Remove bower, upgrade lodash v3 to v4

dcc-portal-ui/README.md

@@ -13,11 +13,10 @@ nvm install 6
 nvm use 6
 ```
 
-Next, install `npm` and `bower` dependencies:
+Next, install `npm` dependencies:
 
 ```shell
 yarn
-npm run bower
 ```
 
 ## Running

dcc-portal-ui/UI.md

@@ -313,7 +313,7 @@ Add your ```helloworld``` module dependency to the ```scripts/app/js/app.js``` f
 
     // angular plugins
     'restangular',
-    'ui.scrollfix',
+    'ui.scrollpoint',
 
     // More modules included here ...
     'helloworld' // <--- Define your module here!

dcc-portal-ui/app/index.html

@@ -229,5 +229,6 @@ <h1><span class="t_badge t_badge_icon" style="background: #dc322f"><i class="ico
 </script>
 <portal-settings></portal-settings>
 <script src="https://cdn.polyfill.io/v2/polyfill.min.js"></script>
+<script src="https://cdn.rawgit.com/lodash/lodash-migrate/master/dist/lodash-migrate.min.js"></script>
 </body>
 </html>

dcc-portal-ui/app/scripts/advanced/js/advanced.js

@@ -638,7 +638,7 @@ angular.module('icgc.advanced.controllers', [
           facets: facets
         });
         _ASDonorService.barDataTypes = HighchartsService.bar({
-          hits: _.map(_.sortByOrder(_ASDonorService.pieDataTypes, 'y', false), (dataType) => ({
+          hits: _.map(_.orderBy(_ASDonorService.pieDataTypes, 'y', false), (dataType) => ({
             y: dataType.y,
             name: $filter('trans')(dataType.name, 'availableDataTypes'),
             term: dataType.name,
@@ -652,7 +652,7 @@ angular.module('icgc.advanced.controllers', [
           facets: facets
         });
         _ASDonorService.barAnalysisTypes = HighchartsService.bar({
-          hits: _.map(_.sortByOrder(_ASDonorService.pieAnalysisTypes, 'y', false), (analysisType) => ({
+          hits: _.map(_.orderBy(_ASDonorService.pieAnalysisTypes, 'y', false), (analysisType) => ({
             y: analysisType.y,
             name: $filter('trans')(analysisType.name, 'analysisTypes'),
             term: analysisType.name,
@@ -675,7 +675,7 @@ angular.module('icgc.advanced.controllers', [
           delete filters.donor.id;
         }
         Donors
-          .one(_.pluck(_ASDonorService.donors.hits, 'id').join(','))
+          .one(_.map(_ASDonorService.donors.hits, 'id').join(','))
           .handler
           .one('mutations', 'counts')
           .get({filters: filters})
@@ -802,7 +802,7 @@ angular.module('icgc.advanced.controllers', [
 
       _ASGeneService.mutationCounts = null;
 
-      var geneIds = _.pluck(_ASGeneService.genes.hits, 'id').join(',');
+      var geneIds = _.map(_ASGeneService.genes.hits, 'id').join(',');
       var projectCachePromise = ProjectCache.getData();
 
 
@@ -980,7 +980,7 @@ angular.module('icgc.advanced.controllers', [
 
     const summarizeData = (items) => {
       const count = _.size(items);
-      const firstItem = _.first(items);
+      const firstItem = _.head(items);
 
       if (count < 2) {
         return items;
@@ -989,7 +989,7 @@ angular.module('icgc.advanced.controllers', [
       return {
         name: `Others (${count} Consequence Types)`,
         color: '#999',
-        y: _.sum(items, 'y'),
+        y: _.sumBy(items, 'y'),
         type: firstItem.type,
         facet: firstItem.facet,
         term: _.map(items, 'name')
@@ -1001,13 +1001,13 @@ angular.module('icgc.advanced.controllers', [
         return [];
       }
 
-      const max = _.max (data, (item) => item.y);
+      const max = _.maxBy (data, (item) => item.y);
       const isBelowGroupPercent = (item) => (item.y / max.y) < (2 / 100);
       const separated = _.partition (data, isBelowGroupPercent);
-      const belowGroupPercent = _.first(separated);
+      const belowGroupPercent = _.head(separated);
       const regular = _.last(separated);
 
-      return _.sortByOrder(regular.concat(summarizeData(belowGroupPercent)), 'y', false);
+      return _.orderBy(regular.concat(summarizeData(belowGroupPercent)), 'y', false);
       };
 
     function _initFacets(facets) {

dcc-portal-ui/app/scripts/advanced/views/advanced.html

@@ -1,4 +1,4 @@
-<h1 data-ui-scrollfix=79><span class="t_badge t_badge_icon t_badge__advanced"><i class="icon-search"></i></span><translate>Advanced Search</translate></h1>
+<h1 data-ui-scrollpoint=79><span class="t_badge t_badge_icon t_badge__advanced"><i class="icon-search"></i></span><translate>Advanced Search</translate></h1>
 <aside class="t_sidebar">
     <div class="t_tabs">
         <div class="t_tabs__tab t_tabs__tab__donor" data-ng-click="AdvancedCtrl.state.setFacetTab('donor')"

dcc-portal-ui/app/scripts/advanced/views/advanced.mutations.observations.html

@@ -102,10 +102,10 @@ <h3><translate>Mutation Occurrences</translate>
             <td>{{occurrence.donorId}}</td>
             <td>{{occurrence.projectId}}</td>
             <td>chr{{occurrence.chromosome}}:g.{{occurrence.start}}{{occurrence.mutation}}</td>
-            <td>{{ (occurrence.observations | pluck:'icgcSampleId').join(',') }}</td>
-            <td>{{ (occurrence.observations | pluck:'matchedICGCSampleId').join(',') }}</td>
-            <td>{{ (occurrence.observations | pluck:'platform').join(',') }}</td>
-            <td>{{ (occurrence.observations | pluck:'verificationStatus').join(',') }}</td>
+            <td>{{ (occurrence.observations | _:"map":'icgcSampleId').join(',') }}</td>
+            <td>{{ (occurrence.observations | _:"map":'matchedICGCSampleId').join(',') }}</td>
+            <td>{{ (occurrence.observations | _:"map":'platform').join(',') }}</td>
+            <td>{{ (occurrence.observations | _:"map":'verificationStatus').join(',') }}</td>
         </tr>
         </tbody>
     </table>

dcc-portal-ui/app/scripts/analysis/js/analysis.js

@@ -271,8 +271,8 @@
      * Add analysis to local storage
      */
     this.addAnalysis = function(analysis, type) {
-      var ids = _.pluck(analysisList, 'id');
-      if (_.contains(ids, analysis.id) === true) {
+      var ids = _.map(analysisList, 'id');
+      if (_.includes(ids, analysis.id) === true) {
         return;
       }
 
@@ -303,9 +303,9 @@
     };
 
     this.remove = function(id) {
-      var ids = _.pluck(analysisList, 'id');
+      var ids = _.map(analysisList, 'id');
 
-      if (_.contains(ids, id)) {
+      if (_.includes(ids, id)) {
         var index = ids.indexOf(id);
         analysisList.splice(index, 1);
         localStorageService.set(ANALYSIS_ENTITY, analysisList);

dcc-portal-ui/app/scripts/analysis/js/analysisSet.js

@@ -101,7 +101,7 @@
         return set.state !== 'FINISHED';
       });
       if (toRemove.length > 0) {
-        SetService.removeSeveral(_.pluck(toRemove, 'id'));
+        SetService.removeSeveral(_.map(toRemove, 'id'));
         _this.checkAll = false; // reset
       }
     };
@@ -116,7 +116,7 @@
 
       var toRemove = _this.selectedSets;
       if (toRemove.length > 0) {
-        SetService.removeSeveral(_.pluck(toRemove, 'id'));
+        SetService.removeSeveral(_.map(toRemove, 'id'));
         _this.checkAll = false; // reset
       }
     };

dcc-portal-ui/app/scripts/analysis/views/analysis.html

@@ -1,5 +1,5 @@
 <div class="h1-wrap">
-   <h1 data-ui-scrollfix=79>
+   <h1 data-ui-scrollpoint=79>
        <i class="t_badge t_badge_icon t_badge__analysis"><i class="icon-beaker"></i></i><translate>Data Analysis</translate>
    </h1>
 </div>

dcc-portal-ui/app/scripts/app/js/app.js

@@ -193,7 +193,7 @@
 
     // angular plugins
     'restangular',
-    'ui.scrollfix',
+    'ui.scrollpoint',
     'ui.bootstrap.modal',
     'ui.bootstrap.position',
     'ui.bootstrap.pagination',
@@ -202,7 +202,6 @@
     'template/pagination/pagination.html',
     'ui.router',
     'infinite-scroll',
-    'angular-lodash',
     'angularytics',
     'angular-loading-bar',
     'hc.marked',

dcc-portal-ui/app/scripts/beacon/views/beacon.html

@@ -1,5 +1,5 @@
 <div class="h1-wrap">
-    <h1 data-ui-scrollfix="79" class="sticky-scrollfix">
+    <h1 data-ui-scrollpoint="79" class="sticky-scrollfix">
     <i class="t_badge t_badge_icon t_badge__search"><i class="icon-fire"></i></i><translate>ICGC GA4GH Beacon</translate>
 </h1>
 </div>

dcc-portal-ui/app/scripts/common/js/abridger.js

@@ -71,9 +71,9 @@
 
       var tokens = [keyword2].concat (words (keyword2));
       var matchKeyword = _(tokens)
-        .unique()
+        .uniq()
         .find (function (token) {
-          return _.contains (sentence2, token);
+          return _.includes (sentence2, token);
         });
 
       return _.isUndefined (matchKeyword) ? {} : {
@@ -114,7 +114,7 @@
     };
 
     this.processLeftAndRight = function (newElements) {
-      var left = _.first (newElements);
+      var left = _.head (newElements);
       var right = _.last (newElements);
 
       if (withinLimit (newElements)) {
@@ -147,7 +147,7 @@
     };
 
     this.processLeftOnly = function (newElements) {
-      var left = _.first (newElements);
+      var left = _.head (newElements);
 
       if (withinLimit (left)) {
         _this.resultArray = [left].concat (_this.resultArray);

dcc-portal-ui/app/scripts/common/js/common.js

@@ -66,7 +66,7 @@ require('../components');
     return function (items, param) {
       var ret = null;
       if (angular.isArray(items)) {
-        ret = _.reduce(_.pluck(items, param), function (sum, num) {
+        ret = _.reduce(_.map(items, param), function (sum, num) {
           return sum + num;
         });
       }
@@ -79,6 +79,7 @@ require('../components');
       var input = arguments[0];
       var method = arguments[1];
       invariant(_.isString(method), 'The first argument must be a string that specifies a lodash method name');
+      invariant(_[method], `_.${method} does not exist`);
       var args = Array.prototype.slice.call(arguments, 2);
       return _[method].apply(null, [input].concat(args));
     };
@@ -187,7 +188,7 @@ require('../components');
         selfLoadState.isLoading = val;
       },
       addContributingLoadState: function (loadState) {
-        if (_.contains(contributingLoadStates, loadState)) {
+        if (_.includes(contributingLoadStates, loadState)) {
           console.warn('load state is already in contributing loadStates, this shouldnt happen');
           return;
         }

dcc-portal-ui/app/scripts/common/js/consequence.js

@@ -72,7 +72,7 @@
 
 
     this.precedence = function() {
-      return _.pluck(dataOrdered, 'id');
+      return _.map(dataOrdered, 'id');
     };
 
     this.translate = function(id) {

dcc-portal-ui/app/scripts/common/js/datatype.js

@@ -53,7 +53,7 @@
     };
 
     this.precedence = function() {
-      return _.pluck(data, 'id');
+      return _.map(data, 'id');
     };
 
     this.translate = function(id) {

dcc-portal-ui/app/scripts/common/js/display.js

@@ -155,7 +155,7 @@
                 uiTerm = predefinedCurated.name;
                 isPredefined = true;
               }
-            } else if (_.contains(['study', 'donorStudy', 'studies'], facetKey)) {
+            } else if (_.includes(['study', 'donorStudy', 'studies'], facetKey)) {
               if (term === '_missing') {
                 uiTerm = 'None';
               }

dcc-portal-ui/app/scripts/common/js/ensure-input.js

@@ -12,9 +12,9 @@ export const partiallyContainsIgnoringCase = (phrase, keyword) => {
 
     const tokens = [capitalizedKeyword].concat (words(capitalizedKeyword));
     const matchKeyword = _(tokens)
-      .unique()
+      .uniq()
       .find (function (token) {
-        return _.contains(capitalizedPhrase, token);
+        return _.includes(capitalizedPhrase, token);
       });
 
     return !_.isUndefined(matchKeyword);

dcc-portal-ui/app/scripts/common/js/pcawg.js

@@ -45,7 +45,7 @@
     };
 
     this.precedence = function() {
-      return _.pluck(data, 'id');
+      return _.map(data, 'id');
     };