Merge branch 'develop' into feature/dccprtl-99-debowerize

icgc-dcc · Jan 9, 2017 · 525cab9 · 525cab9
2 parents 284b8be + 5f25c7a
commit 525cab9
Show file tree

Hide file tree

Showing 19 changed files with 184 additions and 69 deletions.
diff --git a/dcc-portal-ui/app/scripts/advanced/views/advanced.facets.genes.html b/dcc-portal-ui/app/scripts/advanced/views/advanced.facets.genes.html
@@ -48,5 +48,5 @@ <h3 data-ng-if="!AdvancedCtrl.Gene.genes" class="loading loading-icon">
     </li>
 
     <li data-location-facet data-type="gene" data-facet-name="location" data-label="{{'Location' | translate}}"
-        data-placeholder="{{'Enter gene location' | translate}}" data-example="{{'e.g. chr12:43566-3457633' | translate}}"></li>
+        data-placeholder="{{'e.g. chr12:43566-3457633' | translate}}"></li>
 </ul>
diff --git a/dcc-portal-ui/app/scripts/advanced/views/advanced.facets.mutations.html b/dcc-portal-ui/app/scripts/advanced/views/advanced.facets.mutations.html
@@ -34,6 +34,6 @@
            data-facet="AdvancedCtrl.Mutation.mutations.facets.verificationStatus"></terms>
 
     <li data-location-facet data-type="mutation" data-facet-name="location" data-label="{{'Location' | translate}}"
-        data-placeholder="{{'Enter mutation location' | translate}}" data-example="{{'e.g. chr12:43566-3457633' | translate}}"></li>
+        data-placeholder="{{'e.g. chr12:43566-3457633' | translate}}" ></li>
 </ul>
 
diff --git a/dcc-portal-ui/app/scripts/app/js/app.js b/dcc-portal-ui/app/scripts/app/js/app.js
@@ -603,9 +603,9 @@
       if (response.status !== 401 && response.status !== -1) {
         console.error('Response Error: ', toJson (response));
       }
-
+      
       if (response.status === 500) {
-        Notify.setMessage ('' + response.data.message || response.statusText);
+        Notify.setParams(response);
         Notify.showErrors();
       } else if (response.status === 404) {
         console.error(response.data.message);

diff --git a/dcc-portal-ui/app/scripts/common/js/external.js b/dcc-portal-ui/app/scripts/common/js/external.js
@@ -86,20 +86,14 @@
     this.projectSNP = function() {
       return 'http://www.ncbi.nlm.nih.gov/SNP/';
     };
-    this.projectTCGA = function() {
-      return 'http://cancergenome.nih.gov/';
-    };
+    this.projectGDCLegacy = () => 'https://gdc-portal.nci.nih.gov/legacy-archive';
     this.projectGEO = function() {
       return 'http://www.ncbi.nlm.nih.gov/geo/';
     };
     this.projectEGA = function() {
       return 'https://ega-archive.org/';
     };
-    this.projectCGHub = function(diseasesCode) {
-      return 'https://browser.cghub.ucsc.edu/search/?disease_abbr=' + diseasesCode;
-    };
-
-
+    this.projectGDCActive = () => 'https://gdc-portal.nci.nih.gov';
   });
 
 

diff --git a/dcc-portal-ui/app/scripts/common/js/notify.js b/dcc-portal-ui/app/scripts/common/js/notify.js
@@ -26,6 +26,8 @@
       error = false,
       message = '',
       theme = '';
+
+    let params = {};
 
     function isVisible() {
       return !!visible;
@@ -71,6 +73,16 @@
       message = m;
     }
 
+    const setParams = (response) => {
+      if(!_.isEmpty(response)){
+        params.headers = response.headers();
+        params.source = response.config.url;
+        params.message = response.data.message || response.statusText;
+      }
+    };
+
+    const getParams = () => params;
+
     function getMessage() {
       return message;
     }
@@ -95,22 +107,26 @@
     }
 
     return {
-      isVisible: isVisible,
-      show: show,
-      showErrors: showErrors,
-      hide: hide,
-      redirectHome: redirectHome,
-      setMessage: setMessage,
-      getMessage: getMessage,
-      setRemovable: setRemovable,
-      isRemovable: isRemovable,
-      setTheme: setTheme,
-      getTheme: getTheme
+      isVisible,
+      show,
+      showErrors,
+      hide,
+      redirectHome,
+      setParams,
+      getParams,
+      setMessage,
+      getMessage,
+      setRemovable,
+      isRemovable,
+      setTheme,
+      getTheme
     };
   });
 
   module.controller('NotifyCtrl', function ($scope, Page, Notify) {
     $scope.notify = Notify;
+    $scope.responseParams = $scope.notify.getParams();
+
     $scope.$on('$locationChangeSuccess', function() {
       if (Notify.isVisible() && Page.page() !== 'error') {
         Notify.hide();
@@ -124,17 +140,41 @@
       replace: true,
       controller: 'NotifyCtrl',
       scope: true,
-      template: '<div><div data-ng-if="notify.isVisible()" class="t_notify_popup {{notify.getTheme()}}">' +
-                '<div class="t_notify_body pull-left" data-ng-bind-html="notify.getMessage()"></div>' +
-                '<div class="pull-right">' +
-                '<a class="t_notify_link" data-ng-href="" data-ng-click="notify.redirectHome()">'+
-                '<i data-ng-if="notify.isRemovable()" class="icon-home"></i>Home</a>' +
-                '<span>&nbsp;&nbsp;</span>' +
-                '<a class="t_notify_link" data-ng-href="" data-ng-click="notify.hide()">' +
-                '<i data-ng-if="notify.isRemovable()" class="icon-cancel"></i>Close</a>' +
-                '</div>' +
-                '</div>' +
-                '</div>'
+      template: `<div>
+                  <div data-ng-if="notify.isVisible()" class="t_notify_popup {{notify.getTheme()}}">
+                    <div class="t_notify_body pull-left">
+                      <span>
+                        An error occured while performing the requested operation. 
+                        <a class="t_notify_link" href="" data-ng-click="showMessage = !showMessage">See details</a>
+                         for more information.
+                      </span>
+                      <div data-ng-if="showMessage">
+                        <pre><code data-ng-bind="responseParams.message || notify.getMessage()"></code></pre>
+                        <span data-ng-if="responseParams.source && responseParams.headers">
+                          We have created an error report that you can send to help us improve ICGC Portal.
+                          <a class="t_notify_link" 
+                            href="mailto:dcc-support@icgc.org?Subject=ICGC DCC Portal - Error Report
+                              &body=An error occured while {{responseParams.source}} operation.%0A
+Error: {{responseParams.message || notify.getMessage()}}%0A
+Portal Information: %0A
+  API Version: {{responseParams.headers['x-icgc-api-version']}}%0A
+  Index Commit Id: {{responseParams.headers['x-icgc-index-commitid']}}%0A
+  Index Name: {{responseParams.headers['x-icgc-index-name']}}%0A
+  Portal Commit Id: {{responseParams.headers['x-icgc-portal-commitid']}}">Email error report.</a>
+                        </span>
+                      </div>
+                    </div>
+                    <div class="pull-right">
+                      <a class="t_notify_link" data-ng-href="" data-ng-click="notify.redirectHome()">
+                        <i data-ng-if="notify.isRemovable()" class="icon-home"></i>Home
+                      </a>
+                      <span>&nbsp;&nbsp;</span>
+                      <a class="t_notify_link" data-ng-href="" data-ng-click="notify.hide()">
+                        <i data-ng-if="notify.isRemovable()" class="icon-cancel"></i>Close
+                      </a>
+                    </div>
+                  </div>
+                </div>`
     };
   });
 })();
diff --git a/dcc-portal-ui/app/scripts/downloader/js/request.js b/dcc-portal-ui/app/scripts/downloader/js/request.js
@@ -118,7 +118,7 @@
       $scope.dlTotal = 0;
 
       // Compute the total number of donors
-      Donors.handler.get('count', {filters: filters}).then(function (data) {
+      Donors.handler.get('count', {filters: filters}).then( (data) => {
         $scope.totalDonor = data;
       });
 
@@ -133,13 +133,12 @@
 
         // Re-order it based on importance
         $scope.params.dataTypes = $filter('orderBy')($scope.params.dataTypes, sortFunc);
-
-        $scope.params.processing = false;
-      },function (error) {        
+      }, (error) => {
         if(error.status === 503){
-          $scope.params.processing = false;
           $scope.params.downloadEnabled = false;
-        }         
+        }
+      }).finally(() => {
+          $scope.params.processing = false;
       });
     };
 

diff --git a/dcc-portal-ui/app/scripts/facets/js/terms.js b/dcc-portal-ui/app/scripts/facets/js/terms.js
@@ -24,6 +24,7 @@
     function ($scope, $filter, Facets, HighchartsService, ProjectCache, ValueTranslator, LocationService) {
 
       $scope.resetPaginationOnChange = _.isUndefined($scope.resetPaginationOnChange) ? true : $scope.resetPaginationOnChange;  
+      $scope.search = {};
 
     // Translation on UI is slow, do in here
     function addTranslations (terms, facetName, missingText) {
@@ -180,7 +181,10 @@
         iconGetter: '&iconGetter',
         showWhenEmpty: '<',
 
-        resetPaginationOnChange: '<'
+        resetPaginationOnChange: '<',
+
+        //Search Config
+        searchIconShowLimit : '@'
       },
       transclude: true,
       templateUrl: '/scripts/facets/views/terms.html',

diff --git a/dcc-portal-ui/app/scripts/facets/styles/_facets.scss b/dcc-portal-ui/app/scripts/facets/styles/_facets.scss
@@ -21,10 +21,25 @@ $foregroundRed: #ff654b;
     size: 1.1rem;
     weight: 300;
   }
+
+  .t_facets_facet_search_icon{
+    i{
+      font-size: 1.5rem;
+    }
+  }
+
+  .t_facets__facet__search{
+    input{
+      font-size: 1rem;
+    }
+  }
 }
 
 .t_facets__facet__title_active {
   border-left-color: $orangeLight;
+  .t_facets_facet_search_icon{
+    margin-right: -.5rem;
+  }
 }
 
 .t_facets__facet__title__label {
@@ -317,5 +332,5 @@ $togglerFontSize: 10px;
 }
 
 .t_facet_location_search{
-  margin: 0px 0px 10px 0px;
+  margin: 10px 0px 10px 0px;
 }
diff --git a/dcc-portal-ui/app/scripts/facets/views/terms.html b/dcc-portal-ui/app/scripts/facets/views/terms.html
@@ -7,6 +7,19 @@
         <span data-ng-if="actives.length" class="t_facets__facet__terms__inactive__reset t_tools">
             <span data-ng-click="removeFacet()" class="t_tools__tool"><i class="icon-undo"></i></span>
         </span>
+        <span class="t_tools t_facets_facet_search_icon" 
+            data-ng-show="(inactives.length > (searchIconShowLimit || 5)) && !collapsed">
+            <span data-ng-click="showSearch = !showSearch" class="t_tools__tool"><i class="icon-search"></i></span>
+        </span>
+        <div class="t_facets__facet__search t_facets__facet__input" data-ng-if="showSearch && !collapsed">
+            <input class="t_input__block" type="search" placeholder="Filter values" ng-model="search.query" autofocus>
+            <i class="t_suggest__embedded t_suggest__embedded__right t_suggest__embedded__clear icon-cancel"
+                data-ng-click="search.query = ''"
+                data-ng-show="search.query"></i>
+        </div>
+    </li>
+    <li class="t_facets__facet__search" data-ng-show="showSearch">
+
     </li>
     <li class="t_facets__facet__terms">
         <ul class="t_facets__facet__terms__active">
@@ -41,7 +54,7 @@
         </ul>
 
         <ul data-ng-hide="collapsed || inactives.length == 0" class="t_facets__facet__terms__inactive">
-            <li data-ng-repeat="item in inactives | limitTo: (collapsed? 0 : displayLimit)"
+            <li data-ng-repeat="item in inactives | filter: search.query | limitTo: (collapsed? 0 : displayLimit)"
                 class="t_facets__facet__terms__inactive__term">
 
                 <span data-ng-hide="hideCount" data-ng-style="bar(item.count)" class="t_facets__facet__terms__inactive__term__bar"></span>
@@ -58,11 +71,11 @@
                 <span data-ng-if="hideCount" class="t_facets__facet__terms__inactive__term__count t_facets__facet__term__na">{{hideText}}</span>
 
             </li>
-            <li data-ng-show="inactives.length > displayLimit || expanded" class="t_sh__toggle">
+            <li data-ng-show="(inactives | filter: search.query).length > displayLimit || expanded" class="t_sh__toggle">
                 <a data-ng-click="toggle()" href="" class="t_tools__tool">
                   <span>
                      <i class="{{ expanded? 'icon-caret-up': 'icon-caret-down' }}"></i>
-                     {{ expanded? "less" : (inactives.length - displayLimit) + " more" }}
+                     {{ expanded? "less" : ((inactives | filter: search.query).length - displayLimit) + " more" }}
                   </span>
                 </a>
             </li>

diff --git a/dcc-portal-ui/app/scripts/genomemaps/js/viewer.js b/dcc-portal-ui/app/scripts/genomemaps/js/viewer.js
@@ -277,7 +277,7 @@ angular.module('icgc.modules.genomeviewer').directive('genomeViewer', function (
           title: 'ICGC Genes',
           minHistogramRegionSize: 20000000,
           maxLabelRegionSize: 10000000,
-          minTranscriptRegionSize: 300000,
+          minTranscriptRegionSize: 500000,
           height: 100,
           renderer: new GeneRenderer({
             tooltipContainerID: '#genomic',
@@ -633,7 +633,7 @@ angular.module('icgc.modules.genomeviewer').directive('gvembed', function (GMSer
           title: 'ICGC Genes',
           minHistogramRegionSize: 20000000,
           maxLabelRegionSize: 10000000,
-          minTranscriptRegionSize: 300000,
+          minTranscriptRegionSize: 500000,
           height: 100,
           functional_impact: _.get(LocationService.filters(), 'mutation.functionalImpact.is', ''),
           renderer: new GeneRenderer({

diff --git a/dcc-portal-ui/app/scripts/pancancer/views/pancancer.html b/dcc-portal-ui/app/scripts/pancancer/views/pancancer.html
@@ -11,7 +11,8 @@ <h1>
          data-y-label="{{'Donors' | translate}}"
          data-alternate-brightness="true"
          data-items="primarySites"
-         data-is-loading="false">
+         data-is-loading="false"
+         data-current-page="pcawg">
       </stacked>
 
       <section class="well" style="padding-top:0.5rem; padding-bottom:0.5rem">

diff --git a/dcc-portal-ui/app/scripts/projects/views/project.html b/dcc-portal-ui/app/scripts/projects/views/project.html
@@ -164,11 +164,11 @@ <h3><translate>Raw data is available at</translate></h3>
                         <a data-ng-switch-when="dbSNP" target="_blank" href="{{ProjectCtrl.ExternalLinks.projectSNP()}}">
                             <i class="icon-external-link"></i><translate>NCBI dbSNP</translate></a>
 
-                        <a data-ng-switch-when="TCGA" target="_blank" href="{{ProjectCtrl.ExternalLinks.projectTCGA()}}">
-                            <i class="icon-external-link"></i><translate>The Cancer Genome Atlas</translate></a>
+                        <a data-ng-switch-when="TCGA" target="_blank" href="{{ProjectCtrl.ExternalLinks.projectGDCLegacy()}}">
+                            <i class="icon-external-link"></i><translate>Genomic Data Commons (Legacy)</translate></a>
 
-                        <a data-ng-switch-when="CGHub" target="_blank" href="{{ProjectCtrl.ExternalLinks.projectCGHub(ProjectCtrl.project.id.split('-')[0])}}">
-                            <i class="icon-external-link"></i><translate>Cancer Genomics Hub</translate></a>
+                        <a data-ng-switch-when="CGHub" target="_blank" href="{{ProjectCtrl.ExternalLinks.projectGDCActive()}}">
+                            <i class="icon-external-link"></i><translate>Genomic Data Commons (Active)</translate></a>
 
                         <a data-ng-switch-when="GEO" target="_blank" href="{{ProjectCtrl.ExternalLinks.projectGEO()}}">
                             <i class="icon-external-link"></i><translate>Gene Expression Omnibus</translate></a>
@@ -310,10 +310,28 @@ <h3><translate>Available Data Types:</translate></h3>
         </tr>
     </table>
     <div>
-        <span class="open-in"><translate>Open in</translate></span>
-        <a href="{{:: ProjectCtrl.dataReleasesUrl }}/current/Projects/{{ProjectCtrl.project.id}}">
-        <i class="icon-database"></i>{{:: ProjectCtrl.dataReleasesTitle }}
-        </a>
+        <span class="action-toolbar">
+            <span class="action-item">
+                <span>
+                    <i class="icon-database"></i>
+                    <span>
+                        <a href='{{:: ProjectCtrl.dataReleasesUrl }}/current/Projects/{{ProjectCtrl.project.id}}'>
+                            <translate>Open in {{:: ProjectCtrl.dataReleasesTitle }}</translate>
+                        </a>
+                    </span>
+                </span>
+            </span>
+            <span class="action-item">
+                <span>
+                    <i class="icon-download-cloud"></i>
+                    <span>
+                        <a href='/repositories?filters={"file":{"projectCode":{"is":["{{ProjectCtrl.project.id}}"]}}}'>
+                            <translate>View in Data Repositories</translate>
+                        </a>
+                    </span>
+                </span>
+            </span>
+        </span>
     </div>
 </div>
 </section>

diff --git a/dcc-portal-ui/app/scripts/projects/views/projects.summary.html b/dcc-portal-ui/app/scripts/projects/views/projects.summary.html
@@ -31,7 +31,8 @@
                      selected-project-count="ProjectsCtrl.numberOfSelectedProjectsInFilter()"
                      data-title="{{'Top 20 Mutated Genes with High Functional Impact SSMs' | translate}}"
                      data-y-label="{{'Donors Affected' | translate}}"
-                     data-subtitle="{{ProjectsCtrl.ssmTotalDonors | number}} Unique SSM-Tested Donors">
+                     data-subtitle="{{ProjectsCtrl.ssmTotalDonors | number}} Unique SSM-Tested Donors"
+                     data-current-page="projects">
             </stacked>
         </div>
     </section>