webpack done

.jshintrc

@@ -72,7 +72,6 @@
     "devel"         : true,     // Development/debugging (alert, confirm, etc)
     "dojo"          : false,    // Dojo Toolkit
     "jasmine"       : true,    // Jasmine
-    "jquery"        : true,    // jQuery
     "mocha"         : true,     // Mocha
     "mootools"      : false,    // MooTools
     "node"          : true,    // Node.js

R/gemtc.R

@@ -383,6 +383,7 @@ gemtc <- function(params) {
     }
 
     # create network
+    print(is.vector(studies))
     network <- mtc.network(data.ab=data.ab, data.re=data.re, treatments=treatments, studies=studies)
 
     # pair-wise analysis: filter network

R/r-base/Dockerfile

@@ -4,6 +4,7 @@ FROM patavi/worker-amqp
 
 USER root
 
+RUN DEBIAN_FRONTEND=noninteractive apt-get update
 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q r-cran-rjags
 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q r-cran-xml
 
@@ -18,6 +19,6 @@ RUN R -e 'install.packages("truncnorm", repos="http://cran.rstudio.com/"); if (!
 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q r-cran-rglpk
 
 # RUN R -e 'install.packages("gemtc", repos="http://cran.rstudio.com/"); if (!require("gemtc")) quit(save="no", status=8)'
-COPY gemtc_0.8-2.tar.gz gemtc_0.8.tar.gz
+COPY gemtc_0.8-3.tar.gz gemtc_0.8.tar.gz
 RUN R -e 'install.packages("gemtc_0.8.tar.gz", repos=NULL, type="source"); if (!require("gemtc")) quit(save="no", status=8)'
 

app/js/app.js

@@ -1,27 +1,28 @@
 'use strict';
 define(
   ['angular',
-    './analyses/analyses',
-    'angular-patavi-client',
-    'angular-touch',
-    'angular-ui-router',
-    'angular-animate',
-    './constants',
-    './controllers',
-    'core-js',
-    'error-reporting',
-    'export-directive',
-    'help-popup',
-    'jQuery',
-    'angular-foundation-6',
-    './models/models',
-    'angular-sanitize',
-    './patavi/patavi',
-    './services',
-    './util/util'
-  ],
-  function(angular) {
-
+  './analyses/analyses',
+  'angular-patavi-client',
+  'angular-touch',
+  'angular-ui-router',
+  'angular-animate',
+  './constants',
+  './controllers',
+  'core-js',
+  'error-reporting',
+  'export-directive',
+  'help-popup',
+  'jquery',
+  'angular-foundation-6',
+  './models/models',
+  'angular-sanitize',
+  './patavi/patavi',
+  './services',
+  './util/util'
+],
+function(angular) {
+
+  //@require "../views/*.html"
     var dependencies = [
       'ui.router',
       'ngTouch',
@@ -42,8 +43,15 @@ define(
 
     var app = angular.module('gemtc', dependencies);
 
-    app.run(['$rootScope', '$window', '$http', '$location', '$anchorScroll', 'HelpPopupService',
-      function($rootScope, $window, $http, $location, $anchorScroll, HelpPopupService) {
+    app.run(['$rootScope', '$http', '$templateCache', 'HelpPopupService',
+      function($rootScope, $http, $templateCache, HelpPopupService) {
+
+        $templateCache.put('model-settings-section.html', require('../views/model-settings-section.html'));
+        $templateCache.put('convergence-diagnostics-section.html', require('../views/convergence-diagnostics-section.html'));
+        $templateCache.put('meta-regression-section.html', require('../views/meta-regression-section.html'));
+        $templateCache.put('results-section.html', require('../views/results-section.html'));
+        $templateCache.put('model-fit-section.html', require('../views/model-fit-section.html'));
+
         $rootScope.$safeApply = function($scope, fn) {
           var phase = $scope.$root.$$phase;
           if (phase === '$apply' || phase === '$digest') {
@@ -189,4 +197,4 @@ define(
     ]);
 
     return app;
-  });
+  });

app/js/controllers/modelController.js

@@ -1,6 +1,7 @@
 'use strict';
-define(['lodash', 'clipboard'], function(_, Clipboard) {
-  var dependencies = ['$scope', '$q', '$http', '$modal', '$state', '$stateParams', '$window', 'gemtcRootPath', 'ModelResource', 'ModelBaselineResource',
+define(['lodash', 'clipboard', 'jquery'], function(_, Clipboard, $) {
+  var dependencies = ['$scope', '$q', '$http', '$modal', '$state', '$stateParams', 
+    '$window', 'ModelResource', 'ModelBaselineResource',
     'FunnelPlotResource', 
     'PataviService',
     'RelativeEffectsTableService', 
@@ -14,7 +15,8 @@ define(['lodash', 'clipboard'], function(_, Clipboard) {
     'MetaRegressionService',
     'ResultsPlotService'
   ];
-  var ModelController = function($scope, $q, $http, $modal, $state, $stateParams, $window, gemtcRootPath, ModelResource, ModelBaselineResource,
+  var ModelController = function($scope, $q, $http, $modal, $state, $stateParams, 
+    $window, ModelResource, ModelBaselineResource,
     FunnelPlotResource, 
     PataviService,
     RelativeEffectsTableService, 
@@ -47,11 +49,6 @@ define(['lodash', 'clipboard'], function(_, Clipboard) {
     $scope.model = ModelResource.get($stateParams);
     $scope.modelPromise = modelDefer.promise;
     $scope.comparisonAdjustedFunnelPlots = FunnelPlotResource.query($stateParams);
-    $scope.resultsViewTemplate = gemtcRootPath + 'views/results-section.html';
-    $scope.modelSettingsViewTemplate = gemtcRootPath + 'views/model-settings-section.html';
-    $scope.convergenceDiagnosticsViewTemplate = gemtcRootPath + 'views/convergence-diagnostics-section.html';
-    $scope.modelFitViewTemplate = gemtcRootPath + 'views/model-fit-section.html';
-    $scope.metaRegressionTemplate = gemtcRootPath + 'views/meta-regression-section.html';
     $scope.stateParams = $stateParams;
     new Clipboard('.clipboard-button');
     $scope.selectedBaseline = undefined;
@@ -103,7 +100,7 @@ define(['lodash', 'clipboard'], function(_, Clipboard) {
     function openRunLengthDialog() {
       $modal.open({
         windowClass: 'small',
-        templateUrl: gemtcRootPath + 'js/models/extendRunLength.html',
+        templateUrl: 'gemtc-web/models/extendRunLength.html',
         scope: $scope,
         controller: 'ExtendRunLengthController',
         resolve: {
@@ -128,7 +125,7 @@ define(['lodash', 'clipboard'], function(_, Clipboard) {
     function openComparisonAdjustedModal() {
       $modal.open({
         windowClass: 'small',
-        templateUrl: gemtcRootPath + 'js/models/addComparisonFunnelPlot.html',
+        templateUrl: 'gemtc-web/models/addComparisonFunnelPlot.html',
         scope: $scope,
         controller: 'AddComparisonFunnelPlotController',
         resolve: {
@@ -221,7 +218,7 @@ define(['lodash', 'clipboard'], function(_, Clipboard) {
 
     function openBaselineDistributionModal() {
       $modal.open({
-        templateUrl: gemtcRootPath + 'js/models/setBaselineDistribution.html',
+        templateUrl: 'gemtc-web/models/setBaselineDistribution.html',
         controller: 'SetBaselineDistributionController',
         windowClass: 'small',
         resolve: {
@@ -302,4 +299,4 @@ define(['lodash', 'clipboard'], function(_, Clipboard) {
     }
   };
   return dependencies.concat(ModelController);
-});
+});

app/js/models/comparisonAdjustedFunnelPlot/comparisonAdjustedFunnelPlotDirective.js

@@ -17,7 +17,7 @@ define(['d3', 'nvd3', 'lodash'], function(d3, nvd3, _) {
         problemPromise: '=',
         resultsPromise: '='
       },
-      templateUrl: gemtcRootPath + 'js/models/funnelPlot/funnelPlot.html',
+      templateUrl: 'gemtc-web/models/funnelPlot/funnelPlot.html',
       link: function(scope, element) {
         $q.all([scope.resultsPromise, scope.problemPromise]).then(function(promiseResults) {
           var results = promiseResults[0];
@@ -88,4 +88,4 @@ define(['d3', 'nvd3', 'lodash'], function(d3, nvd3, _) {
     };
   };
   return dependencies.concat(FunnelPlot);
-});
+});

app/js/models/funnelPlot/funnelPlotDirective.js

@@ -7,7 +7,7 @@ define(['d3', 'nvd3', 'lodash'], function(d3, nvd3, _) {
       scope: {
         resultsPromise: '='
       },
-      templateUrl: gemtcRootPath + 'js/models/funnelPlot/funnelPlot.html',
+      templateUrl: 'gemtc-web/models/funnelPlot/funnelPlot.html',
       link: function(scope, element) {
 
         scope.resultsPromise.then(function(results) {
@@ -51,4 +51,4 @@ define(['d3', 'nvd3', 'lodash'], function(d3, nvd3, _) {
     };
   };
   return dependencies.concat(FunnelPlot);
-});
+});

app/js/models/funnelPlot/funnelPlotService.js

@@ -1,5 +1,5 @@
 'use strict';
-define(['d3', 'nvd3', 'lodash'], function(d3, nvd3, _) {
+define(['d3', 'nvd3', 'lodash', 'jquery'], function(d3, nvd3, _, $) {
   var dependencies = [];
   var FunnelPlotService = function() {
 
@@ -87,4 +87,4 @@ define(['d3', 'nvd3', 'lodash'], function(d3, nvd3, _) {
   };
 
   return dependencies.concat(FunnelPlotService);
-});
+});

app/js/models/heterogeneityPrior/heterogeneityPriorDirective.js

@@ -4,7 +4,7 @@ define([], function() {
   var HeterogeneityPriorDirective = function(gemtcRootPath) {
     return {
       restrict: 'E',
-      templateUrl: gemtcRootPath + 'js/models/heterogeneityPrior/heterogeneityPrior.html',
+      templateUrl: 'gemtc-web/models/heterogeneityPrior/heterogeneityPrior.html',
       scope: {
         prior: '='
       },

app/js/models/nodeSplitOverviewController.js

@@ -119,7 +119,7 @@ define(['angular', 'lodash'], function(angular, _) {
     function openCreateNetworkDialog() {
       $modal.open({
         windowClass: 'small',
-        templateUrl: gemtcRootPath + 'js/models/createModelFromBase.html',
+        templateUrl: 'gemtc-web/models/createModelFromBase.html',
         scope: $scope,
         controller: 'CreateNetworkModelController',
         resolve: {
@@ -144,7 +144,7 @@ define(['angular', 'lodash'], function(angular, _) {
     function openCreateNodeSplitDialog(comparison) {
       $modal.open({
         windowClass: 'small',
-        templateUrl: gemtcRootPath + 'js/models/createModelFromBase.html',
+        templateUrl: 'gemtc-web/models/createModelFromBase.html',
         scope: $scope,
         controller: 'CreateNodeSplitModelController',
         resolve: {

app/js/models/result/metaRegressionCovPlotsDirective.js

@@ -9,7 +9,7 @@ define([], function() {
         problemPromise: '='
       },
       restrict: 'E',
-      templateUrl: gemtcRootPath + 'js/models/result/metaRegressionCovPlots.html',
+      templateUrl: 'gemtc-web/models/result/metaRegressionCovPlots.html',
       link: function(scope) {
 
         $q.all([scope.modelPromise, scope.resultsPromise, scope.problemPromise])

app/js/models/result/nodeSplitDensityPlotsDirective.js

@@ -9,7 +9,7 @@ define([], function() {
         problemPromise: '='
       },
       restrict: 'E',
-      templateUrl: gemtcRootPath + 'js/models/result/nodeSplitDensityPlots.html',
+      templateUrl: 'gemtc-web/models/result/nodeSplitDensityPlots.html',
       link: function(scope) {
 
         $q.all([scope.modelPromise, scope.resultsPromise, scope.problemPromise])

app/js/models/result/pairwiseForestPlotsDirective.js

@@ -9,7 +9,7 @@ define(['lodash'], function(_) {
         problemPromise: '='
       },
       restrict: 'E',
-      templateUrl: gemtcRootPath + 'js/models/result/pairwiseForestPlots.html',
+      templateUrl: 'gemtc-web/models/result/pairwiseForestPlots.html',
       link: function(scope) {
 
         $q.all([scope.modelPromise, scope.resultsPromise, scope.problemPromise])

app/js/models/result/relativeEffectPlotsDirective.js

@@ -9,7 +9,7 @@ define(['lodash'], function(_) {
         problemPromise: '='
       },
       restrict: 'E',
-      templateUrl: gemtcRootPath + 'js/models/result/relativeEffectPlots.html',
+      templateUrl: 'gemtc-web/models/result/relativeEffectPlots.html',
       link: function(scope) {
 
         function prefixPlots(plots) {

app/js/signin.js

@@ -1,4 +1,3 @@
 define(['bowser', 'css/gemtc-drugis.css'], function(bowser){
   window.bowser = bowser;
-
-});
+});

app/js/util/graphModalDirective/graphModalDirective.js

@@ -9,12 +9,12 @@ define([], function() {
       },
       restrict: 'E',
       // using template because loading teplateUrl irritating in submodule
-      templateUrl: gemtcRootPath + 'js/util/graphModalDirective/graphModalDirective.html',
+      templateUrl: 'gemtc-web/util/graphModalDirective/graphModalDirective.html',
       link: function(scope) {
 
         scope.openModal = function() {
           $modal.open({
-            templateUrl: gemtcRootPath + 'js/util/graphModalDirective/plotNavigation.html',
+            templateUrl: 'gemtc-web/util/graphModalDirective/plotNavigation.html',
             scope: scope,
             windowClass: 'small',
             controller: 'PlotNavigationController'

app/js/util/pagedPngPlotDirective.js

@@ -9,7 +9,7 @@ define([], function() {
       },
       restrict: 'E',
       // using template because loading teplateUrl irritating in submodule
-      templateUrl: gemtcRootPath + 'js/util/pagedPngPlotDirective.html',
+      templateUrl: 'gemtc-web/util/pagedPngPlotDirective.html',
       link: function(scope) {
         scope.selectNextPage = selectNextPage;
         scope.selectPreviousPage = selectPreviousPage;

app/js/util/pagedSvgPlotDirective.js

@@ -9,7 +9,7 @@ define([], function() {
       },
       restrict: 'E',
       // using template because loading templateUrl irritating in submodule
-      templateUrl: gemtcRootPath + 'js/util/pagedSvgPlotDirective.html',
+      templateUrl: 'gemtc-web/util/pagedSvgPlotDirective.html',
       link: function(scope) {
         scope.selectNextPage = selectNextPage;
         scope.selectPreviousPage = selectPreviousPage;

app/views/modelView.html

@@ -15,15 +15,15 @@ <h5>
     </div>
   </div>
 
-  <ng-include src="modelSettingsViewTemplate"></ng-include>
+  <ng-include src="'model-settings-section.html'"></ng-include>
 
-  <ng-include src="convergenceDiagnosticsViewTemplate"></ng-include>
+  <ng-include src="'convergence-diagnostics-section.html'"></ng-include>
 
-  <ng-include ng-show="model.modelType.type === 'regression'" src="metaRegressionTemplate"></ng-include>
+  <ng-include ng-if="model.modelType.type === 'regression'" src="'meta-regression-section.html'"></ng-include>
 
-  <ng-include src="resultsViewTemplate"></ng-include>
+  <ng-include src="'results-section.html'"></ng-include>
 
-  <ng-include src="modelFitViewTemplate"></ng-include>
+  <ng-include src="'model-fit-section.html'"></ng-include>
 
 
 </div ui-view>

standalone-app/loginUtils.js

@@ -52,11 +52,8 @@ module.exports = {
     }
     else if (request.method === 'GET' && // if not then you can get static content or go sign in
       (request.url.startsWith('/css') ||
-        // request.url.startsWith('/dist') ||
         request.url.startsWith('/views') ||
         request.url.startsWith('/img') ||
-        request.url.startsWith('/fonts') ||
-        request.url.startsWith('/font') ||
         request.url === '/signin.html' ||
         request.url === '/signin.bundle.js' ||
         request.url === '/main.bundle.js' ||

standalone-app/pataviTaskRepository.js

@@ -22,14 +22,14 @@ var httpsOptions = {
 try {
   httpsOptions.key = fs.readFileSync(process.env.PATAVI_CLIENT_KEY);
 } catch (e) {
-  logger.warn('could not read patavi client key at: ' + process.env.PATAVI_CLIENT_KEY);
+  logger.error('could not read patavi client key at: ' + process.env.PATAVI_CLIENT_KEY);
   httpsOptions.key = 'empty-key';
 }
 
 try {
   httpsOptions.cert = fs.readFileSync(process.env.PATAVI_CLIENT_CRT);
 } catch (e) {
-  logger.warn('could not read patavi client certivicate key at: ' + process.env.PATAVI_CLIENT_CRT);
+  logger.error('could not read patavi client certivicate key at: ' + process.env.PATAVI_CLIENT_CRT);
   httpsOptions.cert = 'empty-client-crt';
 }
 
@@ -133,4 +133,4 @@ function deleteTask(id, callback) {
     }
   });
   deleteReq.end();
-}
+}