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MISP
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Code Issues Releases Wiki Activity

new: First round of updates to the correlation engine ready 

- node deletion temporarily disabled until a bug is resolved
pull/2547/head
iglocska 2017-10-08 19:50:28 +02:00
parent b5b4652c61
commit fa7d3fdb36
16 changed files with 752 additions and 598 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
app/Controller/EventsController.php
View File

@ -3955,12 +3955,23 @@ class EventsController extends AppController {
$event = $this->Event->fetchEvent($this->Auth->user(), array('eventid' => $id)); $event = $this->Event->fetchEvent($this->Auth->user(), array('eventid' => $id));
if (empty($event)) throw new MethodNotAllowedException('Invalid Event.'); if (empty($event)) throw new MethodNotAllowedException('Invalid Event.');
$this->set('event', $event[0]); $this->set('event', $event[0]);
$this->set('scope', 'event');
$this->set('id', $id); $this->set('id', $id);
} }
/*
public function deleteNode($id) {
if (!$this->request->is('post')) throw new MethodNotAllowedException('Only POST requests are allowed.');
App::uses('CorrelationGraphTool', 'Tools');
$grapher = new CorrelationGraphTool();
$grapher->construct($this->Event, $this->Taxonomy, $this->GalaxyCluster, $this->Auth->user(), $this->request->data);
$json = $grapher->deleteNode($id);
}
*/
public function updateGraph($id, $type = 'event') { public function updateGraph($id, $type = 'event') {
$validTools = array('event', 'galaxy', 'tag'); $validTools = array('event', 'galaxy', 'tag');
if (!in_array($type, $validTools)) throw new NotAllowedException('Invalid type.'); if (!in_array($type, $validTools)) throw new MethodNotAllowedException('Invalid type.');
$this->loadModel('Taxonomy'); $this->loadModel('Taxonomy');
$this->loadModel('GalaxyCluster'); $this->loadModel('GalaxyCluster');
App::uses('CorrelationGraphTool', 'Tools'); App::uses('CorrelationGraphTool', 'Tools');

14
app/Controller/GalaxiesController.php
View File

@ -140,4 +140,18 @@ class GalaxiesController extends AppController {
$this->redirect($this->referer()); $this->redirect($this->referer());
} }
} }
public function viewGraph($id) {
$cluster = $this->Galaxy->GalaxyCluster->find('first', array(
'conditions' => array('GalaxyCluster.id' => $id),
'contain' => array('Galaxy'),
'recursive' => -1
));
if (empty($cluster)) throw new MethodNotAllowedException('Invalid Galaxy.');
$this->set('cluster', $cluster);
$this->set('scope', 'galaxy');
$this->set('id', $id);
$this->set('galaxy_id' , $cluster['Galaxy']['id']);
$this->render('/Events/view_graph');
}
} }

2
app/Controller/GalaxyClustersController.php
View File

@ -113,6 +113,8 @@ class GalaxyClustersController extends AppController {
$cluster['GalaxyCluster']['tag_id'] = $tag['Tag']['id']; $cluster['GalaxyCluster']['tag_id'] = $tag['Tag']['id'];
} }
} }
$this->set('id', $id);
$this->set('galaxy_id' , $cluster['Galaxy']['id']);
$this->set('cluster', $cluster); $this->set('cluster', $cluster);
} }

16
app/Controller/TagsController.php
View File

@ -749,4 +749,20 @@ class TagsController extends AppController {
return $this->RestResponse->saveFailResponse('Tags', 'removeTagFromObject', false, 'Failed to remove tag from object.', $this->response->type()); return $this->RestResponse->saveFailResponse('Tags', 'removeTagFromObject', false, 'Failed to remove tag from object.', $this->response->type());
} }
} }
public function viewGraph($id) {
$tag = $this->Tag->find('first', array(
'conditions' => array('Tag.id' => $id),
'recursive' => -1
));
if (empty($tag)) throw new MethodNotAllowedException('Invalid Tag.');
$this->loadModel('Taxonomy');
$taxonomy = $this->Taxonomy->getTaxonomyForTag($tag['Tag']['name']);
if (!empty($taxonomy)) {
$this->set('taxonomy', $taxonomy);
}
$this->set('scope', 'tag');
$this->set('id', $id);
$this->render('/Events/view_graph');
}
} }

38
app/Lib/Tools/CorrelationGraphTool.php
View File

@ -58,7 +58,6 @@
public function buildGraphJson($id, $type = 'event', $action = 'create') { public function buildGraphJson($id, $type = 'event', $action = 'create') {
if ($action == 'delete') { if ($action == 'delete') {
return $this->__json; return $this->__json;
} }
switch ($type) { switch ($type) {
@ -76,10 +75,8 @@
} }
private function __deleteObject($id) { private function __deleteObject($id) {
unset($this->__json['nodes'][$id]); $this->cleanLinks();
foreach ($this->__json['links'] as $k => $link) { return $this->__json;
debug($link);
}
} }
private function __handleObjects($objects, $anchor_id, $full = false) { private function __handleObjects($objects, $anchor_id, $full = false) {
@ -121,6 +118,14 @@
} }
} }
private function __addTag($id) {
$tag = $this->__eventModel->EventTag->Tag->find('first', array(
'conditions' => array('Tag.id' => $id),
'recursive' => -1
));
return $this->__createNode('tag', $tag['Tag']);
}
private function __handleTags($tags, $anchor_id) { private function __handleTags($tags, $anchor_id) {
foreach ($tags as $tag) { foreach ($tags as $tag) {
if (strpos($tag['name'], 'misp-galaxy:') === 0) { if (strpos($tag['name'], 'misp-galaxy:') === 0) {
@ -143,7 +148,9 @@
private function __expandTag($id) { private function __expandTag($id) {
$current_tag_id = $this->graphJsonContains('tag', array('id' => $id)); $current_tag_id = $this->graphJsonContains('tag', array('id' => $id));
if (empty($current_tag_id)) return false; if (empty($current_tag_id)) {
$current_tag_id = $this->__addTag($id);
}
$this->cleanLinks(); $this->cleanLinks();
$events = $this->__eventModel->EventTag->Tag->fetchSimpleEventsForTag($id, $this->__user); $events = $this->__eventModel->EventTag->Tag->fetchSimpleEventsForTag($id, $this->__user);
foreach ($events as $event) { foreach ($events as $event) {
@ -161,13 +168,17 @@
} }
private function __expandGalaxy($id) { private function __expandGalaxy($id) {
if (!empty($this->__json['nodes'])) {
foreach ($this->__json['nodes'] as $k => $node) { foreach ($this->__json['nodes'] as $k => $node) {
if ($node['type'] == 'galaxy' && $node['id'] == $id) { if ($node['type'] == 'galaxy' && $node['id'] == $id) {
$current_galaxy_id = $k; $current_galaxy_id = $k;
$tag_name = $node['tag_name']; $tag_name = $node['tag_name'];
} }
} }
if (empty($current_galaxy_id)) return false; }
if (empty($current_galaxy_id)) {
$current_galaxy_id = $this->__addGalaxy($id);
}
$this->cleanLinks(); $this->cleanLinks();
$events = $this->__eventModel->EventTag->Tag->fetchSimpleEventsForTag($this->__json['nodes'][$current_galaxy_id]['tag_name'], $this->__user, true); $events = $this->__eventModel->EventTag->Tag->fetchSimpleEventsForTag($this->__json['nodes'][$current_galaxy_id]['tag_name'], $this->__user, true);
foreach ($events as $event) { foreach ($events as $event) {
@ -177,6 +188,15 @@
$this->_json['nodes'][$current_galaxy_id]['expanded'] = 1; $this->_json['nodes'][$current_galaxy_id]['expanded'] = 1;
} }
private function __addGalaxy($id) {
$temp = $this->__galaxyClusterModel->getCluster($id);
// move stuff around to resemble the galaxies attached to events
$galaxy = $temp['GalaxyCluster']['Galaxy'];
unset($temp['GalaxyCluster']['Galaxy']);
$galaxy['GalaxyCluster'][0] = $temp['GalaxyCluster'];
return $this->__createNode('galaxy', $galaxy);
}
private function __addLink($from_id, $to_id, $linkDistance = 150) { private function __addLink($from_id, $to_id, $linkDistance = 150) {
$link = $this->graphJsonContainsLink($from_id, $to_id); $link = $this->graphJsonContainsLink($from_id, $to_id);
if ($link === false) $this->__json['links'][] = array('source' => $from_id, 'target' => $to_id, 'linkDistance' => $linkDistance); if ($link === false) $this->__json['links'][] = array('source' => $from_id, 'target' => $to_id, 'linkDistance' => $linkDistance);
@ -304,8 +324,8 @@
foreach ($this->__json['nodes'] as $k => $node) { foreach ($this->__json['nodes'] as $k => $node) {
if ($link['source'] == $node) $temp['source'] = $k; if ($link['source'] == $node) $temp['source'] = $k;
if ($link['target'] == $node) $temp['target'] = $k; if ($link['target'] == $node) $temp['target'] = $k;
$temp['linkDistance'] = $link['linkDistance'];
} }
$temp['linkDistance'] = $link['linkDistance'];
$links[] = $temp; $links[] = $temp;
} }
$this->__json['links'] = $links; $this->__json['links'] = $links;
@ -333,7 +353,7 @@
if ($type == 'event' && $node['type'] == 'event' && $node['id'] == $element['id']) { if ($type == 'event' && $node['type'] == 'event' && $node['id'] == $element['id']) {
return $k; return $k;
} }
if ($type == 'attribute' && $node['type'] == 'attribute' && $node['id'] == $element['id']) { if ($type == 'attribute' && $node['type'] == 'attribute' && $node['name'] == $element['value']) {
return $k; return $k;
} }
if ($type == 'tag' && $node['type'] == 'tag' && $node['id'] == $element['id']) { if ($type == 'tag' && $node['type'] == 'tag' && $node['id'] == $element['id']) {

2
app/Model/Galaxy.php
View File

@ -49,7 +49,6 @@ class Galaxy extends AppModel{
} }
foreach ($galaxies as $k => $galaxy) { foreach ($galaxies as $k => $galaxy) {
if (isset($existingGalaxies[$galaxy['uuid']])) { if (isset($existingGalaxies[$galaxy['uuid']])) {
//debug($galaxy);
if ( if (
$existingGalaxies[$galaxy['uuid']]['version'] < $galaxy['version'] || $existingGalaxies[$galaxy['uuid']]['version'] < $galaxy['version'] ||
(!empty($galaxy['icon']) && ($existingGalaxies[$galaxy['uuid']]['icon'] != $galaxy['icon'])) (!empty($galaxy['icon']) && ($existingGalaxies[$galaxy['uuid']]['icon'] != $galaxy['icon']))
@ -62,7 +61,6 @@ class Galaxy extends AppModel{
$this->save($galaxy); $this->save($galaxy);
} }
} }
//throw new Exception();
return $this->find('list', array('recursive' => -1, 'fields' => array('type', 'id'))); return $this->find('list', array('recursive' => -1, 'fields' => array('type', 'id')));
} }

28
app/View/Elements/side_menu.ctp
View File

@ -29,7 +29,7 @@
<li class="divider"></li> <li class="divider"></li>
<?php endif;?> <?php endif;?>
<li id='liviewEvent'><a href="<?php echo $baseurl;?>/events/view/<?php echo h($event['Event']['id']);?>">View Event</a></li> <li id='liviewEvent'><a href="<?php echo $baseurl;?>/events/view/<?php echo h($event['Event']['id']);?>">View Event</a></li>
<li id='liviewEventGraph'><a href="<?php echo $baseurl;?>/events/viewGraph/<?php echo h($event['Event']['id']);?>">View Correlation Graph</a></li> <li id='liviewGraph'><a href="<?php echo $baseurl;?>/events/viewGraph/<?php echo h($event['Event']['id']);?>">View Correlation Graph</a></li>
<li id='lieventLog'><a href="<?php echo $baseurl;?>/logs/event_index/<?php echo h($event['Event']['id']);?>">View Event History</a></li> <li id='lieventLog'><a href="<?php echo $baseurl;?>/logs/event_index/<?php echo h($event['Event']['id']);?>">View Event History</a></li>
<li class="divider"></li> <li class="divider"></li>
<?php if ($isSiteAdmin || (isset($mayModify) && $mayModify)): ?> <?php if ($isSiteAdmin || (isset($mayModify) && $mayModify)): ?>
@ -273,13 +273,25 @@
case 'tags': ?> case 'tags': ?>
<li id='liindexfav'><?php echo $this->Html->link('List Favourite Tags', array('action' => 'index', true));?></li> <li id='liindexfav'><?php echo $this->Html->link('List Favourite Tags', array('action' => 'index', true));?></li>
<li id='liindex'><?php echo $this->Html->link('List Tags', array('action' => 'index'));?></li> <li id='liindex'><?php echo $this->Html->link('List Tags', array('action' => 'index'));?></li>
<?php if ($isAclTagEditor): ?> <?php
if ($isAclTagEditor):
?>
<li id='liadd'><?php echo $this->Html->link('Add Tag', array('action' => 'add'));?></li> <li id='liadd'><?php echo $this->Html->link('Add Tag', array('action' => 'add'));?></li>
<?php <?php
endif; endif;
if ($menuItem === 'edit'): if ($menuItem === 'edit'):
?> ?>
<li class="active"><?php echo $this->Html->link('Edit Tag', array('action' => 'edit'));?></li> <li class="active"><?php echo $this->Html->link('Edit Tag', array('action' => 'edit'));?></li>
<?php
endif;
if ($menuItem === 'viewGraph'):
if (!empty($taxonomy)):
?>
<li><a href="<?php echo $baseurl; ?>/taxonomies/view/<?php echo h($taxonomy['Taxonomy']['id']); ?>">View Taxonomy</a></li>
<?php
endif;
?>
<li id='liviewGraph'><a href="<?php echo $baseurl;?>/tags/viewGraph/<?php echo h($id); ?>">View Correlation Graph</a></li>
<?php <?php
endif; endif;
break; break;
@ -350,14 +362,16 @@
<li><?php echo $this->Form->postLink('Update Galaxies', array('controller' => 'galaxies', 'action' => 'update'), null, __('Are you sure you want to reimport all galaxies from the submodule?')); ?></li> <li><?php echo $this->Form->postLink('Update Galaxies', array('controller' => 'galaxies', 'action' => 'update'), null, __('Are you sure you want to reimport all galaxies from the submodule?')); ?></li>
<?php <?php
endif; endif;
if ($menuItem === 'viewGraph' || $menuItem === 'view_cluster'): ?>
<li><a href="<?php echo $baseurl;?>/galaxies/view/<?php echo h($galaxy_id); ?>">View Galaxy</a></li>
<li id='liview_cluster'><a href="<?php echo $baseurl;?>/galaxy_clusters/view/<?php echo h($id); ?>">View Cluster</a></li>
<li id='liviewGraph'><a href="<?php echo $baseurl;?>/galaxies/viewGraph/<?php echo h($id); ?>">View Correlation Graph</a></li>
<?php
endif;
if ($menuItem === 'view'): if ($menuItem === 'view'):
?> ?>
<li class="active"><a href="#">View Galaxy</a></li> <li class="active"><a href="#">View Galaxy</a></li>
<?php
endif;
if ($menuItem === 'view_cluster'):
?>
<li class="active"><a href="#">View Cluster</a></li>
<?php <?php
endif; endif;
break; break;

568
app/View/Events/view_graph.ctp
View File

@ -1,91 +1,13 @@
<?php <?php
if ($scope == 'event') {
$mayModify = (($isAclModify && $event['Event']['user_id'] == $me['id'] && $event['Orgc']['id'] == $me['org_id']) || ($isAclModifyOrg && $event['Orgc']['id'] == $me['org_id'])); $mayModify = (($isAclModify && $event['Event']['user_id'] == $me['id'] && $event['Orgc']['id'] == $me['org_id']) || ($isAclModifyOrg && $event['Orgc']['id'] == $me['org_id']));
$mayPublish = ($isAclPublish && $event['Orgc']['id'] == $me['org_id']); $mayPublish = ($isAclPublish && $event['Orgc']['id'] == $me['org_id']);
}
echo $this->Html->css('font-awesome'); echo $this->Html->css('font-awesome');
echo $this->Html->script('d3'); ?> echo $this->Html->css('correlation-graph');
<style> echo $this->Html->script('d3');
echo $this->Html->script('correlation-graph');
.node circle { ?>
cursor: pointer;
stroke: #3182bd;
stroke-width: 1.5px;
}
.node text {
font: 10px sans-serif;
pointer-events: none;
text-anchor: middle;
}
line.link {
fill: none;
stroke: #9ecae1;
stroke-width: 1.5px;
}
#main {
display: inline-block;
background-color: grey;
position: relative;
}
.menu {
border: 1px solid black;
background-color: grey;
display: none;
position: relative;
}
.menu,
.menu li {
padding: 0px;
margin: 0px;
width: 250px;
}
.menu li {
color: white;
}
.menu > li:hover {
background-color: lightblue;
color: black;
}
.menu li {
display: block;
word-wrap: break-word;
}
.menu li:hover ul {
display:inline-block;
position: relative;
top: 0;
}
.menu > li > span > a {
color:white;
font-weight:bold;
}
.menu > li > span:first-child {
font-weight:bold;
}
.graphMenuTitle {
background-color:#0088cc;
font-weight:bold;
color:white;
}
.graphMenuActions {
background-color:#0088cc;
color:white;
}
.graphMenuAction {
cursor: hand;
}
.menu-container {
position:absolute;
width:300px;
}
.font-white {
color:white;
}
.corrected-icon {
top:-5px;
margin-left:100px;
}
</style>
<div class="view"> <div class="view">
<div id="chart" style="width:100%;height:100%"></div> <div id="chart" style="width:100%;height:100%"></div>
<div id="hover-menu-container" class="menu-container"> <div id="hover-menu-container" class="menu-container">
@ -103,466 +25,26 @@ echo $this->Html->script('d3'); ?>
<li id="context-delete">Delete</li> <li id="context-delete">Delete</li>
</ul> </ul>
</div> </div>
<div id="graph_init" class="hidden" data-id="<?php echo h($id);?>" data-scope="<?php echo h($scope);?>">
</div>
<?php <?php
echo $this->element('side_menu', array('menuList' => 'event', 'menuItem' => 'viewEventGraph', 'mayModify' => $mayModify, 'mayPublish' => $mayPublish)); $scope_list = array(
?> 'event' => 'event',
<script> 'galaxy' => 'galaxies',
var currentMousePos = { x: -1, y: -1 }; 'tag' => 'tags'
$(document).mousemove(function(event) {
currentMousePos.x = event.pageX;
currentMousePos.y = event.pageY;
});
var margin = {top: -5, right: -5, bottom: -5, left: -5},
width = $(window).width() - margin.left - margin.right,
height = $(window).height() - 160 - margin.top - margin.bottom;
var menu_x_buffer_ = width - 150;
var menu_y_buffer = height - 100;
$('.menu-container').css('left', '200px');
$('#hover-menu-container').css('top', '50px');
$('#hover-menu-container').css('z-index', 1);
$('#selected-menu-container').css('top', '400px');
$('#selected-menu-container').css('z-index', 2);
var root;
var highlighted;
var hovered;
var icon_sizes = {
"event": 24,
"object": 12,
"attribute": 12,
"galaxy": 32,
"tag": 24
}
var selection_radius_sizes = {
"event": 18,
"object": 12,
"attribute": 12,
"galaxy": 18,
"tag": 18
}
var force = d3.layout.force()
.linkDistance(function (d) {
return d.linkDistance;
})
.linkStrength(0.9)
.friction(0.5)
.theta(0.9)
.charge(-500)
.gravity(0.21)
.size([width, height])
.on("tick", tick);
var vis = d3.select("#chart");
var svg = vis.append("svg:svg")
.attr("width", width)
.attr("height", height)
.attr("pointer-events", "all");
var rect = svg.append("svg:rect")
.attr('width', width)
.attr('height', height)
.attr('fill', 'white')
.call(d3.behavior.zoom().on("zoom", zoomhandler));
var plotting_area = svg.append("g")
.attr("class", "plotting-area");
var drag1 = d3.behavior.drag()
.on("dragstart", dragstart)
.on("drag", dragmove)
.on("dragend", dragend);
var link = plotting_area.selectAll(".link");
var node = plotting_area.selectAll(".node");
d3.json("/events/updateGraph/<?php echo $id; ?>.json", function(error, json) {
root = json;
update();
});
var graphElementScale = 1;
var graphElementTranslate = [0, 0];
function zoomhandler() {
plotting_area.attr("transform",
"translate(" + d3.event.translate + ")"
+ " scale(" + d3.event.scale + ")");
graphElementScale = d3.event.scale;
graphElementTranslate = d3.event.translate;
}
function update() {
var nodes = root['nodes'], links = root['links'];
// Restart the force layout.
force.nodes(nodes).links(links).start();
// Update links.
link = link.data(links);
link.exit().remove();
link.enter().insert("line", ".node").attr("class", "link");
// Update nodes.
node = node.data(nodes);
node.exit().remove();
var nodeEnter = node.enter().append("g").attr("class", "node").call(drag1);
nodeEnter.attr('id', function(d) { return 'id-' + d.unique_id; })
nodeEnter.insert("circle", ".circle")
.classed("highlighted_circle", true)
.attr("cx", function(d) { return d.x_axis; })
.attr("cy", function(d) { return d.y_axis; })
.attr("r", function(d) { return selection_radius_sizes[d.type] })
.attr("stroke", "red")
.attr("stroke-opacity", "0")
.attr("fill-opacity", "0")
.attr("fill", "red");
nodeEnter.filter(function(d) {return d.image !== undefined})
.append("svg:image")
.attr("class", "circle")
.attr("xlink:href", function(d) {
return d.image
})
.attr("x", function(d) {
return (0 - (icon_sizes[d.type]/2)) + "px";
})
.attr("y", function(d) {
return (0 - (icon_sizes[d.type]/2)) + "px";
})
.attr("width", function(d) {
return ((icon_sizes[d.type])) + "px";
})
.attr("height", function(d) {
return ((icon_sizes[d.type])) + "px";
});
nodeEnter.filter(function(d) {return d.imgClass !== undefined})
.append("g")
.append('svg:foreignObject')
.attr("width", 12)
.attr("height", 12)
.attr("x", function(d) {
if (d.type == 'galaxy' || d.type == 'tag') {
return '-10px';
} else {
return '-6px';
}
}
)
.attr("y", function(d) {
if (d.type == 'galaxy' || d.type == 'tag') {
return '-12px';
} else {
return '-8px';
}
}
)
.append("xhtml:body")
.html(function (d) {
var result = 'fa-' + d.imgClass;
if (d.type == 'galaxy' || d.type == 'tag') result = 'fa-2x ' + result;
return '<i class="fa ' + result + '"></i>';
});
nodeEnter.append("text")
.attr("dy", function(d) {
if (d.type == "event" || d.type == "galaxy") {
return "10px";
} else {
return "0px";
}
})
.attr("fill", function(d) {
if (d.type == "event") {
if (d.expanded == 1) {
return "#0000ff";
} else {
return "#ff0000";
}
}
})
.text(function(d) {
return d.type + ': ' + d.name;
});
node.selectAll("text")
.attr("y", 20);
node.on('mouseover', function(d) {
link.style('stroke', function(l) {
if (d === l.source || d === l.target)
return "#ff0000";
else
return "#9ecae1";
});
link.style('stroke-width', function(l) {
if (d === l.source || d === l.target)
return 2;
else
return 1;
});
showPane(d, 'hover');
});
node.on('mouseout', function() {
link.style('stroke-width', 1);
link.style('stroke', "#9ecae1");
});
node.on("click", function(d) {
showPane(d, 'selected');
});
}
function highlightNode(d) {
d3.selectAll('.highlighted_circle')
.style("stroke-opacity", 0);
d3.select('#id-' + d.unique_id)
.select('.highlighted_circle')
.style("stroke", "red")
.style("stroke-opacity", 0.5);
}
function contextMenu(d, newContext) {
d3.event.preventDefault();
if (d.type == 'event') showPane(d, 'context');
}
function bindExpand(d, type) {
if (!d.expanded) {
var expandName = 'Expand (ctrl+x)';
if (type == 'selected') {
expandName = 'Expand (x)';
}
$("#" + type + "-menu").append('<li id="expand_' + type + '_' + d.id +'" class="graphMenuAction"><span>' + expandName + '</span></li>');
d3.select('#expand_' + type + '_' + d.id)
.on('click', function() {
expand(d);
});
}
}
function bindDelete(d, type) {
var deleteName = 'Delete (ctrl+d)';
if (type == 'selected') {
deleteName = 'Delete (d)';
}
$("#" + type + "-menu").append('<li id="remove_' + type + '_' + d.id +'" class="graphMenuAction"><span>' + deleteName + '</span></li>');
d3.select('#remove_' + type + '_' + d.id)
.on('click', function() {
remove(d);
});
}
function createInfoPane(d, data, type) {
var i = 0;
var view_urls = {
'event': '/events/view/' + parseInt(d.id),
'tag': '/tags/view/' + parseInt(d.id),
'galaxy': '/galaxy_clusters/view/' + parseInt(d.id)
};
data["fields"].forEach(function(e) {
var title = e;
if (i == 0) title = d.type;
title = title.split("_").join(" ");
title = title.charAt(0).toUpperCase() + title.slice(1);
var span1 = $('<span />').text(title + ': ');
var span2 = $('<span />').text(d[e]);
var li = $('<li />');
li.append(span1);
li.append(span2);
if (i == 0) li.addClass('graphMenuTitle');
i++;
$("#" + type + "-menu").append(li);
});
$("#" + type + "-menu").append('<li class="graphMenuActions">Actions</li>');
if ($.inArray("navigate", data["actions"]) !== -1) {
console.log($.inArray("navigate", data["actions"]));
$("#" + type + "-menu").append('<li><span><a href="' + view_urls[d.type] + '">Go to ' + d.type + '</a></span></li>');
}
if ($.inArray("expand", data["actions"]) !== -1) {
bindExpand(d, type);
}
if ($.inArray("delete", data["actions"]) !== -1) {
bindDelete(d, type);
}
}
function showPane(d, type) {
if (type == 'hover') {
hovered = d;
} else {
highlighted = d;
highlightNode(d);
}
$('#' + type + '-header').show();
d3.select("#" + type + "-menu").style('display', 'inline-block');
$("#" + type + "-menu").empty();
if (d.type== 'attribute') {
var data = {
"fields": ["id", "name", "category", "type", "comment"],
"actions": ["delete"]
}
}
if (d.type== 'event') {
var tempid = parseInt(d.id);
var data = {
"fields": ["id", "info", "date", "analysis", "org"],
"actions": ["expand", "delete", "navigate"]
}
}
if (d.type == 'tag') {
var data = {
"fields": ["id", "name"],
"actions": ["expand", "delete"]
}
if (d.taxonomy !== undefined) {
data["fields"].push("taxonomy");
data["fields"].push("taxonomy_description");
if (d.description !== "") {
data["fields"].push("Description");
}
}
}
if (d.type == 'galaxy') {
var data = {
"fields": ["id", "name", "galaxy", "synonyms", "authors", "description", "source"],
"actions": ["expand", "delete", "navigate"]
}
}
if (d.type == 'object') {
var data = {
"fields": ["id", "name", "metacategory", "description", "comment"],
"actions": ["delete"]
}
}
createInfoPane(d, data, type);
}
function expand(d) {
if (d.type == 'event' || d.type == 'galaxy' || d.type == 'tag') {
d3.xhr("/events/updateGraph/" + d.id + "/" + d.type + ".json")
.header("Content-Type", "application/json")
.post(
JSON.stringify(root),
function(err, rawData){
root = JSON.parse(rawData.response);
update();
}
); );
$params = array(
'menuList' => $scope_list[$scope],
'menuItem' => 'viewGraph'
);
if ($scope == 'event') {
$params['mayModify'] = $mayModify;
$params['mayPublish'] = $mayPublish;
}
if ($scope == 'tag') {
if (!empty($taxoomy)) {
$params['taxonomy'] = $taxonomy['Taxonomy']['id'];
} }
} }
echo $this->element('side_menu', $params);
function tick() { ?>
link.attr("x1", function(d) { return d.source.x; })
.attr("y1", function(d) { return d.source.y; })
.attr("x2", function(d) { return d.target.x; })
.attr("y2", function(d) { return d.target.y; });
node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
}
// Returns a list of all nodes under the root.
function flatten(root) {
var nodes = [], i = 0;
function recurse(node) {
if (node.children) node.children.forEach(recurse);
if (!node.id) node.id = ++i;
nodes.push(node);
}
recurse(root);
return nodes;
}
function dragstart(d, i) {
force.stop();
}
function dragmove(d, i) {
d.px += d3.event.dx;
d.py += d3.event.dy;
d.x += d3.event.dx;
d.y += d3.event.dy;
tick();
}
function dragend(d, i) {
d.fixed = true;
tick();
force.resume();
}
function searchArray(arr, val) {
for (var i=0; i < arr.length; i++)
if (arr[i] === val)
return i;
return false;
}
$(document).on('keydown', function(e) {
if (e.which == 69) {
if (highlighted == undefined) {
showPane(root['nodes'][0], 'selected');
} else {
var current = searchArray(root['nodes'], highlighted);
if (current == root['nodes'].length-1) {
showPane(root['nodes'][0], 'selected');
} else {
showPane(root['nodes'][current+1], 'selected');
}
}
}
if (e.which == 81) {
if (highlighted == undefined) {
showPane(root['nodes'][root['nodes'].length-1], 'selected');
} else {
var current = searchArray(root['nodes'], highlighted);
if (current == 0) {
showPane(root['nodes'][root['nodes'].length-1], 'selected');
} else {
showPane(root['nodes'][current-1], 'selected');
}
}
}
});
$(document).on('keydown', function(e) {
if (e.which == 68) {
e.preventDefault();
if (e.ctrlKey) {
if (hovered != undefined) {
remove(hovered);
}
} else {
if (highlighted != undefined) {
remove(highlighted);
}
}
}
});
$(document).on('keydown', function(e) {
if (e.which == 88) {
e.preventDefault();
if (e.ctrlKey) {
if (hovered != undefined) {
expand(hovered);
}
} else {
if (highlighted != undefined) {
expand(highlighted);
}
}
}
});
</script>

5
app/View/Galaxies/view.ctp
View File

@ -4,7 +4,10 @@
<div class="galaxy view"> <div class="galaxy view">
<div class="row-fluid"> <div class="row-fluid">
<div class="span8"> <div class="span8">
<h2><?php echo h($galaxy['Galaxy']['name']); ?> galaxy</h2> <h2>
<span class="fa fa-<?php echo h($galaxy['Galaxy']['icon']); ?>"></span>&nbsp;
<?php echo h($galaxy['Galaxy']['name']); ?> galaxy
</h2>
<dl> <dl>
<dt>Galaxy ID</dt> <dt>Galaxy ID</dt>
<dd><?php echo h($galaxy['Galaxy']['id']); ?></dd> <dd><?php echo h($galaxy['Galaxy']['id']); ?></dd>

1
app/View/GalaxyClusters/ajax/index.ctp
View File

@ -50,6 +50,7 @@
</td> </td>
<td><?php echo h($item['GalaxyCluster']['description']); ?>&nbsp;</td> <td><?php echo h($item['GalaxyCluster']['description']); ?>&nbsp;</td>
<td class="short action-links"> <td class="short action-links">
<?php echo $this->Html->link('', array('controller' => 'galaxies', 'action' => 'viewGraph', $item['GalaxyCluster']['id']), array('class' => 'fa fa-line-chart', 'title' => 'View graph'));?>
<?php echo $this->Html->link('', array('action' => 'view', $item['GalaxyCluster']['id']), array('class' => 'icon-list-alt', 'title' => 'View'));?> <?php echo $this->Html->link('', array('action' => 'view', $item['GalaxyCluster']['id']), array('class' => 'icon-list-alt', 'title' => 'View'));?>
</td> </td>
</tr> </tr>

1
app/View/Tags/index.ctp
View File

@ -104,6 +104,7 @@ foreach ($list as $k => $item): ?>
</td> </td>
<?php if ($isSiteAdmin): ?> <?php if ($isSiteAdmin): ?>
<td class="short action-links"> <td class="short action-links">
<?php echo $this->Html->link('', array('controller' => 'tags', 'action' => 'viewGraph', $item['Tag']['id']), array('class' => 'fa fa-line-chart', 'title' => 'View graph'));?>
<?php echo $this->Html->link('', array('action' => 'edit', $item['Tag']['id']), array('class' => 'icon-edit', 'title' => 'Edit'));?> <?php echo $this->Html->link('', array('action' => 'edit', $item['Tag']['id']), array('class' => 'icon-edit', 'title' => 'Edit'));?>
<?php echo $this->Form->postLink('', array('action' => 'delete', $item['Tag']['id']), array('class' => 'icon-trash', 'title' => 'Delete'), __('Are you sure you want to delete "%s"?', $item['Tag']['name']));?> <?php echo $this->Form->postLink('', array('action' => 'delete', $item['Tag']['id']), array('class' => 'icon-trash', 'title' => 'Delete'), __('Are you sure you want to delete "%s"?', $item['Tag']['name']));?>
</td> </td>

1
app/View/Taxonomies/view.ctp
View File

@ -122,6 +122,7 @@
<a href="<?php echo $url;?>" class="<?php echo $isAclTagger ? 'tagFirstHalf' : 'tag' ?>" style="background-color:<?php echo h($item['existing_tag']['Tag']['colour']);?>;color:<?php echo $this->TextColour->getTextColour($item['existing_tag']['Tag']['colour']);?>"><?php echo h($item['existing_tag']['Tag']['name']); ?></a> <a href="<?php echo $url;?>" class="<?php echo $isAclTagger ? 'tagFirstHalf' : 'tag' ?>" style="background-color:<?php echo h($item['existing_tag']['Tag']['colour']);?>;color:<?php echo $this->TextColour->getTextColour($item['existing_tag']['Tag']['colour']);?>"><?php echo h($item['existing_tag']['Tag']['name']); ?></a>
<?php <?php
endif; endif;
echo '&nbsp;' . $this->Html->link('', array('controller' => 'tags', 'action' => 'viewGraph', $item['existing_tag']['Tag']['id']), array('class' => 'fa fa-line-chart black', 'title' => 'View graph'));
endif; endif;
?> ?>
</td> </td>

80
app/webroot/css/correlation-graph.css Normal file
View File

@ -0,0 +1,80 @@
.node circle {
cursor: pointer;
stroke: #3182bd;
stroke-width: 1.5px;
}
.node text {
font: 10px sans-serif;
pointer-events: none;
text-anchor: middle;
}
line.link {
fill: none;
stroke: #9ecae1;
stroke-width: 1.5px;
}
#main {
display: inline-block;
background-color: grey;
position: relative;
}
.menu {
border: 1px solid black;
background-color: grey;
display: none;
position: relative;
}
.menu,
.menu li {
padding: 0px;
margin: 0px;
width: 250px;
}
.menu li {
color: white;
}
.menu > li:hover {
background-color: lightblue;
color: black;
}
.menu li {
display: block;
word-wrap: break-word;
}
.menu li:hover ul {
display:inline-block;
position: relative;
top: 0;
}
.menu > li > span > a {
color:white;
font-weight:bold;
}
.menu > li > span:first-child {
font-weight:bold;
}
.graphMenuTitle {
background-color:#0088cc;
font-weight:bold;
color:white;
}
.graphMenuActions {
background-color:#0088cc;
color:white;
}
.graphMenuAction {
cursor: hand;
}
.menu-container {
position:absolute;
width:300px;
}
.font-white {
color:white;
}
.corrected-icon {
top:-5px;
margin-left:100px;
}

4
app/webroot/css/main.css
View File

@ -1912,6 +1912,10 @@ table tr:hover .down-expand-button {
border:50px solid black; border:50px solid black;
} }
.action-links > .fa {
color:black;
}
@-webkit-keyframes rotation { @-webkit-keyframes rotation {
from {-webkit-transform: rotate(0deg);} from {-webkit-transform: rotate(0deg);}
to {-webkit-transform: rotate(359deg);} to {-webkit-transform: rotate(359deg);}

507
app/webroot/js/correlation-graph.js Normal file
View File

@ -0,0 +1,507 @@
$(document).ready( function() {
var currentMousePos = { x: -1, y: -1 };
$(document).mousemove(function(event) {
currentMousePos.x = event.pageX;
currentMousePos.y = event.pageY;
});
var margin = {top: -5, right: -5, bottom: -5, left: -5},
width = $(window).width() - margin.left - margin.right,
height = $(window).height() - 160 - margin.top - margin.bottom;
var menu_x_buffer_ = width - 150;
var menu_y_buffer = height - 100;
$('.menu-container').css('left', '200px');
$('#hover-menu-container').css('top', '50px');
$('#hover-menu-container').css('z-index', 1);
$('#selected-menu-container').css('top', '400px');
$('#selected-menu-container').css('z-index', 2);
var root;
var highlighted;
var hovered;
var icon_sizes = {
"event": 24,
"object": 12,
"attribute": 12,
"galaxy": 32,
"tag": 24
}
var selection_radius_sizes = {
"event": 18,
"object": 12,
"attribute": 12,
"galaxy": 18,
"tag": 18
}
var force = d3.layout.force()
.linkDistance(function (d) {
return d.linkDistance;
})
.linkStrength(0.9)
.friction(0.5)
.theta(0.9)
.charge(-500)
.gravity(0.21)
.size([width, height])
.on("tick", tick);
var vis = d3.select("#chart");
var svg = vis.append("svg:svg")
.attr("width", width)
.attr("height", height)
.attr("pointer-events", "all");
var rect = svg.append("svg:rect")
.attr('width', width)
.attr('height', height)
.attr('fill', 'white')
.call(d3.behavior.zoom().on("zoom", zoomhandler));
var plotting_area = svg.append("g")
.attr("class", "plotting-area");
var drag1 = d3.behavior.drag()
.on("dragstart", dragstart)
.on("drag", dragmove)
.on("dragend", dragend);
var link = plotting_area.selectAll(".link");
var node = plotting_area.selectAll(".node");
var scope_id = $('#graph_init').data('id');
var scope = $('#graph_init').data('scope');
d3.json("/events/updateGraph/" + scope_id + "/" + scope + ".json", function(error, json) {
root = json;
update();
});
var graphElementScale = 1;
var graphElementTranslate = [0, 0];
function zoomhandler() {
plotting_area.attr("transform",
"translate(" + d3.event.translate + ")"
+ " scale(" + d3.event.scale + ")");
graphElementScale = d3.event.scale;
graphElementTranslate = d3.event.translate;
}
function update() {
var nodes = root['nodes'], links = root['links'];
// Restart the force layout.
force.nodes(nodes).links(links).start();
// Update links.
link = link.data(links);
link.exit().remove();
link.enter().insert("line", ".node").attr("class", "link");
// Update nodes.
node = node.data(nodes);
node.exit().remove();
var nodeEnter = node.enter().append("g").attr("class", "node").call(drag1);
nodeEnter.attr('id', function(d) { return 'id-' + d.unique_id; })
nodeEnter.insert("circle", ".circle")
.classed("highlighted_circle", true)
.attr("cx", function(d) { return d.x_axis; })
.attr("cy", function(d) { return d.y_axis; })
.attr("r", function(d) { return selection_radius_sizes[d.type] })
.attr("stroke", "red")
.attr("stroke-opacity", "0")
.attr("fill-opacity", "0")
.attr("fill", "red");
nodeEnter.filter(function(d) {return d.image !== undefined})
.append("svg:image")
.attr("class", "circle")
.attr("xlink:href", function(d) {
return d.image
})
.attr("x", function(d) {
return (0 - (icon_sizes[d.type]/2)) + "px";
})
.attr("y", function(d) {
return (0 - (icon_sizes[d.type]/2)) + "px";
})
.attr("width", function(d) {
return ((icon_sizes[d.type])) + "px";
})
.attr("height", function(d) {
return ((icon_sizes[d.type])) + "px";
});
nodeEnter.filter(function(d) {return d.imgClass !== undefined})
.append("g")
.append('svg:foreignObject')
.attr("width", 12)
.attr("height", 12)
.attr("x", function(d) {
if (d.type == 'galaxy' || d.type == 'tag') {
return '-10px';
} else {
return '-6px';
}
}
)
.attr("y", function(d) {
if (d.type == 'galaxy' || d.type == 'tag') {
return '-12px';
} else {
return '-8px';
}
}
)
.append("xhtml:body")
.html(function (d) {
var result = 'fa-' + d.imgClass;
if (d.type == 'galaxy' || d.type == 'tag') result = 'fa-2x ' + result;
return '<i class="fa ' + result + '"></i>';
});
nodeEnter.append("text")
.attr("dy", function(d) {
if (d.type == "event" || d.type == "galaxy") {
return "10px";
} else {
return "0px";
}
})
.attr("fill", function(d) {
if (d.type == "event") {
if (d.expanded == 1) {
return "#0000ff";
} else {
return "#ff0000";
}
}
})
.text(function(d) {
return d.type + ': ' + d.name;
});
node.selectAll("text")
.attr("y", 20);
node.on('mouseover', function(d) {
link.style('stroke', function(l) {
if (d === l.source || d === l.target)
return "#ff0000";
else
return "#9ecae1";
});
link.style('stroke-width', function(l) {
if (d === l.source || d === l.target)
return 2;
else
return 1;
});
showPane(d, 'hover');
});
node.on('mouseout', function() {
link.style('stroke-width', 1);
link.style('stroke', "#9ecae1");
});
node.on("click", function(d) {
showPane(d, 'selected');
});
}
function highlightNode(d) {
d3.selectAll('.highlighted_circle')
.style("stroke-opacity", 0);
d3.select('#id-' + d.unique_id)
.select('.highlighted_circle')
.style("stroke", "red")
.style("stroke-opacity", 0.5);
}
function contextMenu(d, newContext) {
d3.event.preventDefault();
if (d.type == 'event') showPane(d, 'context');
}
function bindExpand(d, type) {
if (!d.expanded) {
var expandName = 'Expand (ctrl+x)';
if (type == 'selected') {
expandName = 'Expand (x)';
}
$("#" + type + "-menu").append('<li id="expand_' + type + '_' + d.id +'" class="graphMenuAction"><span>' + expandName + '</span></li>');
d3.select('#expand_' + type + '_' + d.id)
.on('click', function() {
expand(d);
});
}
}
function remove_node(d) {
var index = root.nodes.indexOf(d);
if (index > -1) {
root.nodes.splice(index, 1);
}
var temp = [];
root['links'].forEach(function(n) {
if (n.source != d && n.target != d) {
temp.push(n);
}
});
root['links'] = temp;
var i = 0;
var links = [];
root.links.forEach(function(l) {
var j = 0;
var temp = {};
root.nodes.forEach(function(n) {
if (l.source == n) {
temp.source = j;
}
if (l.target == n) {
temp.target = j;
}
var j = j+1;
});
temp.linkDistance = l.linkDistance;
links.push(temp);
var i = i+1;
});
root = {
'nodes': root['nodes'],
'links': root['links']
};
update();
}
/*
function bindDelete(d, type) {
var deleteName = 'Delete (ctrl+d)';
if (type == 'selected') {
deleteName = 'Delete (d)';
}
$("#" + type + "-menu").append('<li id="remove_' + type + '_' + d.id +'" class="graphMenuAction"><span>' + deleteName + '</span></li>');
d3.select('#remove_' + type + '_' + d.id)
.on('click', function() {
remove_node(d);
});
}
*/
function createInfoPane(d, data, type) {
var i = 0;
var view_urls = {
'event': '/events/view/' + parseInt(d.id),
'tag': '/tags/view/' + parseInt(d.id),
'galaxy': '/galaxy_clusters/view/' + parseInt(d.id)
};
data["fields"].forEach(function(e) {
var title = e;
if (i == 0) title = d.type;
title = title.split("_").join(" ");
title = title.charAt(0).toUpperCase() + title.slice(1);
var span1 = $('<span />').text(title + ': ');
var span2 = $('<span />').text(d[e]);
var li = $('<li />');
li.append(span1);
li.append(span2);
if (i == 0) li.addClass('graphMenuTitle');
i++;
$("#" + type + "-menu").append(li);
});
$("#" + type + "-menu").append('<li class="graphMenuActions">Actions</li>');
if ($.inArray("navigate", data["actions"]) !== -1) {
$("#" + type + "-menu").append('<li><span><a href="' + view_urls[d.type] + '">Go to ' + d.type + '</a></span></li>');
}
if ($.inArray("expand", data["actions"]) !== -1) {
bindExpand(d, type);
}
if ($.inArray("delete", data["actions"]) !== -1) {
bindDelete(d, type);
}
}
function showPane(d, type) {
if (type == 'hover') {
hovered = d;
} else {
highlighted = d;
highlightNode(d);
}
$('#' + type + '-header').show();
d3.select("#" + type + "-menu").style('display', 'inline-block');
$("#" + type + "-menu").empty();
if (d.type== 'attribute') {
var data = {
"fields": ["id", "name", "category", "type", "comment"],
"actions": ["delete"]
}
}
if (d.type== 'event') {
var tempid = parseInt(d.id);
var data = {
"fields": ["id", "info", "date", "analysis", "org"],
"actions": ["expand", "delete", "navigate"]
}
}
if (d.type == 'tag') {
var data = {
"fields": ["id", "name"],
"actions": ["expand", "delete"]
}
if (d.taxonomy !== undefined) {
data["fields"].push("taxonomy");
data["fields"].push("taxonomy_description");
if (d.description !== "") {
data["fields"].push("Description");
}
}
}
if (d.type == 'galaxy') {
var data = {
"fields": ["id", "name", "galaxy", "synonyms", "authors", "description", "source"],
"actions": ["expand", "delete", "navigate"]
}
}
if (d.type == 'object') {
var data = {
"fields": ["id", "name", "metacategory", "description", "comment"],
"actions": ["delete"]
}
}
createInfoPane(d, data, type);
}
function expand(d) {
if (d.type == 'event' || d.type == 'galaxy' || d.type == 'tag') {
d3.xhr("/events/updateGraph/" + d.id + "/" + d.type + ".json")
.header("Content-Type", "application/json")
.post(
JSON.stringify(root),
function(err, rawData){
root = JSON.parse(rawData.response);
update();
}
);
}
}
function tick() {
link.attr("x1", function(d) { return d.source.x; })
.attr("y1", function(d) { return d.source.y; })
.attr("x2", function(d) { return d.target.x; })
.attr("y2", function(d) { return d.target.y; });
node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
}
// Returns a list of all nodes under the root.
function flatten(root) {
var nodes = [], i = 0;
function recurse(node) {
if (node.children) node.children.forEach(recurse);
if (!node.id) node.id = ++i;
nodes.push(node);
}
recurse(root);
return nodes;
}
function dragstart(d, i) {
force.stop();
}
function dragmove(d, i) {
d.px += d3.event.dx;
d.py += d3.event.dy;
d.x += d3.event.dx;
d.y += d3.event.dy;
tick();
}
function dragend(d, i) {
d.fixed = true;
tick();
force.resume();
}
function searchArray(arr, val) {
for (var i=0; i < arr.length; i++)
if (arr[i] === val)
return i;
return false;
}
$(document).on('keydown', function(e) {
if (e.which == 69) {
if (highlighted == undefined) {
showPane(root['nodes'][0], 'selected');
} else {
var current = searchArray(root['nodes'], highlighted);
if (current == root['nodes'].length-1) {
showPane(root['nodes'][0], 'selected');
} else {
showPane(root['nodes'][current+1], 'selected');
}
}
}
if (e.which == 81) {
if (highlighted == undefined) {
showPane(root['nodes'][root['nodes'].length-1], 'selected');
} else {
var current = searchArray(root['nodes'], highlighted);
if (current == 0) {
showPane(root['nodes'][root['nodes'].length-1], 'selected');
} else {
showPane(root['nodes'][current-1], 'selected');
}
}
}
});
/*
$(document).on('keydown', function(e) {
if (e.which == 68) {
e.preventDefault();
if (e.ctrlKey) {
if (hovered != undefined) {
remove_node(hovered);
}
} else {
if (highlighted != undefined) {
remove_node(highlighted);
}
}
}
});
*/
$(document).on('keydown', function(e) {
if (e.which == 88) {
e.preventDefault();
if (e.ctrlKey) {
if (hovered != undefined) {
expand(hovered);
}
} else {
if (highlighted != undefined) {
expand(highlighted);
}
}
}
});
});