V0.12.0

package.json

@@ -82,6 +82,7 @@
     "react-router-dom": "^4.0.0",
     "rethinkdb": "^2.3.2",
     "serve-favicon": "^2.3.0",
+    "smoothscroll-polyfill": "^0.4.4",
     "soap": "^0.25.0",
     "socket.io": "^2.1.1",
     "socket.io-client": "^2.1.1",
@@ -128,5 +129,5 @@
   "engines": {
     "node": ">=10.0.0"
   },
-  "version": "0.11.0"
+  "version": "0.12.1"
 }

src/client/components/document-management-components.js

@@ -476,16 +476,14 @@ class DocumentManagementDocumentComponent extends React.Component {
             workingMessage: 'Sending...',
             buttonKey: EMAIL_TYPE_INVITE,
             value: EMAIL_TYPE_INVITE,
-            label: _.capitalize( EMAIL_TYPE_INVITE ),
-            disableWhen: doc.initiated() || doc.trashed()
+            label: _.capitalize( EMAIL_TYPE_INVITE )
           }),
           h( DocumentEmailButtonComponent, {
             params: { doc, apiKey },
             workingMessage: 'Sending...',
             buttonKey: EMAIL_TYPE_FOLLOWUP,
             value: EMAIL_TYPE_FOLLOWUP,
-            label: _.upperFirst( EMAIL_TYPE_FOLLOWUP.replace(/([A-Z])/g, (match, letter) => '-' + letter) ),
-            disableWhen: doc.initiated() || doc.trashed()
+            label: _.upperFirst( EMAIL_TYPE_FOLLOWUP.replace(/([A-Z])/g, (match, letter) => '-' + letter) )
           })
         ]);
       }

src/client/components/document-management.js

@@ -9,7 +9,7 @@ import { DocumentManagementDocumentComponent } from './document-management-compo
 import logger from '../logger';
 import DirtyComponent from './dirty-component';
 import Document from '../../model/document';
-import { tryPromise } from '../../util';
+import { makeClassList, tryPromise } from '../../util';
 import Popover from './popover/popover';
 import { checkHTTPStatus } from '../../util';
 import { RequestForm } from './home';
@@ -63,7 +63,8 @@ class DocumentManagement extends DirtyComponent {
       status,
       pageCount: 0,
       limit: 10,
-      offset: 0
+      offset: 0,
+      isLoading: false
     };
 
     this.bus = new EventEmitter();
@@ -100,6 +101,8 @@ class DocumentManagement extends DirtyComponent {
     const url = '/api/document';
     const params = this.getUrlParams();
 
+    this.setState({ isLoading: true });
+
     return fetch(`${url}?${params}`)
       .then( res => {
         const total = res.headers.get('X-Document-Count');
@@ -112,7 +115,10 @@ class DocumentManagement extends DirtyComponent {
         return docs;
       })
       .then( docs => new Promise( resolve => this.setState( { docs }, resolve ) ) )
-      .then( () => this.updateUrlParams() );
+      .then( () => this.updateUrlParams() )
+      .finally( () => {
+        new Promise( resolve => this.setState( { isLoading: false }, resolve ) );
+      });
   }
 
   handleApiKeyFormChange( apiKey ) {
@@ -151,7 +157,7 @@ class DocumentManagement extends DirtyComponent {
   }
 
   render(){
-    let { docs, apiKey, status, validApiKey } = this.state;
+    let { docs, apiKey, status, validApiKey, isLoading } = this.state;
     const header = h('div.page-content-title', [
       h('h1', 'Document management panel')
     ]);
@@ -228,15 +234,22 @@ class DocumentManagement extends DirtyComponent {
       })
     );
 
-    const documentContainer = h( 'div.document-management-document-container', [
-      documentMenu,
-      documentList
-    ]);
-
+    const documentContainer = h( 'div.document-management-document-container',
+      [
+        h('i.icon.icon-spinner.document-management-spinner', {
+          className: makeClassList({ 'document-management-hidden': !isLoading })
+        }),
+        h('div', {
+          className: makeClassList({ 'document-management-hidden': isLoading })
+        }, [documentMenu, documentList])
+      ]
+    );
 
     let body = validApiKey ? documentContainer: apiKeyForm;
 
-    const footer = h('div.document-management-footer', [
+    const footer = h('div.document-management-footer', {
+      className: makeClassList({ 'document-management-hidden': isLoading })
+    }, [
       h( 'div.document-management-paginator', [
         h( ReactPaginate, {
           pageCount: this.state.pageCount,

src/client/components/editor/submit.js

@@ -1,17 +1,27 @@
+import EventEmitter from 'eventemitter3';
+
 import { TaskView } from '../tasks';
 import Popover from '../popover/popover';
 import { makeClassList } from '../../../util';
 import h from 'react-hyperscript';
 
 export const Submit = props => {
+
+  const emitter = new EventEmitter();
   const { document, bus, controller } = props;
 
   if( !document.editable() ){
     return null;
   }
 
+  // emitter.on('close', () => { console.log( 'close triggered'); });
+
   return h('div.editor-submit', [
-    h(Popover, { tippy: { html: h(TaskView, { document, bus, controller } ) } }, [
+    h(Popover, {
+      tippy: {
+        html: h(TaskView, { document, bus, controller, emitter } )
+      }
+    }, [
       h('button.editor-submit-button', {
         disabled: document.trashed(),
         className: makeClassList({

src/client/components/element-info/entity-info.js

@@ -10,6 +10,7 @@ import assocDisp from './entity-assoc-display';
 import CancelablePromise from 'p-cancelable';
 import { isComplex, isGGP, ELEMENT_TYPE } from '../../../model/element/element-type';
 import RelatedPapers from '../related-papers';
+import Organism from '../../../model/organism';
 
 import {
   focusDomElement, makeClassList, initCache, SingleValueCache,
@@ -191,7 +192,7 @@ class EntityInfo extends DataComponent {
       name: name,
       limit: s.limit,
       offset: offset,
-      organismCounts: doc.organismCountsJson()
+      organismCounts: doc.organismCountsJson(el) // exclude el from org count (avoids mid typing biases)
     };
 
     if( s.updatePromise ){
@@ -383,11 +384,10 @@ class EntityInfo extends DataComponent {
         nameChildren.push( matchName() );
       }
 
-      if( complete && m.name.toLowerCase() !== s.name.toLowerCase() ){
+      if( m.organism != null ){
         nameChildren.push(
-          h('br'),
-          h('span', '('),
-          matchName(),
+          h('span', ' ('),
+          Organism.fromId(m.organism).name(),
           h('span', ')')
         );
       }
@@ -467,7 +467,6 @@ class EntityInfo extends DataComponent {
 
         orgMatches = _.sortBy(orgMatches, m => m.organismName);
 
-        const selectedIndex = _.findIndex(orgMatches, match => match.id === m.id && match.namespace === m.namespace);
         const selectedOrg = assoc ? assoc.organism : null;
 
         const getSelectDisplay = (om, includeName = false) => {
@@ -490,20 +489,20 @@ class EntityInfo extends DataComponent {
         organism = h('div.entity-info-section.entity-info-organism-refinement', [
           h('span.entity-info-title', 'Organism'),
           h('select.entity-info-organism-dropdown', {
-            defaultValue: selectedIndex,
+            value: `${m.namespace}:${m.id}`,
             onChange: e => {
               const val = e.target.value;
-              const index = parseInt(val);
-              const om = orgMatches[index];
+              const [ns, id] = val.split(':');
+              const om = s.matches.find(match => match.namespace === ns && match.id === id);
 
               if( om ){
                 this.associate(om);
               } else {
                 this.enableManualMatchMode();
               }
             }
-          }, orgMatches.map((om, index) => {
-            const value = index;
+          }, orgMatches.map((om) => {
+            const value = `${om.namespace}:${om.id}`;
             const orgMatches = orgToMatches.get(om.organism);
             const multOrgMatches = orgMatches.length > 1;
             const isFirstOrgMatch = orgMatches[0].id === om.id && orgMatches[0].namespace === om.namespace;
@@ -514,7 +513,7 @@ class EntityInfo extends DataComponent {
 
             return h('option', { value }, getSelectDisplay(om));
           }).concat([
-            selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
+            // selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
             h('option', { value: -2 }, 'Other')
           ]))
         ]);
@@ -524,30 +523,28 @@ class EntityInfo extends DataComponent {
           const needDisam = ambigGrs && ambigGrs.length > 1;
 
           if( needDisam ){
-            const selectedAmIndex = _.findIndex(ambigGrs, match => match.id === m.id && match.namespace === m.namespace);
-
             disambiguation = h('div.entity-info-section.entity-info-organism-refinement', [
               h('span.entity-info-title', 'Which' + (s.name ? ` ${s.name}` : '') + ''),
               h('select.entity-info-organism-dropdown', {
-                defaultValue: selectedAmIndex,
+                value: `${m.namespace}:${m.id}`,
                 onChange: e => {
                   const val = e.target.value;
-                  const index = parseInt(val);
-                  const om = ambigGrs[index];
+                  const [ns, id] = val.split(':');
+                  const om = s.matches.find(om => om.namespace === ns && om.id === id);
 
                   if( om ){
                     this.associate(om);
                   } else {
                     this.enableManualMatchMode();
                   }
                 }
-              }, ambigGrs.map((om, index) => {
-                const value = index;
+              }, ambigGrs.map((om) => {
+                const value = `${om.namespace}:${om.id}`;
 
                 return h('option', { value }, getDisamtDisplay(om));
               }).concat([
-                selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
-                h('option', { value: -2 }, 'Other')
+                // selectedIndex < 0 ? h('option', { value: -1 }, getSelectDisplay(m, true)) : null,
+                h('option', { value: 'other:other' }, 'Other')
               ]))
             ]);
           }