From aea97205b57118ba51b3c2bbb0b9a2b1205d72c1 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Wed, 4 Jan 2017 15:32:51 -0500 Subject: [PATCH 01/19] Updating stacker click event function --- .../projects/views/projects.summary.html | 1 + .../scripts/repositories/js/repositories.js | 7 +++---- .../scripts/stackedbarchart/js/directives.js | 18 ++++++++++++++---- .../scripts/stackedbarchart/js/stackedbar.js | 4 +--- 4 files changed, 19 insertions(+), 11 deletions(-) diff --git a/dcc-portal-ui/app/scripts/projects/views/projects.summary.html b/dcc-portal-ui/app/scripts/projects/views/projects.summary.html index 5f86b0a52..bcde54125 100644 --- a/dcc-portal-ui/app/scripts/projects/views/projects.summary.html +++ b/dcc-portal-ui/app/scripts/projects/views/projects.summary.html @@ -27,6 +27,7 @@ line-height="lineHeight" data-items="ProjectsCtrl.stacked" data-is-loading="ProjectsCtrl.isLoadingData" + data-is-project-page="true" data-selected="ProjectsCtrl.projectIds" selected-project-count="ProjectsCtrl.numberOfSelectedProjectsInFilter()" data-title="{{'Top 20 Mutated Genes with High Functional Impact SSMs' | translate}}" diff --git a/dcc-portal-ui/app/scripts/repositories/js/repositories.js b/dcc-portal-ui/app/scripts/repositories/js/repositories.js index f2b8f62ca..7f70058af 100644 --- a/dcc-portal-ui/app/scripts/repositories/js/repositories.js +++ b/dcc-portal-ui/app/scripts/repositories/js/repositories.js @@ -108,7 +108,7 @@ angular.module('icgc.repositories.controllers', []) Page.setTitle(gettextCatalog.getString('User Guide')); }) .controller('RepositoriesController', function ($scope, Page, repoAliasMapConstants, - RepositorySearchService, RepositoryService, $stateParams, gettextCatalog) { + RepositorySearchService, RepositoryService, $stateParams, gettextCatalog) { var _ctrl = this, _repoAlias = $stateParams.repoAlias.toLowerCase(), _repoContext = _.get(repoAliasMapConstants, _repoAlias, null), @@ -116,8 +116,7 @@ angular.module('icgc.repositories.controllers', []) _repoCreationDate = null, _filterQueryStr = null, _repoSummaryData = null, - _repoStats = {}; - + _repoStats = {}; function _capitalizeWords(str) { return str.replace(/[^\s]+/g, function(word) { @@ -157,7 +156,7 @@ angular.module('icgc.repositories.controllers', []) function _init() { Page.stopWork(); - Page.setPage('entity'); + Page.setPage(_repoContext); /// ${repoContext} would be a noun Page.setTitle(_.template(gettextCatalog.getString('ICGC in the Cloud - ${repoContext} Repository'))({ repoContext : _capitalizeWords(_repoContext) diff --git a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js index 32cdd45e3..658c07329 100644 --- a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js +++ b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js @@ -19,13 +19,14 @@ 'use strict'; var module = angular.module('icgc.visualization.stackedbar', []); - module.directive('stacked', function ($location, HighchartsService, $window) { + module.directive('stacked', function ($location, HighchartsService, $window, Page) { return { restrict: 'E', replace: true, scope: { items: '=', isLoading: '=', + isProjectPage: '=', alternateBrightness: '=', selected: '=', selectedProjectCount: '=', @@ -56,9 +57,19 @@ label: $scope.yLabel, ticks: 4 }, - onClick: function(link){ + onClick: function(data){ $scope.$emit('tooltip::hide'); - $location.path(link).search({}); + if($scope.isProjectPage){ + $location.path(data.link).search({}); + } else { + let filter = {projectCode: {is: [data.name]}, primarySite: {is: [data.key]}}; + if(_.contains(Page.page(), 'aws')){ + filter = {file: _.extend(filter, {repoName: {is: ['AWS - Virginia']}})}; + } else if(_.contains(Page.page(), 'collaboratory')) { + filter = {file: _.extend(filter, {repoName: {is: ['Collaboratory - Toronto']}})}; + } + $location.path('repositories').search('filters', JSON.stringify(filter)); + } $scope.$apply(); }, tooltipShowFunc: function(elem, d) { @@ -122,7 +133,6 @@ chart.destroy(); } }); - } }; }); diff --git a/dcc-portal-ui/app/scripts/stackedbarchart/js/stackedbar.js b/dcc-portal-ui/app/scripts/stackedbarchart/js/stackedbar.js index 538210fd4..7f6849df3 100644 --- a/dcc-portal-ui/app/scripts/stackedbarchart/js/stackedbar.js +++ b/dcc-portal-ui/app/scripts/stackedbarchart/js/stackedbar.js @@ -194,9 +194,7 @@ config.tooltipHideFunc(); }) .on('click',function(d){ - if (d.link) { - config.onClick(d.link); - } + config.onClick(d); }) .transition() .attr ('y', function (d) {return y (d.y1)}) From 2c171f34325af0e1b62f615574a177bb59a5686f Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Wed, 4 Jan 2017 15:35:44 -0500 Subject: [PATCH 02/19] removed extra code --- dcc-portal-ui/app/scripts/projects/views/projects.summary.html | 1 - dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/dcc-portal-ui/app/scripts/projects/views/projects.summary.html b/dcc-portal-ui/app/scripts/projects/views/projects.summary.html index bcde54125..5f86b0a52 100644 --- a/dcc-portal-ui/app/scripts/projects/views/projects.summary.html +++ b/dcc-portal-ui/app/scripts/projects/views/projects.summary.html @@ -27,7 +27,6 @@ line-height="lineHeight" data-items="ProjectsCtrl.stacked" data-is-loading="ProjectsCtrl.isLoadingData" - data-is-project-page="true" data-selected="ProjectsCtrl.projectIds" selected-project-count="ProjectsCtrl.numberOfSelectedProjectsInFilter()" data-title="{{'Top 20 Mutated Genes with High Functional Impact SSMs' | translate}}" diff --git a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js index 658c07329..6e99884a7 100644 --- a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js +++ b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js @@ -26,7 +26,6 @@ scope: { items: '=', isLoading: '=', - isProjectPage: '=', alternateBrightness: '=', selected: '=', selectedProjectCount: '=', @@ -59,7 +58,7 @@ }, onClick: function(data){ $scope.$emit('tooltip::hide'); - if($scope.isProjectPage){ + if(_.contains(Page.page(), 'projects')){ $location.path(data.link).search({}); } else { let filter = {projectCode: {is: [data.name]}, primarySite: {is: [data.key]}}; From 7e1381097a49e2aad6a4bdb3091eb51ce9de3fce Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Wed, 4 Jan 2017 15:55:11 -0500 Subject: [PATCH 03/19] bug fix --- dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js index 6e99884a7..8009c6b94 100644 --- a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js +++ b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js @@ -61,11 +61,11 @@ if(_.contains(Page.page(), 'projects')){ $location.path(data.link).search({}); } else { - let filter = {projectCode: {is: [data.name]}, primarySite: {is: [data.key]}}; + let filter = {file: {projectCode: {is: [data.name]}, primarySite: {is: [data.key]}}}; if(_.contains(Page.page(), 'aws')){ - filter = {file: _.extend(filter, {repoName: {is: ['AWS - Virginia']}})}; + filter = {file: _.extend(filter.file, {repoName: {is: ['AWS - Virginia']}})}; } else if(_.contains(Page.page(), 'collaboratory')) { - filter = {file: _.extend(filter, {repoName: {is: ['Collaboratory - Toronto']}})}; + filter = {file: _.extend(filter.file, {repoName: {is: ['Collaboratory - Toronto']}})}; } $location.path('repositories').search('filters', JSON.stringify(filter)); } From a742398350f75bfda87044cc8abeecba1a76b40c Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Thu, 5 Jan 2017 10:24:47 -0500 Subject: [PATCH 04/19] added a filter for pcawg stacked bar chart --- .../app/scripts/pancancer/views/pancancer.html | 3 ++- .../scripts/projects/views/projects.summary.html | 3 ++- .../app/scripts/repositories/js/repositories.js | 2 +- .../app/scripts/repositories/views/repos/repos.html | 3 ++- .../app/scripts/stackedbarchart/js/directives.js | 13 ++++++++----- 5 files changed, 15 insertions(+), 9 deletions(-) diff --git a/dcc-portal-ui/app/scripts/pancancer/views/pancancer.html b/dcc-portal-ui/app/scripts/pancancer/views/pancancer.html index bda6e4ad2..ce7353f7f 100644 --- a/dcc-portal-ui/app/scripts/pancancer/views/pancancer.html +++ b/dcc-portal-ui/app/scripts/pancancer/views/pancancer.html @@ -11,7 +11,8 @@

data-y-label="{{'Donors' | translate}}" data-alternate-brightness="true" data-items="primarySites" - data-is-loading="false"> + data-is-loading="false" + data-current-page="pcawg">
diff --git a/dcc-portal-ui/app/scripts/projects/views/projects.summary.html b/dcc-portal-ui/app/scripts/projects/views/projects.summary.html index 5f86b0a52..1de25106f 100644 --- 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">
diff --git a/dcc-portal-ui/app/scripts/repositories/js/repositories.js b/dcc-portal-ui/app/scripts/repositories/js/repositories.js index 7f70058af..acd1086e6 100644 --- a/dcc-portal-ui/app/scripts/repositories/js/repositories.js +++ b/dcc-portal-ui/app/scripts/repositories/js/repositories.js @@ -156,7 +156,7 @@ angular.module('icgc.repositories.controllers', []) function _init() { Page.stopWork(); - Page.setPage(_repoContext); + Page.setPage('entity'); /// ${repoContext} would be a noun Page.setTitle(_.template(gettextCatalog.getString('ICGC in the Cloud - ${repoContext} Repository'))({ repoContext : _capitalizeWords(_repoContext) diff --git a/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html b/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html index 9d32029c4..90699bac1 100644 --- a/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html +++ b/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html @@ -22,7 +22,8 @@

data-y-label="{{'Donors' | translate}}" data-alternate-brightness="true" data-items="repositoryCtrl.getPrimarySites()" - data-is-loading="false"> + data-is-loading="false" + data-current-page="{{repositoryCtrl.getRepoContextID()}}">
diff --git a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js index 8009c6b94..868318ab5 100644 --- a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js +++ b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js @@ -19,7 +19,7 @@ 'use strict'; var module = angular.module('icgc.visualization.stackedbar', []); - module.directive('stacked', function ($location, HighchartsService, $window, Page) { + module.directive('stacked', function ($location, HighchartsService, $window) { return { restrict: 'E', replace: true, @@ -32,7 +32,8 @@ lineHeight: '=', title: '@', subtitle: '@', - yLabel: '@' + yLabel: '@', + currentPage: '@' }, templateUrl: '/scripts/stackedbarchart/views/stackedbarchart.html', link: function ($scope, $element) { @@ -58,14 +59,16 @@ }, onClick: function(data){ $scope.$emit('tooltip::hide'); - if(_.contains(Page.page(), 'projects')){ + if(_.contains($scope.currentPage, 'projects')){ $location.path(data.link).search({}); } else { let filter = {file: {projectCode: {is: [data.name]}, primarySite: {is: [data.key]}}}; - if(_.contains(Page.page(), 'aws')){ + if(_.contains($scope.currentPage, 'aws')){ filter = {file: _.extend(filter.file, {repoName: {is: ['AWS - Virginia']}})}; - } else if(_.contains(Page.page(), 'collaboratory')) { + } else if(_.contains($scope.currentPage, 'collaboratory')) { filter = {file: _.extend(filter.file, {repoName: {is: ['Collaboratory - Toronto']}})}; + } else if (_.contains($scope.currentPage, 'pcawg')) { + filter = {file: _.extend(filter.file, {study: {is: ['PCAWG']}})}; } $location.path('repositories').search('filters', JSON.stringify(filter)); } From bd17d707bc50e2f43d12ed78fd54072ca1271c63 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Thu, 5 Jan 2017 10:59:27 -0500 Subject: [PATCH 05/19] passing the repoName to the directive --- .../app/scripts/repositories/js/repositories.js | 8 ++++++++ .../app/scripts/repositories/views/repos/repos.html | 3 ++- .../app/scripts/stackedbarchart/js/directives.js | 9 ++++----- 3 files changed, 14 insertions(+), 6 deletions(-) diff --git a/dcc-portal-ui/app/scripts/repositories/js/repositories.js b/dcc-portal-ui/app/scripts/repositories/js/repositories.js index acd1086e6..8045f8bd3 100644 --- a/dcc-portal-ui/app/scripts/repositories/js/repositories.js +++ b/dcc-portal-ui/app/scripts/repositories/js/repositories.js @@ -218,6 +218,14 @@ angular.module('icgc.repositories.controllers', []) _ctrl.getFilterQueryStr = function() { return _filterQueryStr; }; + + _ctrl.getRepoName = () => { + if(_.contains(_repoContext, 'aws')){ + return 'AWS - Virginia'; + } else if(_.contains(_repoContext, 'collaboratory')) { + return 'Collaboratory - Toronto'; + } + } }); diff --git a/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html b/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html index 90699bac1..e9b4450fe 100644 --- a/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html +++ b/dcc-portal-ui/app/scripts/repositories/views/repos/repos.html @@ -23,7 +23,8 @@

data-alternate-brightness="true" data-items="repositoryCtrl.getPrimarySites()" data-is-loading="false" - data-current-page="{{repositoryCtrl.getRepoContextID()}}"> + data-current-page="cloud" + data-repo-name="{{repositoryCtrl.getRepoName()}}">
diff --git a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js index 868318ab5..4e2da4695 100644 --- a/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js +++ b/dcc-portal-ui/app/scripts/stackedbarchart/js/directives.js @@ -33,7 +33,8 @@ title: '@', subtitle: '@', yLabel: '@', - currentPage: '@' + currentPage: '@', + repoName: '@' }, templateUrl: '/scripts/stackedbarchart/views/stackedbarchart.html', link: function ($scope, $element) { @@ -63,10 +64,8 @@ $location.path(data.link).search({}); } else { let filter = {file: {projectCode: {is: [data.name]}, primarySite: {is: [data.key]}}}; - if(_.contains($scope.currentPage, 'aws')){ - filter = {file: _.extend(filter.file, {repoName: {is: ['AWS - Virginia']}})}; - } else if(_.contains($scope.currentPage, 'collaboratory')) { - filter = {file: _.extend(filter.file, {repoName: {is: ['Collaboratory - Toronto']}})}; + if(_.contains($scope.currentPage, 'cloud')){ + filter = {file: _.extend(filter.file, {repoName: {is: [$scope.repoName]}})}; } else if (_.contains($scope.currentPage, 'pcawg')) { filter = {file: _.extend(filter.file, {study: {is: ['PCAWG']}})}; } From 2b52f5efa5634344b3b7670348a0ff61d0059000 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Thu, 5 Jan 2017 11:05:30 -0500 Subject: [PATCH 06/19] missing semicolon --- dcc-portal-ui/app/scripts/repositories/js/repositories.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dcc-portal-ui/app/scripts/repositories/js/repositories.js b/dcc-portal-ui/app/scripts/repositories/js/repositories.js index 8045f8bd3..4d7a7f0c2 100644 --- a/dcc-portal-ui/app/scripts/repositories/js/repositories.js +++ b/dcc-portal-ui/app/scripts/repositories/js/repositories.js @@ -225,7 +225,7 @@ angular.module('icgc.repositories.controllers', []) } else if(_.contains(_repoContext, 'collaboratory')) { return 'Collaboratory - Toronto'; } - } + }; }); From 29802efe208be2a4cb23cab2b90b27694950776f Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Thu, 5 Jan 2017 17:21:09 -0500 Subject: [PATCH 07/19] Download donor data message show for any type of error. more detailed Noify message --- dcc-portal-ui/app/scripts/app/js/app.js | 4 +- dcc-portal-ui/app/scripts/common/js/notify.js | 62 +++++++++++++++---- .../app/scripts/downloader/js/request.js | 8 +-- .../app/styles/_modules/_common.scss | 12 ++++ 4 files changed, 68 insertions(+), 18 deletions(-) diff --git a/dcc-portal-ui/app/scripts/app/js/app.js b/dcc-portal-ui/app/scripts/app/js/app.js index 2a97fc6de..7931159bd 100644 --- a/dcc-portal-ui/app/scripts/app/js/app.js +++ b/dcc-portal-ui/app/scripts/app/js/app.js @@ -604,9 +604,9 @@ 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/notify.js b/dcc-portal-ui/app/scripts/common/js/notify.js index 11daee57e..ffdb149da 100644 --- 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; } @@ -100,6 +112,8 @@ showErrors: showErrors, hide: hide, redirectHome: redirectHome, + setParams: setParams, + getParams: getParams, setMessage: setMessage, getMessage: getMessage, setRemovable: setRemovable, @@ -111,6 +125,8 @@ 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: '
' + - '
' + - '
' + - ''+ - 'Home' + - '  ' + - '' + - 'Close' + - '
' + - '
' + - '
' + template: `
+
+
+ + An error occured while performing the requested operation. + See details + for more information. + +
+
+ + We have created an error report that you can send to help us improve ICGC Portal. + Email error report. + +
+
+
+ + Home + +    + + Close + +
+
+
` }; }); })(); diff --git a/dcc-portal-ui/app/scripts/downloader/js/request.js b/dcc-portal-ui/app/scripts/downloader/js/request.js index 7955a3386..5fcf51098 100644 --- a/dcc-portal-ui/app/scripts/downloader/js/request.js +++ b/dcc-portal-ui/app/scripts/downloader/js/request.js @@ -135,11 +135,9 @@ $scope.params.dataTypes = $filter('orderBy')($scope.params.dataTypes, sortFunc); $scope.params.processing = false; - },function (error) { - if(error.status === 503){ - $scope.params.processing = false; - $scope.params.downloadEnabled = false; - } + },function (error) { + $scope.params.processing = false; + $scope.params.downloadEnabled = false; }); }; diff --git a/dcc-portal-ui/app/styles/_modules/_common.scss b/dcc-portal-ui/app/styles/_modules/_common.scss index 95fe28b91..69e550d2c 100644 --- a/dcc-portal-ui/app/styles/_modules/_common.scss +++ b/dcc-portal-ui/app/styles/_modules/_common.scss @@ -230,6 +230,18 @@ h3:hover { font-family: inherit; } +.t_notify_popup { + pre{ + background: #d3741c; + color: #fff; + padding: 10px; + box-shadow: inset 1px 1px 1px 0px rgba(0,0,0,0.5); + overflow: scroll; + max-height: 100px; + line-height: 1rem; + } +} + .t_notify_link { cursor: pointer; color: #FFF; From 97772ab0839b11c507be4df650a8e17ea31729bf Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Fri, 6 Jan 2017 09:25:48 -0500 Subject: [PATCH 08/19] Missing semicolon --- dcc-portal-ui/app/scripts/common/js/notify.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dcc-portal-ui/app/scripts/common/js/notify.js b/dcc-portal-ui/app/scripts/common/js/notify.js index ffdb149da..ada65fbf9 100644 --- a/dcc-portal-ui/app/scripts/common/js/notify.js +++ b/dcc-portal-ui/app/scripts/common/js/notify.js @@ -79,7 +79,7 @@ params.source = response.config.url; params.message = response.data.message || response.statusText; } - } + }; const getParams = () => params; From 80ff616b82568c4a09e60263776799df3341e0de Mon Sep 17 00:00:00 2001 From: Chang Wang Date: Fri, 6 Jan 2017 09:59:41 -0500 Subject: [PATCH 09/19] Increase genome browser minTranscriptRegionSize to 500k --- dcc-portal-ui/app/scripts/genomemaps/js/viewer.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dcc-portal-ui/app/scripts/genomemaps/js/viewer.js b/dcc-portal-ui/app/scripts/genomemaps/js/viewer.js index 319d82aa2..00f4be515 100644 --- 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({ From 6049c60b0a7e7334f4cf1a38a4458aafcee4eed3 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Fri, 6 Jan 2017 10:40:15 -0500 Subject: [PATCH 10/19] TCGA and CGHub links update --- dcc-portal-ui/app/scripts/common/js/external.js | 10 ++-------- dcc-portal-ui/app/scripts/projects/views/project.html | 8 ++++---- 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/dcc-portal-ui/app/scripts/common/js/external.js b/dcc-portal-ui/app/scripts/common/js/external.js index c30255aaf..d31e39e11 100644 --- 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/projects/views/project.html b/dcc-portal-ui/app/scripts/projects/views/project.html index ce601e5f5..7bc0f0649 100644 --- a/dcc-portal-ui/app/scripts/projects/views/project.html +++ b/dcc-portal-ui/app/scripts/projects/views/project.html @@ -164,11 +164,11 @@

Raw data is available at

NCBI dbSNP - - The Cancer Genome Atlas + + Genomic Data Commons (Legacy) - - Cancer Genomics Hub + + Genomic Data Commons (Active) Gene Expression Omnibus From 2bd5115fe4760a988a807a1aafd3d4f9200b744b Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Fri, 6 Jan 2017 10:45:11 -0500 Subject: [PATCH 11/19] Object shorthand --- dcc-portal-ui/app/scripts/common/js/notify.js | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/dcc-portal-ui/app/scripts/common/js/notify.js b/dcc-portal-ui/app/scripts/common/js/notify.js index ada65fbf9..668d36653 100644 --- a/dcc-portal-ui/app/scripts/common/js/notify.js +++ b/dcc-portal-ui/app/scripts/common/js/notify.js @@ -107,19 +107,19 @@ } return { - isVisible: isVisible, - show: show, - showErrors: showErrors, - hide: hide, - redirectHome: redirectHome, - setParams: setParams, - getParams: getParams, - 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 }; }); From 64254d4aab415ad3a9f379adfcf35c7b39319b67 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Fri, 6 Jan 2017 11:46:19 -0500 Subject: [PATCH 12/19] Link to repo added --- dcc-portal-ui/app/scripts/projects/views/project.html | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/dcc-portal-ui/app/scripts/projects/views/project.html b/dcc-portal-ui/app/scripts/projects/views/project.html index ce601e5f5..3cb1b2ec9 100644 --- a/dcc-portal-ui/app/scripts/projects/views/project.html +++ b/dcc-portal-ui/app/scripts/projects/views/project.html @@ -314,6 +314,13 @@

Available Data Types:

{{:: ProjectCtrl.dataReleasesTitle }} + + View in + + + Data Repositories + +
From 7144985d99d25cdff3efbee5956e1d8218ece7b0 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Fri, 6 Jan 2017 12:00:46 -0500 Subject: [PATCH 13/19] Styling change --- .../app/scripts/projects/views/project.html | 31 +++++++++++++------ 1 file changed, 21 insertions(+), 10 deletions(-) diff --git a/dcc-portal-ui/app/scripts/projects/views/project.html b/dcc-portal-ui/app/scripts/projects/views/project.html index dd285922a..00dc87c5a 100644 --- a/dcc-portal-ui/app/scripts/projects/views/project.html +++ b/dcc-portal-ui/app/scripts/projects/views/project.html @@ -310,16 +310,27 @@

Available Data Types:

From 2971b2f4496160a9c9f4341fe6e25a90d2977952 Mon Sep 17 00:00:00 2001 From: Sid Joshi Date: Fri, 6 Jan 2017 13:36:48 -0500 Subject: [PATCH 14/19] Search bar --- dcc-portal-ui/app/scripts/facets/views/terms.html | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/dcc-portal-ui/app/scripts/facets/views/terms.html b/dcc-portal-ui/app/scripts/facets/views/terms.html index da7c673fa..450edf5a1 100644 --- a/dcc-portal-ui/app/scripts/facets/views/terms.html +++ b/dcc-portal-ui/app/scripts/facets/views/terms.html @@ -7,6 +7,12 @@ + + + + +
  • +
  • diff --git a/dcc-portal-ui/app/scripts/facets/js/terms.js b/dcc-portal-ui/app/scripts/facets/js/terms.js index 335c3de97..ca2eb73b7 100644 --- 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) { diff --git a/dcc-portal-ui/app/scripts/facets/styles/_facets.scss b/dcc-portal-ui/app/scripts/facets/styles/_facets.scss index 583c6f484..a5122b453 100644 --- a/dcc-portal-ui/app/scripts/facets/styles/_facets.scss +++ b/dcc-portal-ui/app/scripts/facets/styles/_facets.scss @@ -332,5 +332,5 @@ $togglerFontSize: 10px; } .t_facet_location_search{ - margin: 0px 0px 10px 0px; + margin: 10px 0px 10px 0px; } \ No newline at end of file diff --git a/dcc-portal-ui/app/scripts/facets/views/terms.html b/dcc-portal-ui/app/scripts/facets/views/terms.html index bcce14f17..f252e77fa 100644 --- a/dcc-portal-ui/app/scripts/facets/views/terms.html +++ b/dcc-portal-ui/app/scripts/facets/views/terms.html @@ -11,11 +11,11 @@ data-ng-show="(inactives.length > (searchIconShowLimit || 5)) && !collapsed"> -
    - +
    + + data-ng-click="search.query = ''" + data-ng-show="search.query">
  • @@ -54,7 +54,7 @@