Nal i5 k modernize apollo (#2548)

* adding code to make comments mandatory for sequence modifications * Adding code to replace the Attributes section with a Replaced Models section. Also added a tooltip to the replaced models section. * testing NAthans code to speed up login * add apollo-config.groovy * update .gitignore * Revert "very minor changes" This reverts commit f46de7f. * re-adding the government login text * updateing with upstream * added jbrowse plugin ColorByType and setting jbrowse to a stable release that works with Apollo * adding gov't text to global login dialog * Added our google analytics to grails-app/conf/Config.groovy. Still need to add the federal analytics, will do so through jbrowse. * removing replce tag feature * updating config * updating the config. * updating config * updated apollo-config.groovy for the colorbycds branch * adding this file back in * staging for move to 2.3.0 * savign updated config file * updating config * updating config * updtating config to disable neat features * testing config options * correcting jbrowse version * updated config, reduced session timeout to 30 min * testing updated GA setup * Updated CSS formatting * Added Source Sans Pro font from google and applied to entire body of the page. * Added USWDS Library and added Government Banner Section after the open body tag. * Added NAL Footer from NAL Design System * merged versus dev Co-authored-by: Chris Childers <genetics.guy@gmail.com> Co-authored-by: Yi Hsiao <hsiaoyi0504@gmail.com> Co-authored-by: Yu <12001004033016@FEDIDCARD.GOV>
GMOD · Dec 17, 2020 · 79d19d1 · 79d19d1
1 parent c1b970f
commit 79d19d1
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Showing 17 changed files with 80 additions and 76 deletions.
diff --git a/.gitignore b/.gitignore
@@ -20,7 +20,7 @@ tmp
 version.jsp
 update_client.sh
 *.log
-apollo-config.groovy
+src/java/apollo-config.groovy
 gwt-unitCache/**
 web-app/WEB-INF/deploy/**
 web-app/annotator/**

diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/client/apollo/js/View/Track/AnnotTrack.js
@@ -419,6 +419,7 @@ define([
                     var user = JSON.parse(apolloMainPanel.getCurrentUser());
                     client.subscribe("/topic/AnnotationNotification/" + organism.id + "/" + sequence.id, dojo.hitch(track, 'annotationNotification'));
                     client.subscribe("/topic/AnnotationNotification/user/" + user.email, dojo.hitch(track, 'annotationNotification'));
+                    localStorage.setItem('organism-id', organism.id);
                 });
                 console.log('connection established');
             },

diff --git a/client/apollo/js/View/Track/SequenceTrack.js b/client/apollo/js/View/Track/SequenceTrack.js
@@ -1189,6 +1189,10 @@ function( declare,
                             alert("Input cannot be empty for " + type);
                             ok = false;
                         }
+                        if (commentFieldValue.length == 0) {
+                            alert("Please provide a justification for the sequence modification (" + type + ") in the 'Comment' field.");
+                            ok = false;
+                        }
                         if (ok) {
                             var input = inputField.value.toUpperCase();
                             if (type === "deletion_artifact") {

diff --git a/grails-app/services/org/bbop/apollo/ReportService.groovy b/grails-app/services/org/bbop/apollo/ReportService.groovy
@@ -156,7 +156,7 @@ class ReportService {
 
     AnnotatorSummary generateAnnotatorSummary(User owner) {
         AnnotatorSummary annotatorSummary = new AnnotatorSummary()
-        
+
         // get features created by the annotator
         def geneCount = Gene.executeQuery("select count(distinct g) from Gene g join g.owners owner where owner = :owner", [owner: owner])[0]
         def transposableElementCount = TransposableElement.executeQuery("select count(distinct g) from TransposableElement g join g.owners owner where owner = :owner", [owner: owner])[0]

diff --git a/grails-app/views/auth/login.gsp b/grails-app/views/auth/login.gsp
@@ -5,7 +5,7 @@
     <title>Login</title>
 </head>
 
-<div>
+<body>
     <g:if test="${flash.message}">
         <div class="message">${flash.message}</div>
     </g:if>

diff --git a/grails-app/views/google_analytics.gsp b/grails-app/views/google_analytics.gsp
@@ -5,26 +5,23 @@
   Time: 4:05 PM
 --%>
 
-<script>
-    (function (i, s, o, g, r, a, m) {
-        i['GoogleAnalyticsObject'] = r;
-        i[r] = i[r] || function () {
-            (i[r].q = i[r].q || []).push(arguments)
-        }, i[r].l = 1 * new Date();
-        a = s.createElement(o),
-            m = s.getElementsByTagName(o)[0];
-        a.async = 1;
-        a.src = g;
-        m.parentNode.insertBefore(a, m)
-    })(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
-</script>
+    <script>
+        (function (i, s, o, g, r, a, m) {
+            i['GoogleAnalyticsObject'] = r;
+            i[r] = i[r] || function () {
+                        (i[r].q = i[r].q || []).push(arguments)
+                    }, i[r].l = 1 * new Date();
+            a = s.createElement(o),
+                    m = s.getElementsByTagName(o)[0];
+            a.async = 1;
+            a.src = g;
+            m.parentNode.insertBefore(a, m)
+        })(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
+        <g:each var="google_analytics_id" in="${grailsApplication.config.apollo.google_analytics}">
+                ga('create', '${google_analytics_id}', 'auto');
+        </g:each>
+        ga('send', 'pageview');
+
+    </script>
 
-<script>
-    <g:each var="google_analytics_id" in="${grailsApplication.config.apollo.google_analytics}" status="index">
-    ga('create', '${google_analytics_id}', 'auto', {'name': 'Server${index}'});
-    ga('Server${index}.send', 'pageview');
-    </g:each>
-</script>
-<script>
-</script>
 
diff --git a/grails-app/views/login/doLogin.gsp b/grails-app/views/login/doLogin.gsp
@@ -6,29 +6,23 @@
 --%>
 
 <%@ page contentType="text/html;charset=UTF-8" %>
+
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-<html>
+<html lang="en">
+
 <head>
+
     <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
     <title>Login</title>
-    <!--
-<link rel="stylesheet" type="text/css" href="../styles/login.css" />
--->
-    <!--
-<script src="jslib/jquery-1.7.1.min.js" type="text/javascript"></script>
-<script type="text/javascript" src="jslib/jquery-ui-1.8.9.custom/jquery-ui-1.8.9.custom.min.js"></script>
--->
     <script>
         var context;
         $(document).ready(function () {
             var pathname = location.pathname;
             context = /^\/([^\/]+)\//.exec(pathname)[1];
-//            $("head").append("<link rel='stylesheet' type='text/css' href='/" + context + "/styles/login.css'/>");
             $("#login_button").click(function () {
                 login();
             });
             $("#clear_button").click(function () {
-//                $(".input_field").val("");
                 $("#username").val("");
                 $("#password").val("");
             });
@@ -38,7 +32,6 @@
                     login();
                 }
             });
-//            $("#username").focus();
         });
 
         function login() {
@@ -85,25 +78,25 @@
 
 <body>
 
-<div class="input-group" style="margin-bottom: 5px;margin-top: 5px;">
-    <input class="form-control" type="text" id="username" placeholder="Username" autofocus="autofocus"/>
-</div>
+    <div class="input-group" style="margin-bottom: 5px;margin-top: 5px;">
+        <input class="form-control" type="text" id="username" placeholder="Username" autofocus="autofocus"/>
+    </div>
 
-<div class="input-group" style="margin-bottom: 5px">
-    <input class="form-control" type="password" id="password" placeholder="Password"/>
-</div>
+    <div class="input-group" style="margin-bottom: 5px">
+        <input class="form-control" type="password" id="password" placeholder="Password"/>
+    </div>
 
+    %{-- <div class="button_login"> --}%
+    <button class="btn btn-primary" id="login_button">Login</button>
+    <button class="btn btn-default" id="clear_button" >Clear</button>
+    %{-- <button class="btn btn-default" id="rememberme_button" >Remember Me</button> --}%
 
-%{--<div class="button_login">--}%
-<button class="btn btn-primary" id="login_button">Login</button>
-<button class="btn btn-default" id="clear_button" >Clear</button>
-%{--<button class="btn btn-default" id="rememberme_button" >Remember Me</button>--}%
-<div>
-    Remember me
-    <input type="checkbox" autocomplete="off" id="remember_me" checked>
-</div>
+    <div>
+        Remember me
+        <input type="checkbox" autocomplete="off" id="remember_me" checked>
+    </div>
 
-%{--</div>--}%
-<div id="message"></div>
+    %{--</div>--}%
+    <div id="message"></div>
 </body>
 </html>
diff --git a/index.html b/index.html
@@ -1,3 +1,4 @@
+<!--
 <script>
   (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
      (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
@@ -8,3 +9,5 @@
     ga('send', 'pageview');
 
 </script>
+
+-->
diff --git a/package.json b/package.json
@@ -9,6 +9,7 @@
   "author": "Nathan Dunn",
   "license": "SEE LICENSE IN LICENSE.md",
   "dependencies": {
+    "gradle": "^1.0.9",
     "jquery": "^1.7.2",
     "jqueryui": "^1.8.24"
   },

diff --git a/src/gwt/org/bbop/apollo/gwt/client/LoginDialog.java b/src/gwt/org/bbop/apollo/gwt/client/LoginDialog.java
@@ -21,6 +21,7 @@
 import org.gwtbootstrap3.client.ui.TextBox;
 import org.gwtbootstrap3.client.ui.constants.*;
 import org.bbop.apollo.gwt.client.rest.UserRestService;
+import com.google.gwt.dom.client.Style;
 
 public class LoginDialog extends DialogBox {
     private static final Binder binder = GWT.create(Binder.class);
@@ -53,6 +54,7 @@ interface Binder extends UiBinder<Widget, LoginDialog> {
 
     public LoginDialog() {
         getElement().setId("loginDialogId");
+        getElement().getStyle().setWidth(500, Style.Unit.PX);
         setText("Login");
         setAnimationEnabled(true);
         // Enable glass background.
@@ -74,7 +76,7 @@ public void setError(String errorMessage){
         errorText.setText(errorMessage);
         errorHtml.setVisible(true);
     }
- 
+
     public void clearErrors(){
         errorText.setText("");
         errorHtml.setVisible(false);

diff --git a/src/templates/war/web.xml b/src/templates/war/web.xml
@@ -76,7 +76,9 @@
         <!-- 2 days -->
         <!--<session-timeout>2880</session-timeout>-->
         <!-- 16 hours -->
-        <session-timeout>960</session-timeout>
+        <!--<session-timeout>960</session-timeout>-->
+        <!-- 1 hours  01-21-2020_cpc -->
+        <session-timeout>30</session-timeout>
     </session-config>
 
     <welcome-file-list>

diff --git a/tools/data/add_features_from_gff3_to_annotations.pl b/tools/data/add_features_from_gff3_to_annotations.pl
@@ -4,7 +4,8 @@
 use warnings;
 
 use FindBin qw($RealBin);
-use lib "$RealBin/../../jbrowse/src/perl5";
+#use lib "$RealBin/../../jbrowse/src/perl5";
+use lib "../../src/perl5";
 use JBlibs;
 
 use File::Basename;

diff --git a/web-app/css/Annotator.css b/web-app/css/Annotator.css
@@ -1,6 +1,5 @@
 /** Add css rules here for your application. */
 
-
 /** Example rules used by the template application (remove for your app) */
 h1 {
   font-size: 2em;

diff --git a/web-app/css/chado.css b/web-app/css/chado.css
@@ -1,4 +1,4 @@
-@CHARSET "UTF-8";
+@charset "UTF-8";
 
 table {
 	border-width: 1px;

diff --git a/web-app/css/login.css b/web-app/css/login.css
@@ -1,12 +1,12 @@
-@CHARSET "UTF-8";
+@charset "UTF-8";
 
 .user_login {
 	/* width:30%; */
-	margin:5px;
+	margin: 5px;
 }
 
 .fieldname {
-	margin-right:5px;
+	margin-right: 5px;
 	font-size: 1.3em;
 }
 
@@ -16,7 +16,7 @@
 }
 
 .button_login {
-	text-align:center;
-	margin-top:10px;
+	text-align: center;
+	margin-top: 10px;
 	width: 100%;
-}
+}
diff --git a/web-app/css/search_sequence.css b/web-app/css/search_sequence.css
@@ -1,4 +1,4 @@
-@CHARSET "UTF-8";
+@charset "UTF-8";
 
 .search_sequence_label {
 	font-size: 1.5em;
@@ -75,4 +75,4 @@
 
 .search_sequence {
 	font-size: 12px;
-}
+}
diff --git a/web-app/css/ui-layout.css b/web-app/css/ui-layout.css
@@ -1,4 +1,3 @@
-
 /**
   UI.Layout CSS
 *************************************/
@@ -12,12 +11,12 @@
   overflow: auto;
 }
 
-.ui-splitbar{
-  display: -webkit-box;      /* OLD - iOS 6-, Safari 3.1-6 */
-  display: -moz-box;         /* OLD - Firefox 19- (buggy but mostly works) */
-  display: -ms-flexbox;      /* TWEENER - IE 10 */
-  display: -webkit-flex;     /* NEW - Chrome */
-  display: flex;             /* NEW, Spec - Opera 12.1, Firefox 20+ */
+.ui-splitbar {
+  display: -webkit-box; /* OLD - iOS 6-, Safari 3.1-6 */
+  display: -moz-box; /* OLD - Firefox 19- (buggy but mostly works) */
+  display: -ms-flexbox; /* TWEENER - IE 10 */
+  display: -webkit-flex; /* NEW - Chrome */
+  display: flex; /* NEW, Spec - Opera 12.1, Firefox 20+ */
   -webkit-justify-content: center;
   justify-content: center;
 
@@ -27,15 +26,17 @@
   z-index: 1010;
 }
 
-.ui-layout-row > .ui-splitbar{
-  height: 8px; width: 100%;
+.ui-layout-row > .ui-splitbar {
+  height: 8px;
+  width: 100%;
   cursor: row-resize;
   text-align: center;
   justify-content: center;
   align-items: center;
 }
-.ui-layout-column > .ui-splitbar{
-  width: 8px; height: 100%;
+.ui-layout-column > .ui-splitbar {
+  width: 8px;
+  height: 100%;
   cursor: col-resize;
   -webkit-flex-direction: column;
   flex-direction: column;
@@ -46,4 +47,4 @@
   color: #fff;
   cursor: pointer;
   font-size: 9px;
-}
+}