Update README.md

README.md

@@ -52,10 +52,6 @@ Notes:
 4. Push to the branch: `git push origin my-new-feature`
 5. Submit a pull request
 
-## Author(s)
-
-Neal Conrad <nconrad@anl.gov>
-
 
 ## License
 

app/ctrls/ms-ctrls.js

@@ -18,6 +18,7 @@ function($scope, $state, $stateParams, Auth, $window) {
     // sets method and changes url param
     $scope.switchMethod = function(method) {
         $scope.method = Auth.loginMethod(method);
+        $scope.inValid = false;
         //$state.go('main.home', {login: method});
     }
 
@@ -141,7 +142,7 @@ function($s, $http, config, $rootScope) {
          .then(function(res) { $s.app = true; })
          .catch(function() { $s.app = false; })
 
-    $http.rpc('msSupport', 'list_rast_jobs', {owner: $rootScope.user})
+    $http.rpc('msSupport', 'version', {owner: $rootScope.user})
          .then(function(res) {
              console.log('res', res); $s.msSupport = true;
          })

app/services/auth.js

@@ -88,10 +88,14 @@ function($state, $http, config, $window) {
 
     this.logout = function() {
         $window.localStorage.removeItem('auth');
-        $state.transitionTo('main.home', {}, { reload: true, inherit: true, notify: false })
-              .then(function() {
-                  $window.location.reload();
-              });
+
+        var to_url = window.location.protocol + '//' + window.location.host;
+        if ($state.current.name === 'main.home') {
+            $window.location.reload();
+        } else {
+            to_url = to_url + '/genomes/Plants';
+            $window.location.replace(to_url);
+        }
     }
 
     this.isAuthenticated = function() {

app/services/dialogs.js

@@ -789,7 +789,6 @@ function($rootScope, $dialog, $window, $timeout, Auth, $stateParams) {
                     $s.method = Auth.loginMethod(method);
                     $stateParams.login = method;
                     $s.inValid = false;
-                    $s.creds = {};
                 }
 
                 $s.ok = function(){

app/views/data/model.html

@@ -16,10 +16,6 @@
         </div>
         <md-button class="md-primary md-raised md-button" ng-click="runPlantFBA($event, item)">Run FBA</md-button>
         <md-button class="md-primary md-raised md-button" ng-click="gapfill($event, item)">Run GapFilling</md-button>
-
-            <md-tooltip>View download options</md-tooltip>
-            <i class="icon-file-download"></i>
-        </md-button>
     </div>
 </div>
 <md-divider></md-divider>

app/views/dialogs/auth.html

@@ -5,7 +5,7 @@
         <h3>Please sign in</h3>
         <span flex></span>
         <md-button class="md-icon-button" ng-click="cancel()" ui-sref="main.home" tabindex="1">
-          <md-icon class="material-icons" aria-label="Close signin dialog, go to homepage">close</md-icon>
+          <md-icon class="material-icons" aria-label="Close signIn dialog, go to homepage">close</md-icon>
         </md-button>
       </div>
     </md-toolbar>

app/views/docs/sources.html

@@ -17,25 +17,30 @@ <h2>Data Sources</h2>
     </thead>
     <tbody>
         <tr>
-            <td>Biochemical data and metabolic maps</td>
+            <td>Biochemical data (<a href="https://fairsharing.org/FAIRsharing.Ql6K87" target="_blank">DOI</a>) and metabolic maps</td>
             <td>
-                Kyoto Encyclopedia for Genes and Genomes<br>
-                MetaCyc<br>
-                PlantCyc
+                <a href="https://www.genome.jp/kegg/" target="_blank">KEGG</a>,
+                <a href="https://metacyc.org/" target="_blank"> MetaCyc</a>,
+                <a href="https://plantcyc.org/" target="_blank"> PlantCyc</a>,
+                <a href="https://www.rhea-db.org/" target="_blank"> Rhea</a>
             </td>
         </tr>
         <tr>
             <td>Genome annotations and subsystem data</td>
-            <td>SEED/RAST/MGRAST</td>
+            <td>
+                <a href="https://www.theseed.org/" target="_blank">SEED</a>,
+                <a href="https://rast.nmpdr.org/" target="_blank"> RAST</a>,
+                <a href="https://www.mg-rast.org/" target="_blank"> MGRAST</a>
+            </td>
         </tr>
         <tr>
             <td>Plant Genomes
-            <td><a href="https://phytozome.jgi.doe.gov/pz/portal.html">JGI Phytozome</a></td>
+            <td><a href="https://phytozome.jgi.doe.gov/pz/portal.html" target="_blank">JGI Phytozome</a></td>
         </tr>
         <tr>
             <td>Plant Gene Atlas<br/>
-	    <sub>With thanks to Avinash Sreedasyam of <a href="https://hudsonalpha.org/">HudsonAlpha</a></sub></td>
-            <td><a href="https://phytozome.jgi.doe.gov/phytomine/aspect.do?name=Expression">JGI Gene Atlas</a></td>
+	    <sub>With thanks to Avinash Sreedasyam of <a href="https://hudsonalpha.org/" target="_blank">HudsonAlpha</a></sub></td>
+            <td><a href="https://phytozome.jgi.doe.gov/phytomine/aspect.do?name=Expression" target="_blank">JGI Gene Atlas</a></td>
         </tr>
     </tbody>
 </table>

app/views/home.html

@@ -8,7 +8,18 @@
         <div class="intro-text" flex hide-sm>
             <img src="/img/ModelSEED-logo-horizontal.png" width="280">
             <div class="logo-sub-text text-muted">Metabolic Modeling Made Simple.</div>
-
+            <md-button class="md-raised md-primary" mdbWavesEffect style="
+                height:128px !important;
+                width:280px !important;
+                font-size:28px !important;
+                text-align: center;
+                margin: 46px 0px 0px 0px;
+                padding:26px !important;
+                border-radius: 10px;
+                border: 2px solid black;"
+                ui-sref="app.biochem({chem: 'reactions'})">
+              <span>Biochemistry<br><small>(No login required)</small></span>
+            </md-button>
             <!--
             <div layout-margin ng-controller="Tour">
                 <a ng-click="startTour()">Take a tour!</a>

package.json

@@ -10,7 +10,6 @@
     "type": "git",
     "url": "https://github.com/modelseed/modelseed-ui.git"
   },
-  "author": "nconrad@anl.gov",
   "license": "MIT",
   "bugs": {
     "url": "https://github.com/modelseed/modelseed-ui/issues"