feat(#458): Merging upstream updates

.gitignore

@@ -28,6 +28,7 @@ package-lock.json
 **/**/*.log
 
 # Fuseki
+mockDB/old-fuseki/
 mockDB/fuseki/shiro.ini
 mockDB/fuseki/backups/
 mockDB/fuseki/databases/
@@ -39,7 +40,10 @@ mockDB/fuseki/log4j2.properties
 mockDB/materialsmine_backup/
 mockDB/fuseki/files/
 mockDB/fuseki/
+<<<<<<< HEAD
 mockDB/old-fuseki/
+=======
+>>>>>>> aeed7f9992460ee97924129c5deb1bc0ae161abf
 
 #Sync DB
 mockDB/restore/mongodump/

app/src/components/ChartGallery.vue

@@ -138,14 +138,14 @@
 </template>
 
 <script>
-import spinner from '@/components/Spinner'
-import pagination from '@/components/explorer/Pagination'
-import Dialog from '@/components/Dialog.vue'
-import defaultImg from '@/assets/img/rdf_flyer.svg'
-import { toChartId } from '@/modules/vega-chart'
-import { mapGetters, mapActions, mapMutations } from 'vuex'
-import reducer from '@/mixins/reduce'
-import explorerQueryParams from '@/mixins/explorerQueryParams'
+import spinner from '@/components/Spinner';
+import pagination from '@/components/explorer/Pagination';
+import Dialog from '@/components/Dialog.vue';
+import defaultImg from '@/assets/img/rdf_flyer.svg';
+import { toChartId } from '@/modules/vega-chart';
+import { mapGetters, mapActions, mapMutations } from 'vuex';
+import reducer from '@/mixins/reduce';
+import explorerQueryParams from '@/mixins/explorerQueryParams';
 
 export default {
   name: 'ChartGallery',
@@ -160,7 +160,7 @@ export default {
       default: () => false
     }
   },
-  data () {
+  data() {
     return {
       loading: false,
       loadError: false,
@@ -172,7 +172,7 @@ export default {
         title: 'Test'
       },
       dialogLoading: false
-    }
+    };
   },
   components: {
     pagination,
@@ -194,11 +194,11 @@ export default {
       totalFavorites: 'explorer/gallery/totalFavorites',
       missingCharts: 'explorer/gallery/missingCharts'
     }),
-    galleryChartItems () {
+    galleryChartItems() {
       if (!this.isFavourite) {
-        return this.items
+        return this.items;
       } else {
-        return this.favoriteChartItems
+        return this.favoriteChartItems;
       }
     }
   },
@@ -209,129 +209,129 @@ export default {
       'fetchFavoriteCharts'
     ]),
     ...mapMutations({ toggleDialogBox: 'setDialogBox' }),
-    renderDialog (title, type, result, minWidth) {
+    renderDialog(title, type, result, minWidth) {
       this.dialog = {
         title,
         type,
         minWidth,
         chart: result
-      }
-      this.toggleDialogBox()
+      };
+      this.toggleDialogBox();
     },
-    async deleteChart (chart, retry = false) {
+    async deleteChart(chart, retry = false) {
       try {
-        if (!this.isAdmin) return // temporary safeguard
+        if (!this.isAdmin) return; // temporary safeguard
 
         // Retry is a flag to determine if the function is called from retry action
         if (!retry) {
-          this.dialogLoading = true
+          this.dialogLoading = true;
         }
         await this.$store.dispatch(
           'explorer/curation/deleteEntityNanopub',
           chart.identifier
-        )
+        );
         await this.$store.dispatch('explorer/curation/deleteEntityES', {
           identifier: chart.identifier,
           type: 'charts'
-        })
-        await this.loadItems()
+        });
+        await this.loadItems();
         if (!retry) {
-          this.toggleDialogBox()
-          this.dialogLoading = false
+          this.toggleDialogBox();
+          this.dialogLoading = false;
         }
-        return
+        return;
       } catch (error) {
         if (!retry) {
-          this.toggleDialogBox()
-          this.dialogLoading = false
+          this.toggleDialogBox();
+          this.dialogLoading = false;
         }
         this.$store.commit('setSnackbar', {
           message: error || 'Something went wrong',
           action: () => this.deleteChart(chart, true)
-        })
+        });
       }
     },
-    editChart (chart) {
+    editChart(chart) {
       return this.$router.push(
         `/explorer/chart/editor/edit/${this.getChartId(chart)}`
-      )
+      );
     },
-    async bookmark (chart) {
-      await this.bookmarkChart({ chart })
+    async bookmark(chart) {
+      await this.bookmarkChart({ chart });
     },
-    async localSearchMethod () {
-      await this.loadItems(this.pageNumber)
+    async localSearchMethod() {
+      await this.loadItems(this.pageNumber);
     },
-    async loadItems (page = 1) {
+    async loadItems(page = 1) {
       try {
-        this.loading = true
-        await this.$store.dispatch('explorer/gallery/loadItems', { page })
-        this.loading = false
+        this.loading = true;
+        await this.$store.dispatch('explorer/gallery/loadItems', { page });
+        this.loading = false;
       } catch (error) {
         this.$store.commit('setSnackbar', {
           message: error || 'Something went wrong',
           action: () => this.loadItems(page)
-        })
-        return (this.loading = false)
+        });
+        return (this.loading = false);
       }
     },
-    getChartId (chart) {
-      return toChartId(chart.identifier)
+    getChartId(chart) {
+      return toChartId(chart.identifier);
     },
-    formatMissingFavouriteText () {
-      const message = `${this.missingCharts.length} out of your favourite charts `
+    formatMissingFavouriteText() {
+      const message = `${this.missingCharts.length} out of your favourite charts `;
       return this.missingCharts.length === 1
         ? `${message}is no longer available and has been removed from your favourite list.`
-        : `${message}are no longer available and have been removed from your favourite list.`
+        : `${message}are no longer available and have been removed from your favourite list.`;
     },
-    checkAndRenderDialog () {
-      if (!this.missingCharts.length) return null
-      else this.renderDialog('Missing Charts', 'missingChart', '', 80)
+    checkAndRenderDialog() {
+      if (!this.missingCharts.length) return null;
+      else this.renderDialog('Missing Charts', 'missingChart', '', 80);
     },
-    async loadFavorites () {
-      this.loading = true
+    async loadFavorites() {
+      this.loading = true;
       if (!this.favoriteChartItems.length) {
-        await this.fetchFavoriteCharts(false)
+        await this.fetchFavoriteCharts(false);
       }
-      this.loading = false
-      return this.checkAndRenderDialog()
+      this.loading = false;
+      return this.checkAndRenderDialog();
     },
-    async loadRegularCharts () {
-      const query = this.$route.query
+    async loadRegularCharts() {
+      const query = this.$route.query;
       if (query?.page) {
-        await this.loadParams(this.$route.query, false)
+        await this.loadParams(this.$route.query, false);
       } else {
-        await this.loadItems()
+        await this.loadItems();
       }
     }
   },
-  async mounted () {
+  async mounted() {
     if (this.isFavourite) {
-      await this.loadFavorites()
+      await this.loadFavorites();
     } else {
-      return await this.loadRegularCharts()
+      return await this.loadRegularCharts();
     }
   },
   watch: {
-    newChartExist () {
+    newChartExist() {
       if (!this.isFavourite) {
-        this.$store.commit('explorer/curation/setNewChartExist', false)
-        return this.loadItems()
+        this.$store.commit('explorer/curation/setNewChartExist', false);
+        return this.loadItems();
       }
     },
-    dialogBoxActive () {
+    dialogBoxActive() {
       if (this.dialogBoxActive === false && this.isFavourite) {
         this.$store.commit('explorer/gallery/setMissingCharts', [], {
           root: true
-        })
+        });
       }
     }
   },
-  created () {
+  created() {
     this.$store.commit('setAppHeaderInfo', {
       icon: '',
       name: this.sender
-    })
+    });
   }
-}
+};
 </script>

app/src/components/LoginRequired.vue

@@ -1,10 +1,15 @@
 <template>
   <div class="page-not-found">
-    <i class="material-icons page-not-found-header u--padding-zero" >lock_person</i>
+    <i class="material-icons page-not-found-header u--padding-zero"
+      >lock_person</i
+    >
     <h2 class="u_margin-bottom-small">Login required</h2>
-    <p>The page you are trying to access requires authentication.
-      Would you like to <a>log in</a> or return to the
-      <router-link to=""><a @click="$router.go(-1)">previous page</a></router-link>?
+    <p>
+      The page you are trying to access requires authentication. Would you like
+      to <a href="/secure">log in</a> or return to the
+      <router-link to=""
+        ><a @click="$router.go(-1)">previous page</a></router-link
+      >?
     </p>
   </div>
 </template>

app/src/components/nanomine/HeroHeader.vue

@@ -73,8 +73,12 @@
           </li>
           <li class="u_margin-right-small">
             <div class="nav_menu--container">
-              <a class="u--default-size nav_menu--handler" href="#">Curate</a>
-              <div class="nav_menu--siblings">
+              <a
+                class="u--default-size nav_menu--handler"
+                href="/explorer/curate"
+                >Curate</a
+              >
+              <!-- <div class="nav_menu--siblings">
                 <a
                   href="/explorer/curate/spreadsheet"
                   class="nav_menu--siblings-lists"
@@ -95,7 +99,7 @@
                   class="nav_menu--siblings-lists"
                   ><a>Create Chart</a></router-link
                 >
-              </div>
+              </div> -->
             </div>
           </li>
           <li class="u_margin-right-small">

app/src/modules/vega-chart.js

@@ -379,7 +379,7 @@ async function loadChart (chartUri) {
   const rows = results.bindings
 
   if (rows.length < 1) {
-    throw new Error(`No chart found for uri: ${chartUrl}`)
+    throw new Error(`No data found for the specified chart URI: ${chartUrl}`)
   }
 
   return await readChartSparqlRow(rows[0])

app/src/pages/explorer/Curate.vue

@@ -64,15 +64,32 @@
                   <md-icon class="explorer_page-nav-card_icon"
                     >done_outline</md-icon
                   >
-                  <span class="explorer_page-nav-card_text"
-                    >Submit with SDD</span
-                  >
+                  <span class="explorer_page-nav-card_text">Submit SDD</span>
                   <p class="md-layout-item_para md-layout-item_para_fl">
                     Submit files that use a semantic data dictionary (SDD).
                   </p>
                 </div>
               </router-link>
             </div>
+            <div class="md-layout-item md-layout-item_card">
+              <router-link
+                to="/explorer/curate/xml"
+                v-slot="{ navigate, href }"
+                custom
+              >
+                <div
+                  class="teams_container explorer_page-nav-card md-layout-item_card"
+                  :href="href"
+                  @click="navigate"
+                >
+                  <md-icon class="explorer_page-nav-card_icon">upload</md-icon>
+                  <span class="explorer_page-nav-card_text">Upload an XML</span>
+                  <p class="md-layout-item_para md-layout-item_para_fl">
+                    Directly upload XML files.
+                  </p>
+                </div>
+              </router-link>
+            </div>
             <!-- Extra Div causes misalignment and has no known use -->
             <!-- <div class="md-layout-item md-layout-item_card">
                         </div> -->

app/src/pages/explorer/chart/editor/Chart.vue

@@ -181,13 +181,13 @@ export default {
       querySparql(vm.chart.query)
         .then(this.onQuerySuccess)
         .then((this.loading = false))
+        .catch((this.loading = false))
     },
     onQuerySuccess (results) {
       this.results = results
     },
     onSpecJsonError () {
       // console.log('bad', arguments)
-
     },
     async onNewVegaView (view) {
       const blob = await view
@@ -215,10 +215,12 @@ export default {
         this.actionType = 'Restore Chart'
         this.reloadRestored()
       }
-      getChartPromise.then((chart) => {
-        this.chart = chart
-        return this.getSparqlData()
-      })
+      getChartPromise
+        .then((chart) => {
+          this.chart = chart
+          return this.getSparqlData()
+        })
+        .catch((this.loading = false))
     },
     async reloadRestored () {
       // 1. Fetch backup from mongo