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protein viewer tab added
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Rachel Partridge committed Jul 6, 2016
1 parent 47b04ed commit 7f4ffff
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75 changes: 75 additions & 0 deletions src/main/webapp/citation-frame.xhtml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml"
xmlns:h="http://java.sun.com/jsf/html"
xmlns:f="http://java.sun.com/jsf/core"
xmlns:ui="http://java.sun.com/jsf/facelets"
xmlns:o="http://omnifaces.org/ui"
xmlns:c="http://xmlns.jcp.org/jsp/jstl/core"
lang="en">
<h:head>
<f:facet name="first">
<title><h:outputText value="Dataset Archived by #{dataverseServiceBean.findRootDataverse().displayName}"/></title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<meta http-equiv="Content-Language" content="en"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta http-equiv="X-UA-Compatible" content="IE=edge"/>
<meta name="description" content="#{bundle['head.meta.description']}"/>
</f:facet>
<link type="image/png" rel="icon" href="#{resource['images/favicondataverse.png']}" />
<link type="image/png" rel="image_src" href="#{resource['images/dataverseproject.png']}" />
<link type="text/css" rel="stylesheet" href="#{resource['bs/css/bootstrap.min.css']}?version=#{systemConfig.getVersion()}" />
<link type="text/css" rel="stylesheet" href="#{resource['bs/css/bootstrap-theme.min.css']}?version=#{systemConfig.getVersion()}" />
<link type="text/css" rel="stylesheet" href="#{resource['css/structure.css']}?version=#{systemConfig.getVersion()}" />
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
<ui:fragment rendered="#{!widgetWrapper.widgetView}">
<script>
// Break out of iframe
if (window !== top) top.location = window.location;
</script>
</ui:fragment>
</h:head>

<h:body>
<c:set var="persistentId" value="#{param['persistentId']}"/>
<c:set var="citationRedirectURL" value="#{datasetServiceBean.findByGlobalId(persistentId).owner.citationRedirectURL}"/>

<div id="citation-banner" class="alert alert-warning">
<p class="small pull-left">
<h:outputFormat value="#{bundle['citationFrame.banner.message']}" escape="false">
<o:param value="#{dataverseServiceBean.findRootDataverse().displayName}"/>
<o:param>
<a href="#{systemConfig.dataverseSiteUrl}/dataset.xhtml?persistentId=#{persistentId}" title="#{dataverseServiceBean.findRootDataverse().displayName}">#{bundle['citationFrame.banner.message.here']}</a>
</o:param>
<o:param>
<span id="countdown">&#160;</span>
</o:param>
</h:outputFormat>
</p>
<a class="close" href="#{citationRedirectURL}?persistentId=#{persistentId}" title="#{bundle['citationFrame.banner.closeIcon']}"><span class="glyphicon glyphicon-remove"></span></a>
</div>
<c:if test="${!empty citationRedirectURL}">
<iframe id="citation-forward" src="#{citationRedirectURL}?persistentId=#{persistentId}" width="100%"></iframe>

<script>
$(document).ready(function () {
window.onload = function() {
var countdownElement = document.getElementById('countdown'),
seconds = 10,
second = 0,
interval;
var countdownMessage = "#{bundle['citationFrame.banner.countdownMessage']}";
var countdownMessageSeconds = "#{bundle['citationFrame.banner.countdownMessage.seconds']}";
interval = setInterval(function() {
countdownElement.firstChild.data = countdownMessage + ' ' + (seconds - second) + ' ' + countdownMessageSeconds + '.';
if (second >= seconds) {
window.location.href = "#{citationRedirectURL}?persistentId=#{persistentId}";
}
second++;
}, 1000);
};
});
</script>
</c:if>
</h:body>
</html>
8 changes: 7 additions & 1 deletion src/main/webapp/dataset.xhtml
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<p:tabView id="tabView" widgetVar="content" activeIndex="#{DatasetPage.selectedTabIndex}"
rendered="#{empty DatasetPage.editMode or (DatasetPage.editMode == 'METADATA' or DatasetPage.editMode == 'LICENSE')}">
<p:ajax event="tabChange" listener="#{DatasetPage.tabChanged}" oncomplete="bind_bsui_components();" update="@this" />
<p:tab id="visualizationTab" title="Visualization" rendered="#{true}">
<iframe src ="visualizationFragment.xhtml" id="info" class="iframe" name="info" height="500" width="1100" style="border:none"></iframe>
<!--
<ui:include src="visualizationFragment.xhtml"/>
-->
</p:tab>
<p:tab id="dataFilesTab" title="#{bundle.files}" rendered="#{!DatasetPage.workingVersion.deaccessioned and
(empty DatasetPage.editMode)}">
<ui:include src="filesFragment.xhtml"/>
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</ui:include>
</p:tab>
<!-- 4.2.1: see above -->
<p:tab id="versionsTab" title="#{bundle['file.dataFilesTab.versions']}" rendered="#{empty DatasetPage.editMode}">
<p:tab id="versionsTab" title="#{bundle['file.dataFilesTab.versions']}" rendered="#{!widgetWrapper.widgetView and empty DatasetPage.editMode}">
<ui:include src="dataset-versions.xhtml"></ui:include>
</p:tab>
</p:tabView>
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12 changes: 12 additions & 0 deletions src/main/webapp/resources/js/pv.min.js
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12 changes: 12 additions & 0 deletions src/main/webapp/resources/js/pv/bio-pv.min.js
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206 changes: 206 additions & 0 deletions src/main/webapp/resources/js/pv/formset.js
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/**
* jQuery Formset 1.3-pre
* @author Stanislaus Madueke (stan DOT madueke AT gmail DOT com)
* @requires jQuery 1.2.6 or later
*
* Copyright (c) 2009, Stanislaus Madueke
* All rights reserved.
*
* Licensed under the New BSD License
* See: http://www.opensource.org/licenses/bsd-license.php
*/
;(function($) {
$.fn.formset = function(opts)
{
var options = $.extend({}, $.fn.formset.defaults, opts),
flatExtraClasses = options.extraClasses.join(' '),
totalForms = $('#id_' + options.prefix + '-TOTAL_FORMS'),
maxForms = $('#id_' + options.prefix + '-MAX_NUM_FORMS'),
childElementSelector = 'input,select,textarea,label,div',
$$ = $(this),

applyExtraClasses = function(row, ndx) {
if (options.extraClasses) {
row.removeClass(flatExtraClasses);
row.addClass(options.extraClasses[ndx % options.extraClasses.length]);
}
},

updateElementIndex = function(elem, prefix, ndx) {
var idRegex = new RegExp(prefix + '-(\\d+|__prefix__)-'),
replacement = prefix + '-' + ndx + '-';
if (elem.attr("for")) elem.attr("for", elem.attr("for").replace(idRegex, replacement));
if (elem.attr('id')) elem.attr('id', elem.attr('id').replace(idRegex, replacement));
if (elem.attr('name')) elem.attr('name', elem.attr('name').replace(idRegex, replacement));
},

hasChildElements = function(row) {
return row.find(childElementSelector).length > 0;
},

showAddButton = function() {
return maxForms.length == 0 || // For Django versions pre 1.2
(maxForms.val() == '' || (maxForms.val() - totalForms.val() > 0))
},

insertDeleteLink = function(row) {
if (row.is('TR')) {
// If the forms are laid out in table rows, insert
// the remove button into the last table cell:
row.children(':last').append('<a class="' + options.deleteCssClass +'" href="javascript:void(0)">' + options.deleteText + '</a>');
} else if (row.is('UL') || row.is('OL')) {
// If they're laid out as an ordered/unordered list,
// insert an <li> after the last list item:
row.append('<li><a class="' + options.deleteCssClass + '" href="javascript:void(0)">' + options.deleteText +'</a></li>');
} else {
// Otherwise, just insert the remove button as the
// last child element of the form's container:
row.append('<a class="' + options.deleteCssClass + '" href="javascript:void(0)">' + options.deleteText +'</a>');
}
row.find('a.' + options.deleteCssClass).click(function() {
var row = $(this).parents('.' + options.formCssClass),
del = row.find('input:hidden[id $= "-DELETE"]'),
buttonRow = row.siblings("a." + options.addCssClass + ', .' + options.formCssClass + '-add'),
forms;
if (del.length) {
// We're dealing with an inline formset.
// Rather than remove this form from the DOM, we'll mark it as deleted
// and hide it, then let Django handle the deleting:
del.val('on');
row.hide();
forms = $('.' + options.formCssClass).not(':hidden');
} else {
row.remove();
// Update the TOTAL_FORMS count:
forms = $('.' + options.formCssClass).not('.formset-custom-template');
totalForms.val(forms.length);
}
for (var i=0, formCount=forms.length; i<formCount; i++) {
// Apply `extraClasses` to form rows so they're nicely alternating:
applyExtraClasses(forms.eq(i), i);
if (!del.length) {
// Also update names and IDs for all child controls (if this isn't
// a delete-able inline formset) so they remain in sequence:
forms.eq(i).find(childElementSelector).each(function() {
updateElementIndex($(this), options.prefix, i);
});
}
}
// Check if we need to show the add button:
if (buttonRow.is(':hidden') && showAddButton()) buttonRow.show();
// If a post-delete callback was provided, call it with the deleted form:
if (options.removed) options.removed(row);
return false;
});
};

$$.each(function(i) {
var row = $(this),
del = row.find('input:checkbox[id $= "-DELETE"]');
if (del.length) {
// If you specify "can_delete = True" when creating an inline formset,
// Django adds a checkbox to each form in the formset.
// Replace the default checkbox with a hidden field:
if (del.is(':checked')) {
// If an inline formset containing deleted forms fails validation, make sure
// we keep the forms hidden (thanks for the bug report and suggested fix Mike)
del.before('<input type="hidden" name="' + del.attr('name') +'" id="' + del.attr('id') +'" value="on" />');
row.hide();
} else {
del.before('<input type="hidden" name="' + del.attr('name') +'" id="' + del.attr('id') +'" />');
}
// Hide any labels associated with the DELETE checkbox:
$('label[for="' + del.attr('id') + '"]').hide();
del.remove();
}
if (hasChildElements(row)) {
row.addClass(options.formCssClass);
if (row.is(':visible')) {
insertDeleteLink(row);
applyExtraClasses(row, i);
}
}
});

if ($$.length) {
var hideAddButton = !showAddButton(),
addButton, template;
if (options.formTemplate) {
// If a form template was specified, we'll clone it to generate new form instances:
template = (options.formTemplate instanceof $) ? options.formTemplate : $(options.formTemplate);
template.removeAttr('id').addClass(options.formCssClass + ' formset-custom-template');
template.find(childElementSelector).each(function() {
updateElementIndex($(this), options.prefix, '__prefix__');
});
insertDeleteLink(template);
} else {
// Otherwise, use the last form in the formset; this works much better if you've got
// extra (>= 1) forms (thnaks to justhamade for pointing this out):
template = $('.' + options.formCssClass + ':last').clone(true).removeAttr('id');
template.find('input:hidden[id $= "-DELETE"]').remove();
// Clear all cloned fields, except those the user wants to keep (thanks to brunogola for the suggestion):
template.find(childElementSelector).not(options.keepFieldValues).each(function() {
var elem = $(this);
// If this is a checkbox or radiobutton, uncheck it.
// This fixes Issue 1, reported by Wilson.Andrew.J:
if (elem.is('input:checkbox') || elem.is('input:radio')) {
elem.attr('checked', false);
} else {
elem.val('');
}
});
}
// FIXME: Perhaps using $.data would be a better idea?
options.formTemplate = template;

if ($$.attr('tagName') == 'TR') {
// If forms are laid out as table rows, insert the
// "add" button in a new table row:
var numCols = $$.eq(0).children().length, // This is a bit of an assumption :|
buttonRow = $('<tr><td colspan="' + numCols + '"><a class="' + options.addCssClass + '" href="javascript:void(0)">' + options.addText + '</a></tr>')
.addClass(options.formCssClass + '-add');
$$.parent().append(buttonRow);
if (hideAddButton) buttonRow.hide();
addButton = buttonRow.find('a');
} else {
// Otherwise, insert it immediately after the last form:
$$.filter(':last').after('<a class="' + options.addCssClass + '" href="javascript:void(0)">' + options.addText + '</a>');
addButton = $$.filter(':last').next();
if (hideAddButton) addButton.hide();
}
addButton.click(function() {
var formCount = parseInt(totalForms.val()),
row = options.formTemplate.clone(true).removeClass('formset-custom-template'),
buttonRow = $($(this).parents('tr.' + options.formCssClass + '-add').get(0) || this);
applyExtraClasses(row, formCount);
row.insertBefore(buttonRow).show();
row.find(childElementSelector).each(function() {
updateElementIndex($(this), options.prefix, formCount);
});
totalForms.val(formCount + 1);
// Check if we've exceeded the maximum allowed number of forms:
if (!showAddButton()) buttonRow.hide();
// If a post-add callback was supplied, call it with the added form:
if (options.added) options.added(row);
return false;
});
}

return $$;
}

/* Setup plugin defaults */
$.fn.formset.defaults = {
prefix: 'form', // The form prefix for your django formset
formTemplate: null, // The jQuery selection cloned to generate new form instances
addText: 'add another', // Text for the add link
deleteText: 'remove', // Text for the delete link
addCssClass: 'add-row', // CSS class applied to the add link
deleteCssClass: 'delete-row', // CSS class applied to the delete link
formCssClass: 'dynamic-form', // CSS class applied to each form in a formset
extraClasses: [], // Additional CSS classes, which will be applied to each form in turn
keepFieldValues: '', // jQuery selector for fields whose values should be kept when the form is cloned
added: null, // Function called each time a new form is added
removed: null // Function called each time a form is deleted
};
})(jQuery)
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