@abi-software/flatmapvuer 0.5.9-fccb.3 → 0.5.9

package/package-lock.json

@@ -1,6 +1,6 @@
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     "undici": {
-      "version": "5.27.2",
-      "resolved": "https://registry.npmjs.org/undici/-/undici-5.27.2.tgz",
-      "integrity": "sha512-iS857PdOEy/y3wlM3yRp+6SNQQ6xU0mmZcwRSriqk+et/cwWAtwmIGf6WkoDN2EK/AMdCO/dfXzIwi+rFMrjjQ==",
+      "version": "5.28.1",
+      "resolved": "https://registry.npmjs.org/undici/-/undici-5.28.1.tgz",
+      "integrity": "sha512-xcIIvj1LOQH9zAL54iWFkuDEaIVEjLrru7qRpa3GrEEHk6OBhb/LycuUY2m7VCcTuDeLziXCxobQVyKExyGeIA==",
       "requires": {
         "@fastify/busboy": "^2.0.0"
       }
@@ -18195,6 +18233,11 @@
         }
       }
     },
+    "wicked-good-xpath": {
+      "version": "1.3.0",
+      "resolved": "https://registry.npmjs.org/wicked-good-xpath/-/wicked-good-xpath-1.3.0.tgz",
+      "integrity": "sha512-Gd9+TUn5nXdwj/hFsPVx5cuHHiF5Bwuc30jZ4+ronF1qHK5O7HD0sgmXWSEgwKquT3ClLoKPVbO6qGwVwLzvAw=="
+    },
     "wide-align": {
       "version": "1.1.5",
       "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz",
@@ -18290,6 +18333,11 @@
       "resolved": "https://registry.npmjs.org/xdg-basedir/-/xdg-basedir-4.0.0.tgz",
       "integrity": "sha512-PSNhEJDejZYV7h50BohL09Er9VaIefr2LMAf3OEmpCkjOi34eYyQYAXUTjEQtZJTKcF0E2UKTh+osDLsgNim9Q=="
     },
+    "xmldom-sre": {
+      "version": "0.1.31",
+      "resolved": "https://registry.npmjs.org/xmldom-sre/-/xmldom-sre-0.1.31.tgz",
+      "integrity": "sha512-f9s+fUkX04BxQf+7mMWAp5zk61pciie+fFLC9hX9UVvCeJQfNHRHXpeo5MPcR0EUf57PYLdt+ZO4f3Ipk2oZUw=="
+    },
     "xtend": {
       "version": "4.0.2",
       "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "0.5.9-fccb.3",
+  "version": "0.5.9",
   "license": "Apache-2.0",
   "main": "./dist/flatmapvuer.common.js",
   "files": [
@@ -27,8 +27,8 @@
     "version": "npm run build-bundle;npm run changelog; git add CHANGELOG.md"
   },
   "dependencies": {
-    "@abi-software/flatmap-viewer": "^2.4.2-b.4",
-    "@abi-software/sparc-annotation": "0.0.4",
+    "@abi-software/flatmap-viewer": "^2.4.3",
+    "@abi-software/sparc-annotation": "0.0.5",
     "@abi-software/svg-sprite": "^0.3.0",
     "core-js": "^3.3.2",
     "css-element-queries": "^1.2.2",

package/src/components/AnnotationTool.vue

@@ -29,7 +29,7 @@
             </el-row>
             <div class="entry" v-for="(sub, index) in prevSubs" :key="index">
               <el-row class="dialog-text">
-                <strong>{{ formatTime(sub.created) }}</strong> Anonymous
+                <strong>{{ formatTime(sub.created) }}</strong> {{ sub.creator.name }}
               </el-row>
               <el-row class="dialog-text">
                 <strong>Evidence: </strong> 
@@ -43,9 +43,9 @@
             </div>
           </template>
         </template>
-        <el-row class="dialog-spacer"></el-row>
         <template v-if="authenticated">
           <template v-if="isEditable">
+            <el-row class="dialog-spacer"></el-row>
             <el-row v-if="!editing">
               <i
                 class="el-icon-edit standard-icon"
@@ -115,12 +115,12 @@
                   </el-button>
               </el-row>
             </template>
+            <el-row class="dialog-text" v-if="errorMessage">
+              <strong class="sub-title"> {{ errorMessage }}
+              </strong>
+            </el-row>
           </template>
         </template>
-        <el-row class="dialog-text" v-if="errorMessage">
-          <strong class="sub-title"> {{ errorMessage }}
-          </strong>
-        </el-row>
       </template>
     </div>
   </el-main>
@@ -131,7 +131,7 @@
 /* eslint-disable no-alert, no-console */
 /* eslint-disable no-alert, no-console */
 import Vue from "vue";
-//import { AnnotationService } from "@abi-software/sparc-annotation";
+import { AnnotationService } from "@abi-software/sparc-annotation";
 import { Button, Col, Input, Main, Row, Select } from "element-ui";
 import lang from "element-ui/lib/locale/lang/en";
 import locale from "element-ui/lib/locale";
@@ -171,24 +171,12 @@ export default {
       authenticated: false,
       newEvidence: '',
       comment: '',
-      //prevSubs: [ ],
+      prevSubs: [ ],
       showSubmissions: true,
       errorMessage: "",
-      submissions: [ ],
     }
   },
   computed: {
-    prevSubs: function() {
-      return this.submissions.filter(sub => {
-        if (this.annotationEntry) {
-          if (sub.resource === this.annotationEntry.resourceId && 
-            sub.item === this.annotationEntry.featureId) {
-              return true;
-            }
-        }
-        return false;
-      });
-    },
     isEditable: function() {
       return this.annotationEntry['resourceId'] && this.annotationEntry['featureId'];
     },
@@ -206,7 +194,7 @@ export default {
       return new Date(dateString).toLocaleDateString(undefined, options);
     },
     updatePrevSubmissions: function() {
-      if (this.$annotator) {
+      if (this.$annotator && this.authenticated) {
         if (this.annotationEntry['resourceId'] &&
           this.annotationEntry['featureId']) {
           this.$annotator.itemAnnotations(this.annotationEntry['resourceId'],
@@ -221,7 +209,6 @@ export default {
     },
     submit: function() {
       if ((this.evidence.length > 0) || this.comment) {
-        const now = new Date();
         if (this.annotationEntry['resourceId'] &&
           this.annotationEntry['featureId']) {
           const evidenceURLs = [];
@@ -231,7 +218,7 @@ export default {
               evidenceURLs.push(new URL(link));
             } else if (evidence.includes("PMID:")) {
               const link = evidence.replace("PMID:", "https://pubmed.ncbi.nlm.nih.gov/");
-              evidenceURLs.push(link);
+              evidenceURLs.push(new URL(link));
             }
           });
           const userAnnotation = {
@@ -239,11 +226,7 @@ export default {
             item: this.annotationEntry['featureId'],
             evidence: evidenceURLs,
             comment: this.comment,
-            created: now,
           }
-          this.submissions.push(userAnnotation);
-          this.resetSubmission();
-          /*
           this.$annotator.addAnnotation(userAnnotation).then(() => {
             this.errorMessage = "";
             this.resetSubmission();
@@ -252,7 +235,6 @@ export default {
           .catch(() => {
             this.errorMessage = "There is a problem with the submission, please try again later";
           });
-          */
         }
       }
     },
@@ -270,15 +252,13 @@ export default {
     annotationEntry: {
       handler: function() {
         this.resetSubmission();
-        //this.updatePrevSubmissions();
+        this.updatePrevSubmissions();
       },
       immediate: false,
       deep: false,
     }
   },
   mounted: function() {
-    this.authenticated = true;
-  /*
     if (!this.$annotator) {
       Vue.prototype.$annotator = new AnnotationService(
         `${this.flatmapAPI}annotator`);
@@ -286,11 +266,11 @@ export default {
     this.$annotator.authenticate().then((userData) => {
       if (userData.name && userData.email) {
         this.authenticated = true;
+        this.updatePrevSubmissions();
       } else {
-        this.errorMessage = "You cannot view some of the information as you are not logged in or without the correct permission."
+        this.errorMessage = "";
       }
     })
-    */
   }
 };
 </script>

package/src/components/FlatmapVuer.vue

@@ -197,6 +197,19 @@
           v-popover:checkBoxPopover
         >
           <svg-legends v-if="!isFC" class="svg-legends-container" />
+          <el-popover
+            content="Location of the featured dataset"
+            placement="right"
+            :appendToBody="false"
+            trigger="hover"
+            popper-class="flatmap-popper popper-bump-right right-popper"
+            v-model="hoverVisibilities[9].value"
+            ref="featuredMarkerPopover"
+          >
+          </el-popover>
+          <div v-show="showStarInLegend" v-popover:featuredMarkerPopover class="yellow-star-legend" v-html="yellowstar"></div>
+          <!-- The line below places the yellowstar svg on the left, and the text "Featured markers on the right" with css so they are both centered in the div -->
+
           <el-popover
             content="Find these markers for data"
             placement="right"
@@ -418,8 +431,6 @@
         ref="tooltip"
         class="tooltip"
         :annotationEntry="annotationEntry"
-        @highlightConnectedPaths="highlightConnectedPaths"
-        @onClose="closeTooltip"
         :entry="tooltipEntry"
         :annotationDisplay="viewingMode === 'Annotation'"
       />
@@ -447,10 +458,8 @@ import {
 import lang from "element-ui/lib/locale/lang/en";
 import locale from "element-ui/lib/locale";
 import flatmapMarker from "../icons/flatmap-marker";
-import {
-  FlatmapQueries,
-  findTaxonomyLabel,
-} from "../services/flatmapQueries.js";
+import {FlatmapQueries, findTaxonomyLabel} from "../services/flatmapQueries.js";
+import yellowstar from "../icons/yellowstar";
 
 locale.use(lang);
 Vue.use(Button);
@@ -1221,6 +1230,10 @@ export default {
         ];
       },
     },
+    showStarInLegend: {
+      type: Boolean,
+      default: false
+    },
     isLegacy: {
       type: Boolean,
       default: false,
@@ -1291,7 +1304,9 @@ export default {
         { value: false },
         { value: false },
         { value: false },
+        { value: false },
       ],
+      yellowstar: yellowstar,
       isFC: false,
       inHelp: false,
       currentBackground: "white",
@@ -1606,6 +1621,11 @@ export default {
   padding-left: 8px;
 }
 
+.yellow-star-legend {
+  width: 130px;
+  cursor: pointer;
+}
+
 .settings-group {
   bottom: 16px;
   position: absolute;

package/src/components/MultiFlatmapVuer.vue

@@ -53,6 +53,7 @@
       :helpMode="helpMode"
       :renderAtMounted="renderAtMounted"
       :displayMinimap="displayMinimap"
+      :showStarInLegend="showStarInLegend"
       style="height:100%"
       :flatmapAPI="flatmapAPI"
       :sparcAPI="sparcAPI"
@@ -386,6 +387,10 @@ export default {
       type: Boolean,
       default: false
     },
+    showStarInLegend: {
+      type: Boolean,
+      default: false
+    },
     /**
      * Flag to determine rather open map UI should be
      * presented or not.

package/src/components/ProvenancePopup.vue

@@ -5,9 +5,6 @@
       <div v-if="entry.provenanceTaxonomyLabel && entry.provenanceTaxonomyLabel.length > 0" class="subtitle">
         {{provSpeciesDescription}}
       </div>
-      <el-button @click="showConnectedPaths">
-        Show connected paths
-      </el-button>
     </div>
     <div class="block" v-else>
       <span class="title">{{entry.featureId}}</span>
@@ -182,16 +179,9 @@ export default {
     titleCase: function(title){
       return titleCase(title)
     },
-    showConnectedPaths(){
-      this.$emit('highlightConnectedPaths', this.entry.featureId)
-      this.$emit('onClose')
-    },
     capitalise: function(text){
       return capitalise(text)
     },
-    onClose: function() {
-      this.$emit("onClose")
-    },
     openUrl: function(url){
       window.open(url, '_blank')
     },