Merge branch 'dev' into EEB20/advanced-search

frontend/package.json

@@ -11,7 +11,7 @@
   },
   "dependencies": {
     "@fortawesome/fontawesome-free": "5.2.0",
-    "@source-data/render-rev": "^0.2.0",
+    "@source-data/render-rev": "^0.2.1",
     "axios": "^0.21.4",
     "markdown-it": "^13.0.0",
     "vue": "^2.6.11",

frontend/src/App.vue

@@ -1,5 +1,6 @@
 <template lang="pug">
 v-app
+  Snackbar
   TopNavBar
   v-main.main-padding
     v-container.main-content
@@ -11,6 +12,7 @@ v-app
 <script>
 import TopNavBar from './layouts/top-nav-bar'
 import Banner from './layouts/banner'
+import Snackbar from "./components/helpers/snackbar.vue";
 import Footer from './layouts/footer'
 
 export default {
@@ -19,7 +21,8 @@ export default {
   components: {
     TopNavBar,
     Banner,
-    Footer
+    Footer,
+    Snackbar
   },
   metaInfo: {
     meta: [

frontend/src/components/filtering/by-reviewing-service.vue

@@ -3,7 +3,7 @@ v-card(flat)
   v-card-title Filter by reviewer
   v-card-subtitle Filter the reviewed preprints by the reviewer
   v-card-text
-    v-chip-group(v-model="selectedReviewers" mandatory column multiple)
+    v-chip-group(v-model="selectedReviewers" column multiple)
       span(v-for="service in this.reviewing_services" :key="`${service.id}-chip`")
         v-chip(:value="service.id" :disabled="loadingRecords" filter filter-icon="mdi-check" outlined
                active-class="active-chip" text-color="black")

frontend/src/components/helpers/snackbar.vue

@@ -0,0 +1,39 @@
+<template lang="pug">
+v-snackbar(v-model='show' :top="true" :color='color' timeout="3000" centered)
+  b {{ message }}
+  template(v-slot:action="{ attrs }")
+    v-btn(
+      text
+      v-bind="attrs"
+      @click="show = false" icon)
+        v-icon mdi-close
+</template>
+
+<script>
+  import { mapState } from 'vuex'
+
+  export default {
+    data() {
+      return {
+        show: false,
+
+        message: "",
+        color: ""
+      };
+    },
+    computed: {
+      ...mapState(['snackMessage', 'snackColor']),
+    },
+    watch: {
+      snackMessage(nv, ov) {
+        if (nv != "" && nv != ov) {
+          this.show = true;
+          this.message = this.snackMessage;
+          this.color = this.snackColor;
+
+          this.$store.commit("setSnack", { message: "", color: "" });
+        }
+      }
+    }
+  };
+</script>

frontend/src/components/highlights/article.vue

@@ -1,8 +1,17 @@
 <template lang="pug">
   v-container(fluid).pa-0
+    v-btn(
+      color="primary"
+      fixed
+      bottom
+      right
+      style="bottom: 75px;"
+      fab @click="$vuetify.goTo(0)")
+      v-icon mdi-arrow-up
+
     v-row(v-if="article")
       v-col.d-flex.align-center
-        HighlightedListItem(:article="article" :expandedReview="expandedReview" :open-preprint-boxes=[0, 1, 2] :open-reviewed-boxes=[0, 1, 2]).ml-auto.mr-auto
+        HighlightedListItem(:article="article" :expandedReview="expandedReview" :open-preprint-boxes=[0, 1, 2] :open-reviewed-boxes=[0, 1]).ml-auto.mr-auto
     v-row(v-else)
       v-col
         v-card

frontend/src/components/highlights/index.vue

@@ -1,14 +1,11 @@
 <template lang="pug">
 div(style="max-width: 100%;").d-flex.mr-auto.ml-auto
-  v-container(v-if="showAlert").mt-6
-    v-alert(color="red lighten-2" outlined) {{ error }}
-
   v-container(v-if="loadingRecords").mt-6
     v-progress-circular(:size="70" :width="7" color="primary" indeterminate).ml-auto
 
   span(v-else style="max-width:100%;").mt-3
     v-container(fluid v-if="paging.totalItems > 0" :class="{'highlights-loading': loadingRecords}")
-      h2 {{ paging.totalItems }} reviewed preprints found {{ query != '' ? `for search term "${query}" ` : '' }} in the selected sources
+      h2 {{ paging.totalItems }} reviewed preprints found
     v-container(fluid v-if="paging.totalItems == 0")
       h2 Sorry, we couldn't find any results
       p Try changing some of the filter values.
@@ -46,10 +43,12 @@ div(style="max-width: 100%;").d-flex.mr-auto.ml-auto
                 v-btn(x-small v-bind="attrs" v-on="on" icon aria-label="ascending" value="asc")
                   v-icon(dense) mdi-sort-ascending
               span Sort earliest first
+      v-row(v-if="paging.totalItems > 0")
+        v-switch(v-model="openAbstracts" dense label="Collapse all abstracts").pl-3.mt-0
 
       v-row(v-for="article in records" :key="article.id")
         v-col(cols=12)
-          HighlightedListItem(:article="article" :open-preprint-boxes="[]" :open-reviewed-boxes="[0]")
+          HighlightedListItem(:article="article" :open-preprint-boxes="openedByDefault" :open-reviewed-boxes="[1]")
       v-row(v-if="paging.totalItems > 0" justify="start")
         v-col(cols=6).px-0.d-flex
           v-pagination(
@@ -66,7 +65,8 @@ import { mapState } from 'vuex'
 export default {
   data() {
     return {
-      showAlert: false
+      openAbstracts: false,
+      openedByDefault: [0]
     }
   },
   components: {
@@ -99,15 +99,16 @@ export default {
       }
     }
   },
-  methods: {},
   watch: {
-    error() {
-      this.showAlert = true;
-      window.setInterval(() => {
-        this.showAlert = false;
-      }, 5000)    
+    openAbstracts(nv) {
+      if (nv) {
+        this.openedByDefault = []
+      }
+      else {
+        this.openedByDefault = [0]
+      }
     }
-  }
+  },
 }
 </script>
 

frontend/src/components/highlights/list-item.vue

@@ -11,12 +11,12 @@ v-card(v-if="article" color="tertiary")
         v-list(dense flat outlined)
           v-list-item
             v-list-item-title
-              v-btn(@click="copyFullUrlToClipboard" elevation=0 plain depressed v-ripple="false")
+              v-btn(@click="copyToClipboard(getFullStandaloneDoiUrl)" elevation=0 plain depressed v-ripple="false")
                 v-icon(color="primary") mdi-link-variant
                 span.ml-1 Copy link to clipboard
           v-list-item
             v-list-item-title
-              v-btn(@click="copyCitationToClipboard" elevation=0 plain depressed v-ripple="false")
+              v-btn(@click="copyToClipboard(citationText(true))" elevation=0 plain depressed v-ripple="false")
                 v-icon(color="primary") mdi-content-copy
                 span.ml-2 Copy citation
           v-list-item
@@ -75,51 +75,51 @@ v-card(v-if="article" color="tertiary")
                 v-chip-group(v-if="article.assays.length > 0" :key="3" column)
                   v-chip(v-for="(item, index) in article.assays"  outlined :key="`assays-${index}`").green--text {{ item }}
 
-    v-expansion-panels(accordion multiple v-model="dataOpenReviewedBoxes")
-      v-expansion-panel(readonly)
-        v-expansion-panel-header(hide-actions)
-          span.d-flex.flex-column
-            h3(style="color: black;") Preprint review timeline
-            //- TODO: enable this when the functionality is ready
-              //- v-tooltip(bottom transition="fade-transition")
-              //-   template(v-slot:activator="{ on, hover, attrs }")
-              //-     v-btn(@click="???" v-bind="attrs" v-on="on" icon elevation=0 plain depressed v-ripple="false")
-              //-       v-icon(color="primary") mdi-download-circle
-              //-   span Download all review data
+    v-card.no-bottom-radius
+      v-card-title 
+        span.d-flex.flex-column
+          h4(style="color: black;") Preprint review timeline
+          //- TODO: enable this when the functionality is ready
+            //- v-tooltip(bottom transition="fade-transition")
+            //-   template(v-slot:activator="{ on, hover, attrs }")
+            //-     v-btn(@click="???" v-bind="attrs" v-on="on" icon elevation=0 plain depressed v-ripple="false")
+            //-       v-icon(color="primary") mdi-download-circle
+            //-   span Download all review data
+      v-card-subtitle
+          span.pb-0.d-flex.flex-row.align-center
+            b.mr-3 Reviewed by
+            v-bottom-sheet(v-model="dialog" eager inset)
+              template(v-slot:activator="{ on, attrs }")
+                v-chip-group
+                  v-chip(
+                    v-ripple="false" small
+                    color="secondary"
+                    outlined
+                    @click="selectReviewerInfo(source)"
+                    v-bind="attrs"
+                    v-on="on" v-for='source in article.reviewed_by')
+                    img(v-if="imageFileName(source)" :src="require(`@/assets/partner-logos/` + imageFileName(source))" height="24px" :alt="serviceId2Name(source)").pa-1
+                    span(v-else) {{ serviceId2Name(source) }}
+                    v-icon(right small) mdi-information
 
-            span.pb-0.d-flex.flex-row.align-center
-              b.mr-3 Reviewed by
-              v-bottom-sheet(v-model="dialog" inset)
-                template(v-slot:activator="{ on, attrs }")
-                  v-chip-group
-                    v-chip(
-                      v-ripple="false" small
-                      color="secondary"
-                      outlined
-                      @click="selectReviewerInfo(source)"
-                      v-bind="attrs"
-                      v-on="on" v-for='source in article.reviewed_by')
-                      img(v-if="imageFileName(source)" :src="require(`@/assets/partner-logos/` + imageFileName(source))" height="24px" :alt="serviceId2Name(source)").pa-1
-                      span(v-else) {{ serviceId2Name(service.id) }}
-                      v-icon(right small) mdi-information
-
-                InfoCardsReviewServiceSummaryGraph(
-                  :service_name="serviceId2Name(selectedSource)",
-                  :url="reviewingService(selectedSource).url",
-                  :peer_review_policy="reviewingService(selectedSource).peer_review_policy",
-                  :review_requested_by="reviewingService(selectedSource).review_requested_by",
-                  :reviewer_selected_by="reviewingService(selectedSource).reviewer_selected_by",
-                  :review_coverage="reviewingService(selectedSource).review_coverage",
-                  :reviewer_identity_known_to="reviewingService(selectedSource).reviewer_identity_known_to",
-                  :competing_interests="reviewingService(selectedSource).competing_interests",
-                  :public_interaction="reviewingService(selectedSource).public_interaction",
-                  :opportunity_for_author_response="reviewingService(selectedSource).opportunity_for_author_response",
-                  :recommendation="reviewingService(selectedSource).recommendation",
-                ).px-0.mt-2
-        v-expansion-panel-content(eager).pt-0
-          span.review-process.d-flex.align-start.justify-start
-            render-rev-timeline(:ref='article.doi + "-rev-timeline"')
+              InfoCardsReviewServiceSummaryGraph(
+                :service_name="serviceId2Name(selectedSource)",
+                :url="reviewingService(selectedSource).url",
+                :peer_review_policy="reviewingService(selectedSource).peer_review_policy",
+                :review_requested_by="reviewingService(selectedSource).review_requested_by",
+                :reviewer_selected_by="reviewingService(selectedSource).reviewer_selected_by",
+                :review_coverage="reviewingService(selectedSource).review_coverage",
+                :reviewer_identity_known_to="reviewingService(selectedSource).reviewer_identity_known_to",
+                :competing_interests="reviewingService(selectedSource).competing_interests",
+                :public_interaction="reviewingService(selectedSource).public_interaction",
+                :opportunity_for_author_response="reviewingService(selectedSource).opportunity_for_author_response",
+                :recommendation="reviewingService(selectedSource).recommendation",
+              ).px-0.mt-2
+      v-card-text
+        span.review-process.d-flex.align-start.justify-start
+          render-rev-timeline(:ref='article.doi + "-rev-timeline"')
 
+    v-expansion-panels(accordion multiple v-model="dataOpenReviewedBoxes").no-top-radius
       v-expansion-panel(v-if="maybeReviewSummary")
         v-expansion-panel-header
           span
@@ -144,7 +144,7 @@ v-card(v-if="article" color="tertiary")
             h3 Cite reviewed preprint
             v-tooltip(color="tooltip" bottom transition="fade-transition")
                 template(v-slot:activator="{ on, hover, attrs }")
-                  v-card(@click="copyCitationToClipboard" v-on:click.stop v-bind="attrs" v-on="on" icon elevation=0 plain depressed v-ripple="false").pl-2
+                  v-card(@click="copyToClipboard(citationText(true))" v-on:click.stop v-bind="attrs" v-on="on" icon elevation=0 plain depressed v-ripple="false").pl-2
                     v-icon(color="primary") mdi-content-copy
                 span Click to copy reviewed preprint citation
         v-expansion-panel-content
@@ -158,7 +158,7 @@ import { BASE_URL } from '../../lib/http'
 import { serviceId2Name, normalizeServiceName } from '../../store/by-filters'
 import '@source-data/render-rev'
 import { parse as parseDocmaps } from '@source-data/render-rev/src/docmaps.js'
-import { mapGetters } from 'vuex'
+import { mapState, mapGetters } from 'vuex'
 import InfoCardsReviewServiceSummaryGraph from '../helpers/review-service-summary-graph.vue'
 
 export default {
@@ -225,11 +225,9 @@ export default {
     responseId() {
       return this.article.doi + '#rev0-ar'
     },
-    copyFullUrlToClipboard () {
-      navigator.clipboard.writeText(this.getFullStandaloneDoiUrl);
-    },
-    copyCitationToClipboard () {
-      navigator.clipboard.writeText(this.citationText(true));
+    copyToClipboard (text) {
+      this.$store.commit("setSnack", { message: "Text copied to clipboard!", color: "gray" });
+      return navigator.clipboard.writeText(text);
     },
     selectReviewerInfo(value) {
       this.selectedSource = value;
@@ -262,6 +260,7 @@ export default {
   },
   computed: {
     ...mapGetters('byFilters', ['reviewingService']),
+    ...mapState(['snackMessage, snackColor']),
 
     authorList() {
       // first, clone the authors array because sort() operates in-place on the array it's called on.
@@ -294,6 +293,11 @@ export default {
       return fullLink
     },
   },
+  watch: {
+    openPreprintBoxes: function (newVal) {
+      this.dataOpenPreprintBoxes = newVal
+    },
+  },
   mounted() {
     const doi = this.article.doi;
     const highlightDoi = this.expandedReview ? this.expandedReview.doi : null;
@@ -367,9 +371,17 @@ export default {
   .v-expansion-panel-header:not(.v-expansion-panel-header--active) .hide-when-not-expanded {
     display: none;
   }
-
   .paper-title {
     letter-spacing: normal;
     line-height: normal;
   }
+
+  .no-bottom-radius {
+    border-radius: 4px 4px 0 0 !important;
+  }
+
+  .no-top-radius>:first-child {
+    border-radius: 0 0 !important;
+    border-top: 1px solid rgb(0, 0, 0, 0.1);
+  }
 </style>

frontend/src/layouts/top-nav-bar.vue

@@ -4,7 +4,8 @@
     height=90
     color="tertiary"
     hide-on-scroll
-    scroll-off-screen
+    scroll-threshold=0
+    scroll-off-screen tile elevation=1
   )
     v-row
       v-col(cols=3)