ','} `
+      }
+    }
+    return sql
+  }
+
+  this.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
+  }
+
+  this.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())]
+  }
+
+  this.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()
+  }
+
+  this.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
+  }
+
+  this.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 {
+            resolve(false)
+          }
+        })
+        .catch((error) => {
+          console.error('Error:', error)
+          resolve(false)
+        })
+    })
+    let prom2 = await this.pubmedQueryOnIds(eventData)
+    let results = await Promise.all([prom1, prom2])
+    return results
+  }
+
+  this.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
+    }
+  }
+
+  this.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
+  }
+
+  this.flattenAndFindDatasets = function (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
+    )
+  }
+
+  this.processConnectivity = function (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)
+      })
+    })
+  }
+
+  this.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()
+  }
+
+  this.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
+  }
+
+  this.stripPMIDPrefix = function (pubmedId) {
+    return pubmedId.split(':')[1]
+  }
+
+  this.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
+  }
+
+  this.buildPubmedSqlStatementForModels = function (model) {
+    return `select distinct publication from publications where entity = '${model}'`
+  }
+
+  this.flatmapQuery = function (sql) {
+    const data = { sql: sql }
+    return fetch(`${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)
+      })
+  }
+  // Note that this functin WILL run to the end, as it doesn not catch the second level of promises
+  this.pubmedQueryOnIds = function (eventData) {
+    return new Promise((resolve) => {
+      const keastIds = eventData.resource
+      const source = eventData.feature.source
+      if (!keastIds || keastIds.length === 0) return
+      const sql = this.buildPubmedSqlStatement(keastIds)
+      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]))
+            ),
+          ]
+          resolve(true)
+        } else {
+          // Create pubmed url on models
+          this.pubmedQueryOnModels(source).then((result) => {
+            resolve(result)
+          })
+        }
+      })
+    })
+  }
+
+  this.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]))
+          ),
+        ]
+        return true
+      } else {
+        this.urls = [] // Clears the pubmed search button
+      }
+      return false
+    })
+  }
+
+  this.pubmedSearchUrl = function (ids) {
+    let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
+    let params = new URLSearchParams()
+    params.append('term', ids)
+    return url + params.toString()
+  }
+}
+
+export { FlatmapQueries, findTaxonomyLabel }