@abi-software/map-side-bar 1.3.26-staging → 1.3.27

package/package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-side-bar",
-  "version": "1.3.26",
+  "version": "1.3.6",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-side-bar",
-  "version": "1.3.26-staging",
+  "version": "1.3.27",
   "main": "./dist/map-side-bar.common.js",
   "files": [
     "dist/*",

package/src/algolia/algolia.js

@@ -79,10 +79,10 @@ export class AlgoliaClient {
       newResult = { ...res }
       newResult = {
         doi: res.item.curie.split(':')[1],
-        name: res.item.dataset.name,
-        description: res.item.dataset.description,
-        updated: res.pennsieve ? res.pennsieve.updatedAt : 'Unkown',
-        publishDate: res.pennsieve? res.pennsieve.publishDate : 'Uknown',
+        name: res.item.name,
+        description: res.item.description,
+        updated: res.pennsieve.updatedAt,
+        publishDate: res.pennsieve.publishDate,
         datasetId: res.objectID,
         detailsReady: false
       }
@@ -133,20 +133,20 @@ export class AlgoliaClient {
           page: page - 1,
           filters: filter,
           attributesToHighlight: [],
-          // attributesToRetrieve: [
-          //   'pennsieve.publishDate',
-          //   'pennsieve.updatedAt',
-          //   'item.curie',
-          //   'item.name',
-          //   'item.description',
-          //   'objectID',
-          // ],
+          attributesToRetrieve: [
+            'pennsieve.publishDate',
+            'pennsieve.updatedAt',
+            'item.curie',
+            'item.name',
+            'item.description',
+            'objectID',
+          ],
         })
         .then(response => {
           let searchData = {
             items: this._processResultsForCards(response.hits),
             total: response.nbHits,
-            discoverIds: response.hits.map(r => r.pennsieve ? r.pennsieve.identifier : undefined),
+            discoverIds: response.hits.map(r => r.pennsieve.identifier),
             dois: response.hits.map(r => r.item.curie.split(':')[1])
           }
           resolve(searchData)

package/src/components/ContextCard.vue

@@ -1,11 +1,11 @@
 <template>
   <div class="context-card-container"  ref="container">
     <div v-show="showContextCard">
-      <div v-show="showDetails" class="hide" @click="showDetails = !showDetails">Hide information<i class="el-icon-arrow-up"></i></div>
-      <div v-show="!showDetails" class="hide" @click="showDetails = !showDetails">Show information<i class="el-icon-arrow-down"></i></div>
+      <div v-show="showDetails" class="hide" @click="showDetails = !showDetails">Hide information panel<i class="el-icon-arrow-up"></i></div>
+      <div v-show="!showDetails" class="hide" @click="showDetails = !showDetails">Show information panel<i class="el-icon-arrow-down"></i></div>
       <el-card v-if="showDetails && Object.keys(contextData).length !== 0" v-loading="loading" class="context-card" >
         <div class="card-left">
-          <img :src="entry.banner" class="context-image">
+          <img :src="banner" class="context-image">
         </div>
         <div class="card-right scrollbar">
           <div class="title">{{contextData.heading}}</div>
@@ -140,11 +140,8 @@ export default {
   computed: {
     samplesUnderViews: function(){
       if (this.contextData){
-        if (!this.contextData.views || !this.contextData.samples){
-          return false
-        }
         if (this.contextData.samplesUnderViews){
-          return this.contextData.samplesUnderViews
+          return true
         } else {
           let viewId = this.contextData.views.map(v=>v.id)
           let samplesView = this.contextData.samples.map(s=>s.view)
@@ -161,6 +158,16 @@ export default {
       }
       else return false
     },
+    banner: function(){
+      if (this.contextData.banner){
+        this.getFileFromPath(this.contextData.banner) 
+      } else if (this.contextData && this.contextData.views) {
+        if(this.contextData.views[0].thumbnail){
+          return this.getFileFromPath(this.contextData.views[0].thumbnail)
+        }
+      } 
+      return this.entry.banner
+    }
   },
   methods: {
     samplesMatching: function(viewId){

package/src/components/DatasetCard.vue

@@ -4,8 +4,8 @@
       <div class="seperator-path"></div>
       <div v-loading="loading" class="card" >
         <span class="card-left">
-          <image-gallery v-if="!loading" 
-            :datasetId="String(discoverId)"
+          <image-gallery v-if="!loading && discoverId" 
+            :datasetId="discoverId"
             :datasetVersion="version"
             :entry="entry"
             :envVars="envVars"
@@ -172,11 +172,9 @@ export default {
     splitDOI: function(doi){
       return [doi.split('/')[doi.split('/').length-2], doi.split('/')[doi.split('/').length-1]]
     },
-    getBanner: function () { // NOTE! This getBanner uses the pennsieve api to retrive the banner. Only use for curation!
-      if (this.entry.datasetId.length > 4){
-        this.loading = true
-        this.getPennsieveBanner()
-      } else if (this.lastDoi !== this.entry.doi) {
+    getBanner: function () {
+      // Only load banner if card has changed
+      if (this.lastDoi !== this.entry.doi) {
         this.lastDoi = this.entry.doi
         this.loading = true
         let doi = this.splitDOI(this.entry.doi)
@@ -193,7 +191,7 @@ export default {
             this.discoverId = data.id
             this.version = data.version
             this.dataLocation = `https://sparc.science/datasets/${data.id}?type=dataset`
-            if (this.discoverId.length < 5) this.getBiolucidaInfo(this.discoverId)
+            this.getBiolucidaInfo(this.discoverId)
             this.loading = false
           })
           .catch(() => {
@@ -202,67 +200,9 @@ export default {
             this.discoverId = Number(this.entry.datasetId)
             this.loading = false
           });
-      } 
-    },
-    getPennsieveBanner: function(){
-      // authenticate with pennsieve
-      fetch('https://cognito-idp.us-east-1.amazonaws.com/', {
-        method: 'POST',
-        headers: {
-          'Accept': 'application/json, text/plain, */*',
-          'Content-Type': 'application/x-amz-json-1.1',
-          'X-Amz-Target': 'AWSCognitoIdentityProviderService.InitiateAuth',
-          'X-Amz-User-Agent': 'aws-amplify/0.1.x js',
-        },
-        body: JSON.stringify({"AuthFlow":"USER_PASSWORD_AUTH","ClientId":"670mo7si81pcc3sfub7o1914d8","AuthParameters":{"USERNAME":"jessekhorasanee@gmail.com","PASSWORD":"Asameswayhey@666","DEVICE_KEY":"us-east-1_0d4e8de7-6079-470d-bedd-62043ba70f7e"},"ClientMetadata":{}})
-      }).then(res => res.json())
-        .then(res => {
-            console.log(res)
-            let token = res.AuthenticationResult.AccessToken
-            let proxy = `${this.envVars.API_LOCATION}proxy/?url=` // set up proxy 
-
-            // call pennsieve api via proxy
-            fetch(`${proxy}https://api.pennsieve.io/datasets/N%3Adataset%3A${this.entry.datasetId}/banner?api_key=${token}`
-            ).then(res=>res.json()).then(res=>{
-              console.log('success!')
-              this.thumbnail = res.banner
-              this.discoverId = this.entry.datasetId
-              this.loading = false
-            })
-        })
+      }
 
     },
-    // getBanner: function () {
-    //   // Only load banner if card has changed
-    //   if (this.lastDoi !== this.entry.doi) {
-    //     this.lastDoi = this.entry.doi
-    //     this.loading = true
-    //     let doi = this.splitDOI(this.entry.doi)
-    //     fetch(`${this.envVars.PENNSIEVE_API_LOCATION}/discover/datasets/doi/${doi[0]}/${doi[1]}`)
-    //       .then((response) =>{
-    //         if (!response.ok){
-    //           throw Error(response.statusText)
-    //         } else {
-    //           return response.json()
-    //         }
-    //       })
-    //       .then((data) => {
-    //         this.thumbnail = data.banner
-    //         this.discoverId = data.id
-    //         this.version = data.version
-    //         this.dataLocation = `https://sparc.science/datasets/${data.id}?type=dataset`
-    //         this.getBiolucidaInfo(this.discoverId)
-    //         this.loading = false
-    //       })
-    //       .catch(() => {
-    //         //set defaults if we hit an error
-    //         this.thumbnail = require('@/../assets/missing-image.svg')
-    //         this.discoverId = Number(this.entry.datasetId)
-    //         this.loading = false
-    //       });
-    //   }
-
-    // },
     lastName: function(fullName){
       return fullName.split(',')[0]
     },

package/src/components/ImageGallery.vue

@@ -28,7 +28,7 @@ const capitalise = function (string) {
   return string.replace(/\b\w/g, (v) => v.toUpperCase());
 };
 
-import GalleryHelper from "../mixins/GalleryHelpers";
+import GalleryHelper from "@abi-software/gallery/src/mixins/GalleryHelpers";
 import Gallery from "@abi-software/gallery";
 import "@abi-software/gallery/dist/gallery.css";
 
@@ -58,8 +58,8 @@ export default {
       },
     },
     datasetId: {
-      type: String,
-      default: "",
+      type: Number,
+      default: -1,
     },
     datasetVersion: {
       type: Number,
@@ -215,6 +215,7 @@ export default {
     },
     createScaffoldItems: function () {
       if (this.entry.scaffolds) {
+        window.entry = this.entry
         let index = 0;
         this.entry.scaffolds.forEach((scaffold, i) => {
           const filePath = scaffold.dataset.path;
@@ -228,7 +229,12 @@ export default {
           let mimetype = '';
           let thumbnailURL = undefined;
           if (thumbnail) {
-            thumbnailURL = `${this.envVars.API_LOCATION}s3-resource/${this.datasetId}/${this.datasetVersion}/files/${filePath}`
+            thumbnailURL = this.getImageURLFromS3(this.envVars.API_LOCATION, {
+              id,
+              datasetId: this.datasetId,
+              datasetVersion: this.datasetVersion,
+              file_path: thumbnail.dataset.path,
+            });
             mimetype = thumbnail.mimetype.name;
           }
           let action = {
@@ -344,7 +350,7 @@ export default {
         return undefined
       } else {
         // The line below checks if there is a context file for each scaffold. If there is not, we use the first context card for each scaffold.
-        let contextIndex = this.entry.contextualInformation.length == this.entry.scaffolds.length ? scaffoldIndex : 0
+        let contextIndex = this.entry['abi-contextual-information'].length == this.entry.scaffolds.length ? scaffoldIndex : 0
         return `${this.envVars.API_LOCATION}s3-resource/${this.datasetId}/${this.datasetVersion}/files/${this.entry.contextualInformation[contextIndex]}`
       }
     }

package/src/components/SidebarContent.vue

@@ -311,12 +311,9 @@ export default {
       }
       data.results.forEach(element => {
         // match the scicrunch result with algolia result
-        let i = this.results.findIndex(res=> (res.datasetId === element.dataset_identifier) || (res.identifier === element.dataset_identifier))
-        console.log('i: ', i)
-        let name = this.results[i].name
+        let i = this.results.findIndex(res => element.doi ? element.doi.includes(res.doi) : false )
         // Assign scicrunch results to the object
         Object.assign(this.results[i], element)
-        this.results[i].name = name
         // Assign the attributes that need some processing
         Object.assign(this.results[i],{
           numberSamples: element.sampleSize
@@ -325,8 +322,8 @@ export default {
           numberSubjects: element.subjectSize
             ? parseInt(element.subjectSize)
             : 0,
-          updated: element.updated ? element.updated[0].timestamp.split("T")[0] : undefined,
-          url: element.uri? element.uri[0] : undefined,
+          updated: (element.updated && element.updated.length) > 0 ? element.updated[0].timestamp.split("T")[0] : "",
+          url: element.uri[0],
           datasetId: element.dataset_identifier,
           datasetRevision: element.dataset_revision,
           datasetVersion: element.dataset_version,

package/dist/img/logo-sparc-wave-primary.8ed83a51.svg

@@ -1 +0,0 @@
-<svg id="logo-sparc-wave-primary" data-name="logo-sparc-wave-primary" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 400 190.5854"><defs><linearGradient id="linear-gradient" y1="96.3505" x2="400" y2="96.3505" gradientUnits="userSpaceOnUse"><stop offset="0" stop-color="#0b00bf"/><stop offset="1" stop-color="#bc00fc"/></linearGradient></defs><title>SPARC Logo</title><path d="M396.6976,128.6248l-146.2735-3.38a6.5358,6.5358,0,0,0-6.1378,3.9236l-.0612.1407-13.673,31.4482L202.9416,9.5333l-.01-.0685a8.9823,8.9823,0,0,0-17.6624-.0114L163.673,125.3819,3.298,129.2886a3.38,3.38,0,0,0,.0269,6.7592L169.34,138.7635a6.5939,6.5939,0,0,0,6.5373-5.1457l.0571-.2546,17.8534-79.5649L221.26,185.1237l.0256.1243A6.7593,6.7593,0,0,0,234.092,186.52L254.9005,138.66l141.7971-3.2762a3.3805,3.3805,0,0,0,0-6.7592Z" style="fill:url(#linear-gradient)"/><path d="M25.6793,0C41.3957,0,51.057,10.0926,51.057,26.0972v9.5162H36.2053V26.0972c0-7.3532-3.8945-11.8219-10.526-11.8219-6.7768,0-10.6691,4.4687-10.6691,11.8219,0,3.8945,1.2982,7.3533,5.4786,11.3908l19.754,18.601C46.5861,62.1441,52.21,68.7778,52.21,79.88c0,16.0047-9.95,26.0973-25.9543,26.0973C10.108,105.9776.1585,95.885.1585,79.88V70.362H15.01V79.88c0,7.3533,4.0375,11.822,11.2455,11.822,7.065,0,11.1025-4.4687,11.1025-11.822,0-4.4709-2.1628-8.6514-6.0551-12.2576L11.1158,48.7357C3.043,41.2372.1585,34.8939.1585,25.666.1585,10.0926,9.82,0,25.6793,0Z" style="fill:#0e0e19"/><path d="M99.7971,69.7856v35.1821H84.9454V1.01h25.3755c16.0047,0,26.0973,10.0926,26.0973,26.0973V43.6883c0,16.15-10.0926,26.0973-26.0973,26.0973Zm10.3808-13.9849c7.2081,0,11.3908-4.3257,11.3908-11.6789V26.6759c0-7.21-4.1827-11.6811-11.3908-11.6811H99.7971V55.8007Z" style="fill:#0e0e19"/><path d="M278.5812,108.147H263.73V4.1893h26.0972c16.0047,0,26.0973,10.0926,26.0973,26.0972v14.13c0,9.95-4.3257,17.7363-11.3908,22.205,4.1827,12.6889,10.0926,29.9917,13.8418,41.5254h-15.14L290.6914,70.3708h-12.11Zm11.1-51.7632c7.21,0,11.3907-4.3257,11.3907-11.5338V29.8553c0-7.21-4.18-11.6812-11.3907-11.6812h-11.1v38.21Z" style="fill:#0e0e19"/><path d="M399.844,73.5414V83.06c0,16.0047-9.9474,26.0973-25.9521,26.0973-16.15,0-26.0972-10.0926-26.0972-26.0973V29.2766c0-16.0046,9.9473-26.0972,26.0972-26.0972,16.0047,0,25.9521,10.0926,25.9521,26.0972v9.5161h-14.85V29.2766c0-7.3532-4.0374-11.822-11.1025-11.822-7.21,0-11.2477,4.4688-11.2477,11.822V83.06c0,7.3533,4.0375,11.822,11.2477,11.822,7.0651,0,11.1025-4.4687,11.1025-11.822V73.5414Z" style="fill:#0e0e19"/></svg>

package/src/mixins/GalleryHelpers.js

@@ -1,104 +0,0 @@
-import axios from 'axios'
-
-export default {
-  //this mixin is not used by this code base but it can be used by other
-  //projects to get a handle to various resources
-  data() {
-    return {
-      defaultImg: require('../../assets/logo-sparc-wave-primary.svg'),
-    }
-  },
-  methods: {
-    async getRequest(url, params, timeout) {
-      return await axios({
-        method: 'get',
-        url,
-        params,
-        timeout,
-      })
-    },
-    /**
-     * Returns a file path for S3.
-     * @param {String} dataset_id dataset id.
-     * @param {String} dataset_version dataset version.
-     * @param {String} file_path file path.
-     * @returns {String} full path to S3 file.
-     */
-    getS3FilePath(dataset_id, dataset_version, file_path) {
-      const encoded_file_path = encodeURIComponent(file_path)
-      return `${dataset_id}/${dataset_version}/files/${encoded_file_path}`
-    },
-    /**
-     * Find data path in the array that matches the provide path
-     */
-    findEntryWithPathInArray(array, path) {
-      if (path && array) {
-        for (let i = 0; i < array.length; i++) {
-          if (path === array[i].dataset.path) return array[i]
-        }
-      }
-      return undefined
-    },
-    getThumbnailForPlot(plot, thumbnails) {
-      if (thumbnails && plot) {
-        return this.findEntryWithPathInArray(thumbnails, plot.datacite.isSourceOf.path[0])
-      }
-      return undefined
-    },
-    /**
-     * Use the scaffoldViews to help with finding the correct thumbnails.
-     * Use the index if the workflow stated above fails.
-     */
-    getThumbnailForScaffold(scaffold, scaffoldViews, thumbnails, index) {
-      if (thumbnails && thumbnails.length > 0) {
-        let thumbnail = undefined
-        if (scaffold && scaffoldViews) {
-          const view = this.findEntryWithPathInArray(scaffoldViews, scaffold.datacite.isSourceOf.path[0])
-          if (view) {
-            thumbnail = this.findEntryWithPathInArray(thumbnails, view.datacite.isSourceOf.path[0])
-          }
-        }
-        if (thumbnail) {
-          return thumbnail
-        } else if (index < thumbnails.length) {
-          return thumbnails[index]
-        }
-      }
-      return undefined
-    },
-    getImageURLFromS3(apiEndpoint, info) {
-      return `${apiEndpoint}/s3-resource/${info.datasetId}/${info.datasetVersion}/files/${info.file_path}?encodeBase64=true`
-    },
-    getSegmentationThumbnailURL(apiEndpoint, info) {
-      let endpoint = `${apiEndpoint}/thumbnail/neurolucida`
-      endpoint = endpoint + `?datasetId=${info.datasetId}`
-      endpoint = endpoint + `&version=${info.datasetVersion}`
-      endpoint = endpoint + `&path=files/${info.segmentationFilePath}`
-      return endpoint
-    },
-    getThumbnailURLFromBiolucida(apiEndpoint, info) {
-      return `${apiEndpoint}/thumbnail/${info.id}`
-    },
-    getImageInfoFromBiolucida(apiEndpoint, items, info) {
-      const endpoint = `${apiEndpoint}/image/${info.id}`
-      const params = {}
-      this.getRequest(endpoint, params, 20000).then(
-        (response) => {
-          let item = items.find((x) => x.id === info.id)
-          const name = response.name
-          if (name) {
-            item.title = name
-          }
-        },
-        (reason) => {
-          if (reason.message.includes('timeout') && reason.message.includes('exceeded') && info.fetchAttempts < 3) {
-            info.fetchAttempts += 1
-            this.getImageInfoFromBiolucida(apiEndpoint, items, info)
-          }
-
-          return Promise.reject('Maximum iterations reached.')
-        }
-      )
-    },
-  },
-}