@abi-software/map-side-bar 1.3.34 → 1.3.36

package/package-lock.json

@@ -1,13 +1,13 @@
 {
   "name": "@abi-software/map-side-bar",
-  "version": "1.3.34",
+  "version": "1.3.36",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
     "@abi-software/gallery": {
-      "version": "0.3.1",
-      "resolved": "https://registry.npmjs.org/@abi-software/gallery/-/gallery-0.3.1.tgz",
-      "integrity": "sha512-ED5ppMiXfHbobM073SnDiUhomviLH+dSQ6jgk6b9ULBkdTmF6r0cE6WbPHYJHdNgZVJDbYokBieO/URrff8QhQ==",
+      "version": "0.3.2",
+      "resolved": "https://registry.npmjs.org/@abi-software/gallery/-/gallery-0.3.2.tgz",
+      "integrity": "sha512-YvLlBQVQY7mKyytfsYKX838ulpzlHo8THYEiDwBOT4xSdBVzl+t1cNvFC4Fip+QcXw96LLDJLKCiZXtU+7JDTw==",
       "requires": {
         "@babel/code-frame": "^7.12.11",
         "axios": "^0.26.1",
@@ -19,19 +19,19 @@
       },
       "dependencies": {
         "@babel/code-frame": {
-          "version": "7.16.7",
-          "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.16.7.tgz",
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+          "version": "7.18.6",
+          "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.18.6.tgz",
+          "integrity": "sha512-TDCmlK5eOvH+eH7cdAFlNXeVJqWIQ7gW9tY1GJIpUtFb6CmjVyq2VM3u71bOyR8CRihcCgMUYoDNyLXao3+70Q==",
           "requires": {
-            "@babel/highlight": "^7.16.7"
+            "@babel/highlight": "^7.18.6"
           }
         },
         "@babel/highlight": {
-          "version": "7.17.12",
-          "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.17.12.tgz",
-          "integrity": "sha512-7yykMVF3hfZY2jsHZEEgLc+3x4o1O+fYyULu11GynEUQNwB6lua+IIQn1FiJxNucd5UlyJryrwsOh8PL9Sn8Qg==",
+          "version": "7.18.6",
+          "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.18.6.tgz",
+          "integrity": "sha512-u7stbOuYjaPezCuLj29hNW1v64M2Md2qupEKP1fHc7WdOA3DgLh37suiSrZYY7haUB7iBeQZ9P1uiRF359do3g==",
           "requires": {
-            "@babel/helper-validator-identifier": "^7.16.7",
+            "@babel/helper-validator-identifier": "^7.18.6",
             "chalk": "^2.0.0",
             "js-tokens": "^4.0.0"
           }
@@ -55,14 +55,14 @@
           }
         },
         "core-js": {
-          "version": "3.22.8",
-          "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.22.8.tgz",
-          "integrity": "sha512-UoGQ/cfzGYIuiq6Z7vWL1HfkE9U9IZ4Ub+0XSiJTCzvbZzgPA69oDF2f+lgJ6dFFLEdjW5O6svvoKzXX23xFkA=="
+          "version": "3.29.1",
+          "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.29.1.tgz",
+          "integrity": "sha512-+jwgnhg6cQxKYIIjGtAHq2nwUOolo9eoFZ4sHfUH09BLXBgxnH4gA0zEd+t+BO2cNB8idaBtZFcFTRjQJRJmAw=="
         },
         "element-ui": {
-          "version": "2.15.9",
-          "resolved": "https://registry.npmjs.org/element-ui/-/element-ui-2.15.9.tgz",
-          "integrity": "sha512-dx45nQLt4Hn87/Z9eRr3ex6KFZbxlFAwEU3QoW3wA5EsYftvHTyL9Pq7VnXXD7hu1Eiaup2jcs6kp+/VSFmXuA==",
+          "version": "2.15.13",
+          "resolved": "https://registry.npmjs.org/element-ui/-/element-ui-2.15.13.tgz",
+          "integrity": "sha512-LJoatEYX6WV74FqXBss8Xfho9fh9rjDSzrDrTyREdGb1h1R3uRvmLh5jqp2JU137aj4/BgqA3K06RQpQBX33Bg==",
           "requires": {
             "async-validator": "~1.8.1",
             "babel-helper-vue-jsx-merge-props": "^2.0.0",
@@ -535,9 +535,9 @@
       }
     },
     "@babel/helper-validator-identifier": {
-      "version": "7.16.7",
-      "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.16.7.tgz",
-      "integrity": "sha512-hsEnFemeiW4D08A5gUAZxLBTXpZ39P+a+DGDsHw1yxqyQ/jzFEnxf5uTEGp+3bzAbNOxU1paTgYS4ECU/IgfDw=="
+      "version": "7.19.1",
+      "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.19.1.tgz",
+      "integrity": "sha512-awrNfaMtnHUr653GgGEs++LlAvW6w+DcPrOliSMXWCKo597CwL5Acf/wWdNkf/tfEQE3mjkeD1YOVZOUV/od1w=="
     },
     "@babel/helper-wrap-function": {
       "version": "7.7.4",
@@ -3100,14 +3100,14 @@
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         },
         "json5": {
-          "version": "2.2.1",
-          "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.1.tgz",
-          "integrity": "sha512-1hqLFMSrGHRHxav9q9gNjJ5EXznIxGVO09xQRrwplcS8qs28pZ8s8hupZAmqDwZUmVZ2Qb2jnyPOWcDH8m8dlA=="
+          "version": "2.2.3",
+          "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz",
+          "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg=="
         },
         "loader-utils": {
-          "version": "2.0.2",
-          "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.2.tgz",
-          "integrity": "sha512-TM57VeHptv569d/GKh6TAYdzKblwDNiumOdkFnejjD0XwTH87K90w3O7AiJRqdQoXygvi1VQTJTLGhJl7WqA7A==",
+          "version": "2.0.4",
+          "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.4.tgz",
+          "integrity": "sha512-xXqpXoINfFhgua9xiqD8fPFHgkoq1mmmpE92WlDbm9rNRd/EbRb+Gqf908T2DMfuHjjJlksiK2RbHVOdD/MqSw==",
           "requires": {
             "big.js": "^5.2.2",
             "emojis-list": "^3.0.0",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-side-bar",
-  "version": "1.3.34",
+  "version": "1.3.36",
   "main": "./dist/map-side-bar.common.js",
   "files": [
     "dist/*",
@@ -17,7 +17,7 @@
     "start": "vue-cli-service serve"
   },
   "dependencies": {
-    "@abi-software/gallery": "^0.3.1",
+    "@abi-software/gallery": "^0.3.2",
     "@abi-software/svg-sprite": "^0.1.14",
     "algoliasearch": "^4.10.5",
     "element-ui": "^2.13.0",

package/src/algolia/utils.js

@@ -8,16 +8,16 @@ export const facetPropPathMapping = {
   'item.modalities.keyword' : 'Experimental Approach',
   'attributes.subject.sex.value' : 'Sex',
   'attributes.subject.ageCategory.value' : 'Age Categories',
-  'item.keywords.keyword' : 'Keywords'
+  'item.types.name' : 'Data type',
 }
 
 // Same as above, but these show on the sidebar filters
 export const shownFilters = {
   'anatomy.organ.name' : 'Anatomical Structure',
   'organisms.primary.species.name' : 'Species',
-  'item.modalities.keyword' : 'Experimental Approach',
   'attributes.subject.sex.value' : 'Sex',
   'attributes.subject.ageCategory.value' : 'Age Categories',
+  'item.types.name' : 'Data type',
 }
 
 /* Returns filter for searching algolia. All facets of the same category are joined with OR,

package/src/components/ContextCard.vue

@@ -71,6 +71,9 @@ import locale from "element-ui/lib/locale";
 import EventBus from "./EventBus"
 import hardcoded_info from './hardcoded-context-info'
 
+//provide the s3Bucket related methods and data.
+import S3Bucket from "../mixins/S3Bucket";
+
 import { marked } from 'marked'
 import xss from 'xss'
 
@@ -105,6 +108,7 @@ const convertBackslashToForwardSlash = function(path){
 
 export default {
   name: "contextCard",
+  mixins: [S3Bucket],
   props: {
     /**
      * Object containing information for
@@ -138,6 +142,12 @@ export default {
         }
       },
       immediate: true
+    },
+    'entry.s3uri': {
+      handler(val){
+        this.updateS3Bucket(val);
+      },
+      immediate: true
     }
   },
   computed: {
@@ -228,7 +238,7 @@ export default {
         return path
       }
       path = this.removeDoubleFilesPath(path)
-      return  `${this.envVars.API_LOCATION}s3-resource/${this.entry.discoverId}/${this.entry.version}/files/${path}`
+      return  `${this.envVars.API_LOCATION}s3-resource/${this.entry.discoverId}/${this.entry.version}/files/${path}${this.getS3Args()}`
     },
     //  This is used later when generateing links to the resource on sparc.science (see generateFileLink)
     addDiscoverIdsToContextData(){
@@ -263,7 +273,7 @@ export default {
     },
     openViewFile: function(view){
       // note that we assume that the view file is in the same directory as the scaffold (viewUrls take relative paths)
-      this.entry.viewUrl = `${this.envVars.API_LOCATION}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.getS3Args()}`
       this.entry.type = 'Scaffold View'
       EventBus.$emit("PopoverActionClick", this.entry)
     }

package/src/components/ImageGallery.vue

@@ -30,12 +30,14 @@ const capitalise = function (string) {
 
 import GalleryHelper from "@abi-software/gallery/src/mixins/GalleryHelpers";
 import Gallery from "@abi-software/gallery";
+//provide the s3Bucket related methods and data.
+import S3Bucket from "../mixins/S3Bucket";
 import "@abi-software/gallery/dist/gallery.css";
 
 export default {
   name: "ImageGallery",
   components: { Gallery },
-  mixins: [GalleryHelper],
+  mixins: [GalleryHelper, S3Bucket],
   props: {
     datasetBiolucida: {
       type: Object,
@@ -107,7 +109,7 @@ export default {
       imageStyle: { maxWidth: '160px', maxHeight: '160px'},
       shadow: "never",
       bottomSpacer: { minHeight: '0rem' },
-      resetIndex: false
+      resetIndex: false,
     };
   },
   methods: {
@@ -115,6 +117,7 @@ export default {
       this.$emit('card-clicked', payload);
     },
     createSciCurnchItems: function () {
+      this.updateS3Bucket(this.entry.s3uri);
       this.createDatasetItem();
       this.createScaffoldItems();
       this.createSimulationItems();
@@ -170,12 +173,13 @@ export default {
               datasetId: this.datasetId,
               datasetVersion: this.datasetVersion,
               file_path: thumbnail.dataset.path,
+              s3Bucket: this.s3Bucket,
             });
             mimetype = thumbnail.mimetype.name;
           }
           const plotAnnotation = plot.datacite;
           const filePathPrefix = `${this.envVars.API_LOCATION}/s3-resource/${this.datasetId}/${this.datasetVersion}/files/`;
-          const sourceUrl = filePathPrefix + plot.dataset.path;
+          const sourceUrl = filePathPrefix + plot.dataset.path + this.getS3Args();
 
           const metadata = JSON.parse(
             plotAnnotation.supplemental_json_metadata.description
@@ -197,6 +201,7 @@ export default {
           let action = {
             label: capitalise(this.label),
             resource: resource,
+            s3uri: this.entry.s3uri,
             title: "View plot",
             type: "Plot",
             discoverId: this.discoverId,
@@ -234,18 +239,20 @@ export default {
               datasetId: this.datasetId,
               datasetVersion: this.datasetVersion,
               file_path: thumbnail.dataset.path,
+              s3Bucket: this.s3Bucket,
             });
             mimetype = thumbnail.mimetype.name;
           }
           let action = {
             label: capitalise(this.label),
-            resource: `${this.envVars.API_LOCATION}s3-resource/${this.datasetId}/${this.datasetVersion}/files/${filePath}`,
+            resource: `${this.envVars.API_LOCATION}s3-resource/${this.datasetId}/${this.datasetVersion}/files/${filePath}${this.getS3Args()}`,
             title: "View 3D scaffold",
             type: "Scaffold",
             discoverId: this.datasetId,
             apiLocation: this.envVars.API_LOCATION,
             version: this.datasetVersion,
             banner: this.datasetThumbnail,
+            s3uri: this.entry.s3uri,
             contextCardUrl: this.getContextCardUrl(i)
           };
           this.items['Scaffolds'].push({
@@ -275,6 +282,7 @@ export default {
             label: capitalise(this.label),
             resource: resource,
             datasetId: this.datasetId,
+            s3uri: this.entry.s3uri,
             title: "View segmentation",
             type: "Segmentation",
           };
@@ -285,6 +293,7 @@ export default {
               datasetId: this.datasetId,
               datasetVersion: this.datasetVersion,
               segmentationFilePath: filePath,
+              s3Bucket: this.s3Bucket,
             }
           );
           this.items['Segmentations'].push({
@@ -304,6 +313,7 @@ export default {
         let action = {
           label: undefined,
           apiLocation: this.envVars.API_LOCATION,
+          s3uri: this.entry.s3uri,
           version: this.datasetVersion,
           title: "View simulation",
           type: "Simulation",
@@ -351,7 +361,7 @@ export default {
       } else {
         // The line below checks if there is a context file for each scaffold. If there is not, we use the first context card for each scaffold.
         let contextIndex = this.entry['abi-contextual-information'].length == this.entry.scaffolds.length ? scaffoldIndex : 0
-        return `${this.envVars.API_LOCATION}s3-resource/${this.datasetId}/${this.datasetVersion}/files/${this.entry.contextualInformation[contextIndex]}`
+        return `${this.envVars.API_LOCATION}s3-resource/${this.datasetId}/${this.datasetVersion}/files/${this.entry.contextualInformation[contextIndex]}${this.getS3Args()}`
       }
     }
   },

package/src/components/SearchFilters.vue

@@ -178,7 +178,6 @@ export default {
                   this.createCascaderItemValue(facet.label, facetItem.label);
               });
             });
-            this.createDataTypeFacet();
           })
           .finally(() => {
             resolve();
@@ -290,28 +289,6 @@ export default {
       }
       return event;
     },
-    createDataTypeFacet: function(){
-      let dataFacet = {...this.facets[2]} // copy the 'Experiemental approach' facet
-      let count = this.facets.at(-1).id // get the last id count
-
-      // Step through the children that are valid data types, switch thier values 
-      let newChildren = dataFacet.children.filter( el=> {
-        if (el.label === 'Scaffold' || el.label === 'Simulation' || el.label === 'Show all'){
-          el.key = el.label
-          el.id = count
-          el.value = el.value.replace('Experimental approach', 'Data type')
-          count++
-          return el
-        }
-      })
-      dataFacet.id = count
-      dataFacet.key = 'Data type'
-      // Add 'duplicate' so that the key is unique. This is removed in the cascade event for filtering
-      dataFacet.value += 'duplicate' 
-      dataFacet.children = newChildren
-      dataFacet.label = 'Data type'
-      this.facets.push(dataFacet)
-    },
     cascadeExpandChange: function (event) {
       //work around as the expand item may change on modifying the cascade props
       this.__expandItem__ = event;

package/src/mixins/S3Bucket.vue

@@ -0,0 +1,31 @@
+<script>
+export default {
+  name: "S3Bucket",
+  data() {
+    return {
+      s3Bucket: undefined,
+    };
+  },
+  methods: {
+    updateS3Bucket: function(s3uri) {
+      this.s3Bucket = undefined;
+      if (s3uri) {
+        const substring = s3uri.split("//")[1];
+        if (substring) {
+          this.s3Bucket = substring.split("/")[0];
+          return;
+        }
+      }
+    },
+    getS3Args: function() {
+      if (this.s3Bucket) {
+        return `?s3BucketName=${this.s3Bucket}`
+      }
+      return "";
+    },
+  },
+
+};
+</script>
+
+