Merge pull request #204 from VariantEffect/release-2024.1.1

Release 2024.1.1
VariantEffect · May 21, 2024 · 75cb551 · 75cb551
2 parents d4ab241 + 9a603a3
commit 75cb551
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Showing 15 changed files with 4,306 additions and 1,699 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -41,7 +41,7 @@
     "pluralize": "^8.0.0",
     "primeflex": "^3.3.1",
     "primeicons": "^6.0.1",
-    "primevue": "3.32.2",
+    "primevue": "3.52.0",
     "universal-base64url": "~1.1.0",
     "uuid": "^9.0.1",
     "vee-validate": "^4.12.2",

diff --git a/src/assets/app.css b/src/assets/app.css
@@ -23,3 +23,7 @@ body .p-inputtext {
 body .p-button {
   min-width: 10px;
 }
+
+.p-badge {
+  text-align: center;
+}
diff --git a/src/assets/forms.css b/src/assets/forms.css
@@ -1,7 +1,3 @@
-.field {
-  margin: 10px 0;
-}
-
 /* Field types */
 
 .field:deep(.p-chips) {

diff --git a/src/components/common/EmailPrompt.vue b/src/components/common/EmailPrompt.vue
@@ -7,7 +7,7 @@
         </div>
         <div><span v-if="emailValidationError" class="mave-field-error">{{ emailValidationError }}</span></div>
         <div class="flex justify-content-end gap-2">
-            <Button type="button" label="Now now" severity="secondary" @click="ignoreEmail"></Button>
+            <Button type="button" label="Not now" severity="secondary" @click="ignoreEmail"></Button>
             <Button type="button" label="Add email" @click="saveEmail"></Button>
         </div>
     </Dialog>

diff --git a/src/components/layout/Toolbar.vue b/src/components/layout/Toolbar.vue
@@ -18,6 +18,19 @@
           </div>
         </div>
       </template>
+      <template #item="{item, props, hasSubmenu}">
+        <router-link v-if="item.route" v-slot="{href, navigate}" :to="item.route" custom>
+          <a v-bind="props.action" class="p-menuitem-link" :href="href" @click="navigate">
+            <span v-if="item.icon" :class="['p-menuitem-icon', item.icon]"></span>
+            <span class="p-menuitem-text">{{ item.label }}</span>
+          </a>
+        </router-link>
+        <a v-else class="p-menuitem-link" :href="item.url" :target="item.target" v-bind="props.action">
+          <span v-if="item.icon" :class="['p-menuitem-icon', item.icon]"></span>
+          <span class="p-menuitem-text">{{ item.label }}</span>
+          <span v-if="hasSubmenu" class="pi pi-fw pi-angle-down ml-2"></span>
+        </a>
+      </template>
       <template #end>
       </template>
     </Menubar>
@@ -76,35 +89,35 @@ export default {
     menuItems: function() {
       return [{
         label: 'Dashboard',
-        to: '/dashboard',
+        route: '/dashboard',
         available: ({authenticated}) => authenticated
       }, {
         label: 'Home',
-        to: '/'
+        route: '/'
       }, {
         label: 'Search',
-        to: '/search'
+        route: '/search',
       }, {
         label: 'Documentation',
-        to: '/docs'
+        route: '/docs'
       }, {
         label: 'New experiment',
-        to: '/create-experiment',
+        route: '/create-experiment',
         available: ({authenticated}) => authenticated
       }, {
         label: 'New score set',
-        to: '/create-score-set',
+        route: '/create-score-set',
         available: ({authenticated}) => authenticated
       }, {
         label: 'Users',
-        to: '/users',
+        route: '/users',
         available: ({roles}) => roles.includes('admin')
       }, {
         label: this.userName,
         icon:'pi pi-fw pi-user',
         items:[{
           label: 'Settings',
-          to: '/settings',
+          route: '/settings',
           available: ({authenticated}) => authenticated
         }, {
           label: 'Sign out',
@@ -127,7 +140,6 @@ export default {
     },
 
     filterAvailableMenuItems(menuItems) {
-      const self = this
       return menuItems.map((item) => {
         if (item.items) {
           let newSubitems = this.filterAvailableMenuItems(item.items)

diff --git a/src/components/screens/ExperimentEditor.vue b/src/components/screens/ExperimentEditor.vue
@@ -106,7 +106,7 @@
                     <template #item="slotProps">
                       <div>
                           <div>Title: {{ slotProps.item.title }}</div>
-                          <div>DOI: {{ slotProps.item.publicationDoi || slotProps.item.preprintDoi }}</div>
+                          <div>DOI: {{ slotProps.item.doi }}</div>
                           <div>Identifier: {{ slotProps.item.identifier }}</div>
                           <div>Database: {{ slotProps.item.dbName }}</div>
                       </div>
@@ -130,7 +130,7 @@
                     <template #option="slotProps">
                           <div>
                               <div>Title: {{ slotProps.option.title }}</div>
-                              <div>DOI: {{ slotProps.option.publicationDoi || slotProps.option.preprintDoi }}</div>
+                              <div>DOI: {{ slotProps.option.doi }}</div>
                               <div>Identifier: {{ slotProps.option.identifier }}</div>
                               <div>Database: {{ slotProps.option.dbName }}</div>
                           </div>

diff --git a/src/components/screens/ExperimentSetView.vue b/src/components/screens/ExperimentSetView.vue
@@ -46,6 +46,7 @@ import Button from 'primevue/button'
 import DefaultLayout from '@/components/layout/DefaultLayout'
 import PageLoading from '@/components/common/PageLoading'
 import ItemNotFound from '@/components/common/ItemNotFound'
+import useAuth from '@/composition/auth'
 import useItem from '@/composition/item'
 import useFormatters from '@/composition/formatters'
 
@@ -54,9 +55,12 @@ export default {
   components: {Button, DefaultLayout, PageLoading, ItemNotFound},
 
   setup: () => {
+    const {userIsAuthenticated} = useAuth()
+
     return {
       ...useFormatters(),
-      ...useItem({itemTypeName: 'experimentSet'})
+      ...useItem({itemTypeName: 'experimentSet'}),
+      userIsAuthenticated
     }
   },
 

diff --git a/src/components/screens/PublicationIdentifierView.vue b/src/components/screens/PublicationIdentifierView.vue
@@ -9,14 +9,9 @@
         <div class="mave-1000px-col">
           <div v-if="item.creationDate">Created {{formatDate(item.creationDate)}}, updated {{ formatDate(item.modificationDate) }} </div>
           <div v-if="item.publicationJournal">Published {{item.publicationYear}} in {{item.publicationJournal}} </div>
-          <div v-if="item.publicationDoi">DOI:
+          <div v-if="item.doi">DOI:
             <span>
-              <a :href="`${item.url}`" target="blank">{{ item.publicationDoi }}</a>
-            </span>
-          </div>
-          <div v-if="item.preprintDoi">DOI:
-            <span>
-              <a :href="`${item.url}`" target="blank">{{ item.preprintDoi }}</a>
+              <a :href="`${item.url}`" target="blank">{{ item.doi }}</a>
             </span>
           </div>