@abi-software/flatmapvuer 0.3.8 → 0.3.10-beta

package/src/components/PubmedViewer.vue

@@ -1,199 +1,150 @@
-<template>
-  <div class="pubmed-container">
-      <div v-loading="loading.response" class="block">
-        <div class="attribute-title">Pubmed Resources</div>
-        <br/>
-        <el-carousel 
-          :autoplay="false" 
-          indicator-position="outside"
-          height="250px" width="200px"
-        >
-          <el-carousel-item v-for="(pub, i) in pubmeds" :key="i">
-            <div class="attribute-content">
-                <div v-html="pub.html"/>
-                <el-link :href="pub.url" :underline="false" class="el-link" target="_blank">{{pub.url}}</el-link>
-            </div>
-          </el-carousel-item>
-        </el-carousel>
-      </div>
-  </div>
-</template>
-
-
-<script>
-/* eslint-disable no-alert, no-console */
-import Vue from "vue";
-import {
-  Link,
-  Carousel,
-  CarouselItem,
-  Button
-} from "element-ui";
-import lang from "element-ui/lib/locale/lang/en";
-import locale from "element-ui/lib/locale";
-locale.use(lang);
-Vue.use(Link);
-Vue.use(Carousel);
-Vue.use(CarouselItem);
-Vue.use(Button);
-
-
-export default {
-  name: "Tooltip",
-  props: {
-    entry: {
-      type: Object,
-      default: () => {}
-    },
-  },
-  watch: {
-    'entry.featureId': function (val){
-      this.flatmapQuery(val).then(pb => this.pubmeds = pb)
-    },
-    'entry.featureIds': {
-      handler: function(ids) {
-        this.flatmapQuery(ids)
-      }
-    }
-  },
-  inject: ['flatmapAPI'],
-  data: function() {
-    return {
-      data: {},
-      pubmeds: [],
-      pubmedIds: [],
-      loading: {response: true, publications: true}
-    };
-  },
-  mounted: function() {
-    if (this.entry.featureIds)
-      this.flatmapQuery(this.entry.featureIds)
-  },
-  methods: {
-    stripPMIDPrefix: function (pubmedId){
-      return pubmedId.split(':')[1]
-    },
-    titleFromPubmed: function (pubmedId){
-      return new Promise((resolve) => {
-        fetch(`https://api.ncbi.nlm.nih.gov/lit/ctxp/v1/pubmed/?format=citation&contenttype=json&id=${pubmedId}`)
-        .then(response => response.json())
-        .then(data => {
-          resolve(data.apa.format)
-        })
-        .catch((error) => {
-          console.error('Error:', error)
-        });
-      })
-    },
-    splitLink(bibliographyString){
-      let split = bibliographyString.split('https')
-      return [split[0], 'https' + split[1]]
-    },
-    buildPubmedSqlStatement: function(keastIds) {
-      let sql = 'select distinct publication from publications where entity in ('
-      if (keastIds.length === 1) {
-        sql += `'${keastIds[0]}')`
-      } else if (keastIds.length > 1) {
-        for (let i in keastIds) {
-          sql += `'${keastIds[i]}'${i >= keastIds.length - 1 ? ')' : ','} `
-        }
-      }
-      return sql
-    },
-    flatmapQuery: function(keastIds){
-      if(!keastIds || keastIds.length === 0) return
-      this.pubmeds = []
-      this.loading.response = true
-
-      // fetch pubmed publications for the given ids
-      const data = { sql: this.buildPubmedSqlStatement(keastIds)};
-      fetch(`${this.flatmapAPI}knowledge/query/`, {
-        method: 'POST',
-        headers: {
-          'Content-Type': 'application/json',
-        },
-        body: JSON.stringify(data),
-      })
-      .then(response => response.json())
-      .then(data => {
-        this.responseData = data
-        this.loading.response = false
-
-        // create links for each pubmedId
-        if (data.values.length > 0){
-          data.values.forEach(identifier => {
-            let ids = this.stripPMIDPrefix(identifier[0])
-            this.titleFromPubmed(ids).then( bib=>{
-              let [html, link] = this.splitLink(bib)
-              this.pubmeds.push({identifier: identifier[0] , html: html, url: link})
-            })
-          });
-          this.$emit('pubmedSearchUrl', this.pubmedSearchUrl(data.values.map(id=>this.stripPMIDPrefix(id[0]))))
-        } else {
-           this.$emit('pubmedSearchUrl', '') // Clears the pubmed search button 
-        }
-      })
-      .catch((error) => {
-        console.error('Error:', error)
-    })
-    },
-    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: $app-primary-color;
-    color: #fff; 
-  }
-}
-
+<template>
+  <div class="pubmed-container">
+    <!-- To view old pubmed display go to: https://github.com/Tehsurfer/flatmapvuer/commit/eca131f8d32cdcac4d136d1722d7fe4df25f6c3a -->
+  </div>
+</template>
+
+
+<script>
+/* eslint-disable no-alert, no-console */
+
+export default {
+  name: "Tooltip",
+  props: {
+    entry: {
+      type: Object,
+      default: () => {}
+    },
+  },
+  watch: {
+    'entry.featureIds': {
+      handler: function(ids) {
+        this.pubmedQueryOnIds(ids)
+      }
+    }
+  },
+  inject: ['flatmapAPI'],
+  data: function() {
+    return {
+      pubmeds: [],
+      pubmedIds: [],
+    };
+  },
+  mounted: function() {
+    if (this.entry.featureIds)
+      this.pubmedQueryOnIds(this.entry.featureIds)
+  },
+  methods: {
+    stripPMIDPrefix: function (pubmedId){
+      return pubmedId.split(':')[1]
+    },
+    buildPubmedSqlStatement: function(keastIds) {
+      let sql = 'select distinct publication from publications where entity in ('
+      if (keastIds.length === 1) {
+        sql += `'${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>