@abi-software/map-side-bar 1.3.18 → 1.3.19

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-side-bar",
-  "version": "1.3.18",
+  "version": "1.3.19",
   "main": "./dist/map-side-bar.common.js",
   "files": [
     "dist/*",

package/src/components/ContextCard.vue

@@ -48,7 +48,7 @@
                 <div class="view-description">{{view.description}}<i class="el-icon-warning-outline info"></i> </div>
               </span>
               <div v-if="sampleDetails[i]" v-html="samplesMatching(view.id).description" :key="i+'_2'"/>
-              <a v-bind:key="i+'_5'" v-if="sampleDetails[i]" :href="generateFileLink(samplesMatching(view.id).path)" target="_blank">View Source</a>
+              <a v-bind:key="i+'_5'" v-if="sampleDetails[i]" :href="generateFileLink(samplesMatching(view.id))" target="_blank">View Source</a>
               <div :key="i" class="padding"/>
 
               <!-- Extra padding if sample details is open -->
@@ -79,6 +79,26 @@ Vue.use(Button);
 Vue.use(Select);
 Vue.use(Input);
 
+const addFilesToPathIfMissing = function(path){
+  if (!path.includes('files')){
+    return 'files/' + path
+  } else {
+    return path
+  }
+}
+
+const convertBackslashToForwardSlash = function(path){
+  path = path.replaceAll('\\','/')
+  path = path.replaceAll('\\\\', '/')
+  return path
+}
+
+// const switchPathToDirectory = function(path){
+//   let newPath = path.split('/')
+//   newPath.pop()
+//   return newPath.join('/')
+// }
+
 
 export default {
   name: "contextCard",
@@ -88,6 +108,7 @@ export default {
      * the required viewing.
      */
     entry: Object,
+    envVars: Object,
   },
   data: function () {
     return {
@@ -162,9 +183,11 @@ export default {
         .then((data) => {
           this.contextData = data
           this.loading = false
+          this.addDiscoverIdsToContextData() 
         })
-        .catch(() => {
+        .catch((err) => {
           //set defaults if we hit an error
+          console.error('caught error!', err)
           this.thumbnail = require('@/../assets/missing-image.svg')
           this.discoverId = undefined
           this.loading = false
@@ -192,15 +215,39 @@ export default {
         return path
       }
       path = this.removeDoubleFilesPath(path)
-      return  `${this.entry.apiLocation}s3-resource/${this.entry.discoverId}/${this.entry.version}/files/${path}`
+      return  `${this.envVars.API_LOCATION}s3-resource/${this.entry.discoverId}/${this.entry.version}/files/${path}`
     },
-    generateFileLink(path){
-      return `https://sparc.science/file/${this.entry.discoverId}/${this.entry.version}?path=${encodeURI(path)}`
+    //  This is used later when generateing links to the resource on sparc.science (see generateFileLink)
+    addDiscoverIdsToContextData(){
+      this.contextData.samples.forEach((sample, i)=>{
+        if (sample && sample.doi && sample.doi !== ""){
+          fetch(`${this.envVars.PENNSIEVE_API_LOCATION}/discover/datasets/doi/${this.splitDoiFromUrl(sample.doi)}`)
+          .then((response) => response.json())
+          .then((data) => {
+            this.contextData.samples[i].discoverId = data.id
+            this.contextData.samples[i].version = data.version
+          })
+        } else {
+            this.contextData.samples[i].discoverId = this.entry.discoverId
+            this.contextData.samples[i].version = this.entry.version
+        }
+      })
+    },
+    processPathForUrl(path){
+      path = convertBackslashToForwardSlash(path)
+      path = addFilesToPathIfMissing(path)
+      return encodeURI(path)
+    },
+    splitDoiFromUrl(url){
+      return url.split('https://doi.org/').pop()
+    },
+    generateFileLink(sample){
+      return `https://sparc.science/file/${sample.discoverId}/${sample.version}?path=${this.processPathForUrl(sample.path)}`
 
     },
     openViewFile: function(view){
       // note that we assume that the view file is in the same directory as the scaffold (viewUrls take relative paths)
-      this.entry.viewUrl = `${this.entry.apiLocation}s3-resource/${this.entry.discoverId}/${this.entry.version}/${view.path}`
+      this.entry.viewUrl = `${this.envVars.API_LOCATION}s3-resource/${this.entry.discoverId}/${this.entry.version}/${view.path}`
       this.entry.type = 'Scaffold View'
       EventBus.$emit("PopoverActionClick", this.entry)
     }
@@ -237,7 +284,7 @@ export default {
 
 .view-image {
   width: 34px;
-  height: auto;
+  height: 34px;
   flex: 1;
   margin-right: 4px;
 }

package/src/components/SidebarContent.vue

@@ -1,7 +1,7 @@
 <template>
   <el-card :body-style="bodyStyle" class="content-card">
     <div slot="header" class="header">
-      <context-card v-if="contextCardEntry && contextCardEnabled" :entry="contextCardEntry" />
+      <context-card v-if="contextCardEntry && contextCardEnabled" :entry="contextCardEntry" :envVars="envVars"/>
       <el-input
         class="search-input"
         placeholder="Search"

package/src/components/delte.json

@@ -0,0 +1,27 @@
+{
+    "description": "Mean luminal pressure (represented by a color field with red as high pressure and blue as low pressure) recorded from the proximal, transverse and distal sections of the pig colon are mapped on the scaffold. \n\nBaseline data was collected for 30min, followed by 15min of stimulation and 30min of post-stimulation.",
+    "heading": "Direct proximal colon stimulation",
+    "id": "sparc.science.context_data",
+    "samples": [
+        {
+            "annotation": "",
+            "description": "Manometry data recorded from pigs under direct proximal colon stimulation.",
+            "doi": "https://doi.org/10.26275/up27-ibcr",
+            "heading": "Proximal direct stimulation samples",
+            "id": "Sample 1",
+            "path": "derivative\\stim_proximal-colon_manometry.csv",
+            "view": "View 1"
+        }
+    ],
+    "version": "0.1.0",
+    "views": [
+        {
+            "annotation": "--",
+            "description": "Sections of pig colon scaffold with mapped manometry data where the data are collected from. ",
+            "id": "View 1",
+            "path": "colon_Layout1_view.json",
+            "sample": "Sample 1",
+            "thumbnail": "derivative\\pig_colon_main_thumbnail.jpeg"
+        }
+    ]
+}