From 81af31760ea7ae9480a4574fd2e560bf9153dbae Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Tue, 4 Aug 2020 12:50:56 -0500
Subject: [PATCH 01/10] log out from anywhere including User Data/Build Model
 redirected to Reference Data/Plants tab; signin on RAST on User Data/Build
 Model stay where it is

---
 app/services/auth.js        | 3 ++-
 app/services/dialogs.js     | 1 -
 app/views/dialogs/auth.html | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/services/auth.js b/app/services/auth.js
index 45b850f0..100b44ba 100644
--- a/app/services/auth.js
+++ b/app/services/auth.js
@@ -90,7 +90,8 @@ function($state, $http, config, $window) {
         $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+'/genomes/Plants';
+                  $window.location.replace(to_url);
               });
     }
 
diff --git a/app/services/dialogs.js b/app/services/dialogs.js
index 4416e949..4fbc2ab3 100644
--- a/app/services/dialogs.js
+++ b/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(){
diff --git a/app/views/dialogs/auth.html b/app/views/dialogs/auth.html
index 89529077..2bf35dcb 100644
--- a/app/views/dialogs/auth.html
+++ b/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>

From f48ad4dd0461261bfb301a0c6e469c8b9d9f537d Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Tue, 4 Aug 2020 13:51:01 -0500
Subject: [PATCH 02/10] fixed the home page login behavior

---
 app/ctrls/ms-ctrls.js |  1 +
 app/services/auth.js  | 13 ++++++++-----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/app/ctrls/ms-ctrls.js b/app/ctrls/ms-ctrls.js
index 34d04017..73b03905 100755
--- a/app/ctrls/ms-ctrls.js
+++ b/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});
     }
 
diff --git a/app/services/auth.js b/app/services/auth.js
index 100b44ba..7c5ab914 100644
--- a/app/services/auth.js
+++ b/app/services/auth.js
@@ -88,11 +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() {
-                  var to_url = window.location.protocol + '//' + window.location.host+'/genomes/Plants';
-                  $window.location.replace(to_url);
-              });
+
+        var to_url = window.location.protocol + '//' + window.location.host;
+        if ($state.current.name === 'main.home') {
+            $window.location.reload();
+        } else {
+            to_url = to_url + '/genomes/Plants';
+            $window.location.replace(to_url);
+        }
     }
 
     this.isAuthenticated = function() {

From 9d5b80bff2baabac736e95eb686d150c2bd74ba8 Mon Sep 17 00:00:00 2001
From: Sam Seaver <samseaver@gmail.com>
Date: Thu, 17 Sep 2020 11:34:42 -0500
Subject: [PATCH 03/10] Removing useless arrow icon

---
 app/views/data/model.html | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/app/views/data/model.html b/app/views/data/model.html
index 0bcd7fb4..cafa3204 100755
--- a/app/views/data/model.html
+++ b/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>

From bd89cbc16a3a8d0caeb8a803c3b2e5e5e81b916d Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Thu, 15 Oct 2020 15:51:51 -0500
Subject: [PATCH 04/10] added the big-fat biochemistry button on the homepage

---
 app/views/home.html | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/app/views/home.html b/app/views/home.html
index 2f96032e..3d3fed11 100755
--- a/app/views/home.html
+++ b/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>

From ad00abce26d0fb5f2f39989a12ce36353aa0c5c4 Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Mon, 25 Jan 2021 15:03:06 -0600
Subject: [PATCH 05/10] adding Biochemistry Database DOI link

---
 app/views/docs/sources.html | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/views/docs/sources.html b/app/views/docs/sources.html
index f7f331ff..9334291b 100644
--- a/app/views/docs/sources.html
+++ b/app/views/docs/sources.html
@@ -21,7 +21,8 @@ <h2>Data Sources</h2>
             <td>
                 Kyoto Encyclopedia for Genes and Genomes<br>
                 MetaCyc<br>
-                PlantCyc
+                PlantCyc<br>
+                <a href="https://fairsharing.org/FAIRsharing.Ql6K87" target="_blank">DOI</a>
             </td>
         </tr>
         <tr>

From 2686a9c8d7cd127e526f55873c10629e8c5439a1 Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Mon, 25 Jan 2021 15:10:01 -0600
Subject: [PATCH 06/10] adding Biochemistry Database DOI link

---
 app/views/docs/sources.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/views/docs/sources.html b/app/views/docs/sources.html
index 9334291b..d2aba702 100644
--- a/app/views/docs/sources.html
+++ b/app/views/docs/sources.html
@@ -17,12 +17,12 @@ <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<br>
+            </td>
             <td>
                 Kyoto Encyclopedia for Genes and Genomes<br>
                 MetaCyc<br>
-                PlantCyc<br>
-                <a href="https://fairsharing.org/FAIRsharing.Ql6K87" target="_blank">DOI</a>
+                PlantCyc
             </td>
         </tr>
         <tr>

From 93a7222118b8bd7aaad4015e21b15d67fa9da844 Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Fri, 4 Mar 2022 13:50:40 -0600
Subject: [PATCH 07/10] updating about/data-source by adding Rhea and other
 links

---
 app/views/docs/sources.html | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/app/views/docs/sources.html b/app/views/docs/sources.html
index d2aba702..f724f558 100644
--- a/app/views/docs/sources.html
+++ b/app/views/docs/sources.html
@@ -17,17 +17,21 @@ <h2>Data Sources</h2>
     </thead>
     <tbody>
         <tr>
-            <td>Biochemical data (<a href="https://fairsharing.org/FAIRsharing.Ql6K87" target="_blank">DOI</a>) and metabolic maps<br>
-            </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

From 1b358bf2ec3a4b73c3c837fb6915c5156b5e01f2 Mon Sep 17 00:00:00 2001
From: qzzhang <qzhang@anl.gov>
Date: Mon, 7 Mar 2022 12:02:49 -0600
Subject: [PATCH 08/10] a minor change

---
 app/views/docs/sources.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/views/docs/sources.html b/app/views/docs/sources.html
index f724f558..e371e4bb 100644
--- a/app/views/docs/sources.html
+++ b/app/views/docs/sources.html
@@ -35,12 +35,12 @@ <h2>Data Sources</h2>
         </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>

From 84bf8d2abbcc83d2dcfcd987357a5e21899abcc8 Mon Sep 17 00:00:00 2001
From: Sam Seaver <samseaver@gmail.com>
Date: Thu, 14 Jul 2022 11:22:24 -0500
Subject: [PATCH 09/10] changing version checking for support service

---
 app/ctrls/ms-ctrls.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/ctrls/ms-ctrls.js b/app/ctrls/ms-ctrls.js
index 73b03905..b5eeedf7 100755
--- a/app/ctrls/ms-ctrls.js
+++ b/app/ctrls/ms-ctrls.js
@@ -142,7 +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;
          })

From 39188afb629400ded40bb48db07d5393817aad6a Mon Sep 17 00:00:00 2001
From: nconrad <1194246+nconrad@users.noreply.github.com>
Date: Fri, 1 Sep 2023 12:50:14 -0500
Subject: [PATCH 10/10] Update README.md

Remove email to avoid confusion
---
 README.md    | 4 ----
 package.json | 1 -
 2 files changed, 5 deletions(-)

diff --git a/README.md b/README.md
index cfb891a6..bf2b9527 100755
--- a/README.md
+++ b/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
 
diff --git a/package.json b/package.json
index fb44d194..d7d79a7c 100644
--- a/package.json
+++ b/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"