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nathandunnchildershsiaoyi0504Yu
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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 <[email protected]> Co-authored-by: Yi Hsiao <[email protected]> Co-authored-by: Yu <[email protected]>
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‎.gitignore

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version.jsp
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update_client.sh
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*.log
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apollo-config.groovy
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src/java/apollo-config.groovy
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gwt-unitCache/**
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web-app/WEB-INF/deploy/**
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web-app/annotator/**

‎client/apollo/js/View/Track/AnnotTrack.js

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

‎client/apollo/js/View/Track/SequenceTrack.js

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alert("Input cannot be empty for " + type);
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ok = false;
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}
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if (commentFieldValue.length == 0) {
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alert("Please provide a justification for the sequence modification (" + type + ") in the 'Comment' field.");
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ok = false;
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}
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if (ok) {
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var input = inputField.value.toUpperCase();
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if (type === "deletion_artifact") {

‎grails-app/services/org/bbop/apollo/ReportService.groovy

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

‎grails-app/views/auth/login.gsp

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<title>Login</title>
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</head>
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<div>
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<body>
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<g:if test="${flash.message}">
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<div class="message">${flash.message}</div>
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</g:if>

‎grails-app/views/google_analytics.gsp

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Time: 4:05 PM
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--%>
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<script>
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(function (i, s, o, g, r, a, m) {
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i['GoogleAnalyticsObject'] = r;
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i[r] = i[r] || function () {
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(i[r].q = i[r].q || []).push(arguments)
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}, i[r].l = 1 * new Date();
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a = s.createElement(o),
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m = s.getElementsByTagName(o)[0];
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a.async = 1;
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a.src = g;
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m.parentNode.insertBefore(a, m)
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})(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
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</script>
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<script>
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(function (i, s, o, g, r, a, m) {
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i['GoogleAnalyticsObject'] = r;
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i[r] = i[r] || function () {
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(i[r].q = i[r].q || []).push(arguments)
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}, i[r].l = 1 * new Date();
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a = s.createElement(o),
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m = s.getElementsByTagName(o)[0];
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a.async = 1;
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a.src = g;
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m.parentNode.insertBefore(a, m)
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})(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
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<g:each var="google_analytics_id" in="${grailsApplication.config.apollo.google_analytics}">
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ga('create', '${google_analytics_id}', 'auto');
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</g:each>
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ga('send', 'pageview');
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</script>
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<script>
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<g:each var="google_analytics_id" in="${grailsApplication.config.apollo.google_analytics}" status="index">
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ga('create', '${google_analytics_id}', 'auto', {'name': 'Server${index}'});
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ga('Server${index}.send', 'pageview');
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</g:each>
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</script>
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<script>
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</script>
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‎grails-app/views/login/doLogin.gsp

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--%>
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<%@ page contentType="text/html;charset=UTF-8" %>
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<html>
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<html lang="en">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
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<title>Login</title>
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<!--
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<link rel="stylesheet" type="text/css" href="../styles/login.css" />
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-->
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<!--
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<script src="jslib/jquery-1.7.1.min.js" type="text/javascript"></script>
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<script type="text/javascript" src="jslib/jquery-ui-1.8.9.custom/jquery-ui-1.8.9.custom.min.js"></script>
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-->
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<script>
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var context;
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$(document).ready(function () {
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var pathname = location.pathname;
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context = /^\/([^\/]+)\//.exec(pathname)[1];
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// $("head").append("<link rel='stylesheet' type='text/css' href='/" + context + "/styles/login.css'/>");
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$("#login_button").click(function () {
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login();
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});
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$("#clear_button").click(function () {
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// $(".input_field").val("");
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$("#username").val("");
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$("#password").val("");
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});
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login();
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}
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});
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// $("#username").focus();
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});
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function login() {
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<body>
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<div class="input-group" style="margin-bottom: 5px;margin-top: 5px;">
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<input class="form-control" type="text" id="username" placeholder="Username" autofocus="autofocus"/>
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</div>
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<div class="input-group" style="margin-bottom: 5px;margin-top: 5px;">
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<input class="form-control" type="text" id="username" placeholder="Username" autofocus="autofocus"/>
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</div>
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<div class="input-group" style="margin-bottom: 5px">
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<input class="form-control" type="password" id="password" placeholder="Password"/>
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</div>
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<div class="input-group" style="margin-bottom: 5px">
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<input class="form-control" type="password" id="password" placeholder="Password"/>
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</div>
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%{-- <div class="button_login"> --}%
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<button class="btn btn-primary" id="login_button">Login</button>
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<button class="btn btn-default" id="clear_button" >Clear</button>
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%{-- <button class="btn btn-default" id="rememberme_button" >Remember Me</button> --}%
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%{--<div class="button_login">--}%
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<button class="btn btn-primary" id="login_button">Login</button>
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<button class="btn btn-default" id="clear_button" >Clear</button>
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%{--<button class="btn btn-default" id="rememberme_button" >Remember Me</button>--}%
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<div>
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Remember me
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<input type="checkbox" autocomplete="off" id="remember_me" checked>
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</div>
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<div>
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Remember me
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<input type="checkbox" autocomplete="off" id="remember_me" checked>
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</div>
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%{--</div>--}%
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<div id="message"></div>
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%{--</div>--}%
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<div id="message"></div>
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</body>
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</html>

‎index.html

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<!--
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<script>
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(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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ga('send', 'pageview');
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</script>
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-->

‎package.json

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"author": "Nathan Dunn",
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"license": "SEE LICENSE IN LICENSE.md",
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"dependencies": {
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"gradle": "^1.0.9",
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"jquery": "^1.7.2",
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"jqueryui": "^1.8.24"
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},

‎src/gwt/org/bbop/apollo/gwt/client/LoginDialog.java

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import org.gwtbootstrap3.client.ui.TextBox;
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import org.gwtbootstrap3.client.ui.constants.*;
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import org.bbop.apollo.gwt.client.rest.UserRestService;
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import com.google.gwt.dom.client.Style;
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public class LoginDialog extends DialogBox {
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private static final Binder binder = GWT.create(Binder.class);
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public LoginDialog() {
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getElement().setId("loginDialogId");
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getElement().getStyle().setWidth(500, Style.Unit.PX);
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setText("Login");
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setAnimationEnabled(true);
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// Enable glass background.
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errorText.setText(errorMessage);
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errorHtml.setVisible(true);
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}
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public void clearErrors(){
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errorText.setText("");
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errorHtml.setVisible(false);

‎src/templates/war/web.xml

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<!-- 2 days -->
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<!--<session-timeout>2880</session-timeout>-->
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<!-- 16 hours -->
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<session-timeout>960</session-timeout>
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<!--<session-timeout>960</session-timeout>-->
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<!-- 1 hours 01-21-2020_cpc -->
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<session-timeout>30</session-timeout>
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</session-config>
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<welcome-file-list>

‎tools/data/add_features_from_gff3_to_annotations.pl

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use warnings;
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use FindBin qw($RealBin);
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use lib "$RealBin/../../jbrowse/src/perl5";
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#use lib "$RealBin/../../jbrowse/src/perl5";
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use lib "../../src/perl5";
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use JBlibs;
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use File::Basename;

‎web-app/css/Annotator.css

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/** Add css rules here for your application. */
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/** Example rules used by the template application (remove for your app) */
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h1 {
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font-size: 2em;

‎web-app/css/chado.css

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@CHARSET "UTF-8";
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@charset "UTF-8";
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table {
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border-width: 1px;

‎web-app/css/login.css

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@CHARSET "UTF-8";
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@charset "UTF-8";
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.user_login {
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/* width:30%; */
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margin:5px;
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margin: 5px;
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}
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.fieldname {
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margin-right:5px;
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margin-right: 5px;
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font-size: 1.3em;
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}
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}
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.button_login {
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text-align:center;
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margin-top:10px;
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text-align: center;
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margin-top: 10px;
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width: 100%;
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}
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}

‎web-app/css/search_sequence.css

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@CHARSET "UTF-8";
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@charset "UTF-8";
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.search_sequence_label {
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font-size: 1.5em;
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.search_sequence {
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font-size: 12px;
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}
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}

‎web-app/css/ui-layout.css

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/**
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UI.Layout CSS
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*************************************/
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overflow: auto;
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}
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.ui-splitbar{
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display: -webkit-box; /* OLD - iOS 6-, Safari 3.1-6 */
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display: -moz-box; /* OLD - Firefox 19- (buggy but mostly works) */
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display: -ms-flexbox; /* TWEENER - IE 10 */
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display: -webkit-flex; /* NEW - Chrome */
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display: flex; /* NEW, Spec - Opera 12.1, Firefox 20+ */
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.ui-splitbar {
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display: -webkit-box; /* OLD - iOS 6-, Safari 3.1-6 */
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display: -moz-box; /* OLD - Firefox 19- (buggy but mostly works) */
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display: -ms-flexbox; /* TWEENER - IE 10 */
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display: -webkit-flex; /* NEW - Chrome */
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display: flex; /* NEW, Spec - Opera 12.1, Firefox 20+ */
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-webkit-justify-content: center;
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justify-content: center;
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z-index: 1010;
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}
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.ui-layout-row > .ui-splitbar{
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height: 8px; width: 100%;
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.ui-layout-row > .ui-splitbar {
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height: 8px;
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width: 100%;
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cursor: row-resize;
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text-align: center;
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justify-content: center;
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align-items: center;
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}
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.ui-layout-column > .ui-splitbar{
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width: 8px; height: 100%;
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.ui-layout-column > .ui-splitbar {
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width: 8px;
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height: 100%;
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cursor: col-resize;
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-webkit-flex-direction: column;
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flex-direction: column;
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color: #fff;
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cursor: pointer;
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font-size: 9px;
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}
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}

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