mirror of
https://github.com/galaxyproject/galaxy.git
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Init files
This commit is contained in:
Matej Trojak
@@ -0,0 +1,16 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
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<visualization name="Transition system visualization" embeddable="false">
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<description>- visjs-based interactive visualization of transition system in graph form.</description>
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<data_sources>
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<data_source>
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<model_class>HistoryDatasetAssociation</model_class>
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<test type="isinstance" test_attr="datatype" result_type="datatype">text.BCSLts</test>
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<to_param param_attr="id">dataset_id</to_param>
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</data_source>
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</data_sources>
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<params>
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<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
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</params>
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<entry_point entry_point_type="mako">ts_visjs.mako</entry_point>
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</visualization>
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@@ -0,0 +1,13 @@
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{
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"name": "ts_visjs",
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"version": "1.0.0",
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"license": "MIT",
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"dependencies": {
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"plotly.js": "^2.11.1",
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"pca-js": "^1.0.2",
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"d3": "^7.4.4"
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},
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"scripts": {
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"build": "mkdir -p static/dist && cp node_modules/pca-js/pca.min.js node_modules/plotly.js/dist/plotly.min.js node_modules/d3/dist/d3.min.js static/dist"
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}
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}
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@@ -0,0 +1,174 @@
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#mynetwork {
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||||
width: 94%;
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||||
height: 100%;
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||||
border: 1px solid #000;
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||||
float: left;
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||||
}
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||||
|
||||
#rectangle {
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||||
text-align: center;
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||||
font-weight: bold;
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||||
}
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||||
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||||
#loadingBar {
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||||
position:absolute;
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||||
top:1px;
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||||
left:1px;
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||||
width: 94%;
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||||
height: 93%;
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||||
background-color:rgba(200,200,200,0.8);
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||||
-webkit-transition: all 0.5s ease;
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||||
-moz-transition: all 0.5s ease;
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||||
-ms-transition: all 0.5s ease;
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||||
-o-transition: all 0.5s ease;
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||||
transition: all 0.5s ease;
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||||
opacity:1;
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||||
}
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||||
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||||
#wrapper {
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||||
position:relative;
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||||
width:900px;
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||||
height:900px;
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||||
}
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||||
|
||||
#text {
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position:absolute;
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top:8px;
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left:530px;
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width:30px;
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height:50px;
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margin:auto auto auto auto;
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font-size:22px;
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color: #000000;
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}
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||||
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div.outerBorder {
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position:relative;
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top:400px;
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width:600px;
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height:44px;
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margin:auto auto auto auto;
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border:8px solid rgba(0,0,0,0.1);
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background: rgb(252,252,252); /* Old browsers */
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background: -moz-linear-gradient(top, rgba(252,252,252,1) 0%, rgba(237,237,237,1) 100%); /* FF3.6+ */
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background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,rgba(252,252,252,1)), color-stop(100%,rgba(237,237,237,1))); /* Chrome,Safari4+ */
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background: -webkit-linear-gradient(top, rgba(252,252,252,1) 0%,rgba(237,237,237,1) 100%); /* Chrome10+,Safari5.1+ */
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background: -o-linear-gradient(top, rgba(252,252,252,1) 0%,rgba(237,237,237,1) 100%); /* Opera 11.10+ */
|
||||
background: -ms-linear-gradient(top, rgba(252,252,252,1) 0%,rgba(237,237,237,1) 100%); /* IE10+ */
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background: linear-gradient(to bottom, rgba(252,252,252,1) 0%,rgba(237,237,237,1) 100%); /* W3C */
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filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#fcfcfc', endColorstr='#ededed',GradientType=0 ); /* IE6-9 */
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border-radius:72px;
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box-shadow: 0px 0px 10px rgba(0,0,0,0.2);
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}
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|
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#border {
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||||
position:absolute;
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top:10px;
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left:10px;
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width:500px;
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height:23px;
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margin:auto auto auto auto;
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box-shadow: 0px 0px 4px rgba(0,0,0,0.2);
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border-radius:10px;
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||||
}
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||||
|
||||
#bar {
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||||
position:absolute;
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||||
top:0px;
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left:0px;
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||||
width:20px;
|
||||
height:20px;
|
||||
margin:auto auto auto auto;
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||||
border-radius:11px;
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||||
border:2px solid rgba(30,30,30,0.05);
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||||
background: rgb(0, 173, 246); /* Old browsers */
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||||
box-shadow: 2px 0px 4px rgba(0,0,0,0.4);
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||||
}
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||||
|
||||
html {
|
||||
height: 100%;
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||||
}
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||||
|
||||
body {
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||||
height: 90%;
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||||
}
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||||
|
||||
/* The switch - the box around the slider */
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||||
.switch {
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||||
position: relative;
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||||
display: inline-block;
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width: 60px;
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||||
height: 34px;
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||||
}
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||||
|
||||
/* Hide default HTML checkbox */
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||||
.switch input {
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||||
opacity: 0;
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||||
width: 0;
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||||
height: 0;
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||||
}
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||||
|
||||
/* The slider */
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||||
.slider {
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||||
position: absolute;
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||||
cursor: pointer;
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||||
top: 0;
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||||
left: 0;
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||||
right: 0;
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||||
bottom: 0;
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||||
background-color: #ccc;
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||||
-webkit-transition: .4s;
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transition: .4s;
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||||
}
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||||
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||||
.slider:before {
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||||
position: absolute;
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||||
content: "";
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||||
height: 26px;
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||||
width: 26px;
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||||
left: 4px;
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||||
bottom: 4px;
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||||
background-color: white;
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||||
-webkit-transition: .4s;
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||||
transition: .4s;
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||||
}
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||||
|
||||
input:checked + .slider {
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||||
background-color: #2196F3;
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||||
}
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||||
|
||||
input:focus + .slider {
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||||
box-shadow: 0 0 1px #2196F3;
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||||
}
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||||
|
||||
input:checked + .slider:before {
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||||
-webkit-transform: translateX(26px);
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||||
-ms-transform: translateX(26px);
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transform: translateX(26px);
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||||
}
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||||
|
||||
/* Rounded sliders */
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||||
.slider.round {
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||||
border-radius: 34px;
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||||
}
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||||
|
||||
.slider.round:before {
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||||
border-radius: 50%;
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||||
}
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||||
|
||||
aside {
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||||
float: right;
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||||
width: 5%;
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||||
}
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||||
|
||||
table {
|
||||
border-collapse: collapse;
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||||
}
|
||||
|
||||
td.switch_td {
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||||
padding-bottom: 6px;
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||||
}
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||||
|
||||
.switch_button {
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||||
border-bottom: 2px solid black;
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}
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@@ -0,0 +1,462 @@
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<%!
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import collections
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import json
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import sys
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from numpy import inf
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%>
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<%
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def to_counter(state, ordering):
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"""
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Transforms given state to Counter using given ordering
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:param state: str representation of state
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:param ordering: enumeration of agents
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:return: Counter representing the state
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"""
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state = eval(state)
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if state[0] == inf:
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return inf
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return +collections.Counter({ordering[i]: state[i] for i in range(len(ordering))})
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def node_to_string(node):
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"""
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Creates string representation of Counter of agents.
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:param node: given Counter of agents.
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:return: string representation of Counter
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"""
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if node == inf:
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return "inf"
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return "<br>".join([str(int(v)) + " " + str(k) for k, v in node.items()])
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|
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|
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def side_to_string(side):
|
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"""
|
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Another string representation of Counter, this time used as side in reaction
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:param side: given Counter
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:return: string representation of Counter
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||||
"""
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if side == inf:
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return "inf"
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return " + ".join([str(int(v)) + " " + str(k) for k, v in side.items()])
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def create_sides(lhs, rhs):
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"""
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From given substrates and products counters creates their mutual differences
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:param lhs: dict of substrates
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:param rhs: dict of products
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:return: two counters representing differences
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"""
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if lhs == inf:
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return inf, inf
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if rhs == inf:
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return collections.Counter(), inf
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left = lhs - rhs
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right = rhs - lhs
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return left, right
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|
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|
||||
def write_node(ID, label, node_class):
|
||||
"""
|
||||
Creates string representation of a node
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||||
|
||||
:param ID: ID of given node
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:param label: enumeration of agents
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:return: string representation
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||||
"""
|
||||
if label == "inf":
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||||
node_class = "hell"
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||||
return "\t\t{{id: {0}, label: '{0}', class: '{2}', shape: 'ellipse', title: '{0}', text: '{1}'}},\n".format(
|
||||
ID, label, node_class)
|
||||
|
||||
|
||||
def write_reaction(edge_id, left_index, right_index, substrates, products, rate, label):
|
||||
"""
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||||
Creates string representation of a reaction
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||||
|
||||
:param edge_id: ID of given reaction
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:param left_index: ID of FROM node
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||||
:param right_index: ID of TO node
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||||
:param substrates: enumeration of substrates
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||||
:param products: enumeration of products
|
||||
:param rate: rate of the reaction (if any)
|
||||
:param label: used rule label
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||||
:return: string representation
|
||||
"""
|
||||
rate = " @ " + str(rate) if rate else ""
|
||||
label = label + " ~ " if label else ""
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||||
return "\t\t{{id: {}, from: {}, to: {}, arrows: 'to', text: '{}{} => {}{}'}},\n".format(
|
||||
edge_id, left_index, right_index, label, side_to_string(substrates), side_to_string(products), rate)
|
||||
|
||||
|
||||
def create_HTML_graph(): #data):
|
||||
output_file = firstpart
|
||||
|
||||
data = ''.join(list(hda.datatype.dataprovider(hda, 'line', strip_lines=True, strip_newlines=True)))
|
||||
data = json.loads(data)
|
||||
|
||||
# data = json.load(data)
|
||||
|
||||
ordering = data['ordering']
|
||||
nodes = {int(key): to_counter(data['nodes'][key], ordering) for key in data['nodes'].keys()}
|
||||
|
||||
border_nodes = set()
|
||||
|
||||
edges = []
|
||||
self_loops = []
|
||||
for edge_id, edge in enumerate(data['edges'], 1):
|
||||
substrates, products = create_sides(nodes[edge['s']], nodes[edge['t']])
|
||||
if edge['s'] == edge['t']:
|
||||
self_loops.append((edge_id, edge['s'], edge['t'], substrates,
|
||||
products, edge.get('p', None), edge.get('label', None)))
|
||||
edges.append((edge_id, edge['s'], edge['t'], substrates, products,
|
||||
edge.get('p', None), edge.get('label', None)))
|
||||
if products == inf and substrates != inf:
|
||||
border_nodes.add(edge['s'])
|
||||
|
||||
border_nodes_write = []
|
||||
for id, state in nodes.items():
|
||||
if id in border_nodes:
|
||||
node_class = "border"
|
||||
border_nodes_write.append((id, node_to_string(state), node_class))
|
||||
else:
|
||||
node_class = "default"
|
||||
output_file += write_node(id, node_to_string(state), node_class)
|
||||
|
||||
output_file += mid_1
|
||||
|
||||
for node in border_nodes_write:
|
||||
output_file += write_node(*node)
|
||||
|
||||
output_file += mid_2
|
||||
|
||||
for edge in edges:
|
||||
output_file += write_reaction(*edge)
|
||||
|
||||
output_file += mid_3
|
||||
|
||||
for edge in self_loops:
|
||||
output_file += write_reaction(*edge)
|
||||
|
||||
initial = data['initial']
|
||||
|
||||
iterations = (len(nodes)//100+1) * 100
|
||||
step = iterations//100
|
||||
|
||||
output_file += secondpart_1_1
|
||||
output_file += stabil_physics.format(iterations, step)
|
||||
output_file += secondpart_1_2
|
||||
|
||||
output_file += "\tvar fromNode = " + str(int(initial)) + ";\n"
|
||||
|
||||
output_file += secondpart_2_1
|
||||
output_file += stabil_bar.format(iterations, step)
|
||||
output_file += secondpart_2_2
|
||||
return output_file
|
||||
|
||||
|
||||
firstpart = \
|
||||
'''<!doctype html>
|
||||
<html>
|
||||
<head>
|
||||
<title>TS network visualisation</title>
|
||||
|
||||
${h.javascript_link(app_root + "dist/vis.min.js")}
|
||||
# da sa to?
|
||||
${h.stylesheet_link(app_root + "dist/vis.min.css")}
|
||||
${h.stylesheet_link(app_root + "style.css")}
|
||||
|
||||
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/vis/4.21.0/vis.min.js"></script>
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/vis/4.21.0/vis.min.css" rel="stylesheet" type="text/css"/>
|
||||
|
||||
</style>
|
||||
</head>
|
||||
<body>
|
||||
|
||||
<div id="mynetwork"></div>
|
||||
|
||||
<aside>
|
||||
<table>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td>
|
||||
<img src="static/icons/border.png" alt="border states" style="display: block; width: 60px;">
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="switch_button">
|
||||
<td class="switch_td">
|
||||
<label class="switch">
|
||||
<input type="checkbox" name="check" id='border_nodes'>
|
||||
<span class="slider round"></span>
|
||||
</label>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>
|
||||
<img src="static/icons/loop.png" alt="self-loop" style="display: block; width: 60px;">
|
||||
</td>
|
||||
</tr>
|
||||
<tr class="switch_button">
|
||||
<td class="switch_td">
|
||||
<label class="switch">
|
||||
<input type="checkbox" name="check" id="loop_edges" checked>
|
||||
<span class="slider round"></span>
|
||||
</label>
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>
|
||||
<img src="static/icons/fire.png" alt="hell state" style="display: block; width: 60px;">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td class="switch_td">
|
||||
<label class="switch">
|
||||
<input type="checkbox" name="check" id="hell_node" checked>
|
||||
<span class="slider round"></span>
|
||||
</label>
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</aside>
|
||||
|
||||
<div id="rectangle"style="width:94%;border:1px solid #000;"> </div>
|
||||
<div id="loadingBar">
|
||||
<div class="outerBorder">
|
||||
<div id="text">0%</div>
|
||||
<div id="border">
|
||||
<div id="bar"></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<script type="text/javascript">
|
||||
setTimeout(function () {
|
||||
// create an array with nodes
|
||||
var nodes = new vis.DataSet([
|
||||
'''
|
||||
|
||||
|
||||
mid_1 = '''
|
||||
]);
|
||||
var border_nodes = [
|
||||
|
||||
'''
|
||||
|
||||
mid_2 = '''
|
||||
];
|
||||
|
||||
var edges = new vis.DataSet([
|
||||
|
||||
'''
|
||||
|
||||
mid_3 = '''
|
||||
]);
|
||||
|
||||
var self_loops = [
|
||||
'''
|
||||
|
||||
secondpart_1_1 = '''
|
||||
];
|
||||
|
||||
// create a network
|
||||
var container = document.getElementById('mynetwork');
|
||||
|
||||
var options = {
|
||||
layout: {improvedLayout: true},
|
||||
physics: {
|
||||
enabled: true,
|
||||
barnesHut: {
|
||||
gravitationalConstant: -25000,
|
||||
centralGravity: 0.5,
|
||||
springConstant: 0.5,
|
||||
springLength: 200,
|
||||
damping: 0.15
|
||||
},
|
||||
maxVelocity: 50,
|
||||
minVelocity: 7.5,
|
||||
solver: 'barnesHut',
|
||||
timestep: 0.5,
|
||||
stabilization: {
|
||||
enabled: true,
|
||||
'''
|
||||
|
||||
secondpart_1_2 = ''' },
|
||||
},
|
||||
nodes: {
|
||||
size: 15,
|
||||
font: {
|
||||
size: 20
|
||||
},
|
||||
borderWidth: 2,
|
||||
borderWidthSelected: 4,
|
||||
color:{highlight:{border: '#B20F0F', background: 'red'}}
|
||||
},
|
||||
edges: {
|
||||
width: 4,
|
||||
selectionWidth: function (width) {return width*2.5;},
|
||||
color:{color:'#2B7CE9', hover:'#2B7CE9', highlight: 'red'}
|
||||
},
|
||||
interaction: {
|
||||
navigationButtons: true,
|
||||
keyboard: true,
|
||||
hover: true,
|
||||
tooltipDelay: 500,
|
||||
multiselect: true
|
||||
}
|
||||
};
|
||||
|
||||
// data filters
|
||||
hell_filter = document.getElementById('hell_node')
|
||||
loops_filter = document.getElementById('loop_edges')
|
||||
border_filter = document.getElementById('border_nodes')
|
||||
|
||||
let noHell = false
|
||||
const nodesFilter = (node) => {
|
||||
if (noHell) {
|
||||
return (node.class != 'hell')
|
||||
} else {
|
||||
return true
|
||||
}
|
||||
}
|
||||
|
||||
var nodesView = new vis.DataView(nodes, { filter: nodesFilter })
|
||||
|
||||
// remove hell
|
||||
hell_filter.addEventListener('change', (e) => {
|
||||
if (hell_filter.checked){
|
||||
noHell = false
|
||||
} else {
|
||||
noHell = true
|
||||
}
|
||||
nodesView.refresh()
|
||||
});
|
||||
|
||||
data = {
|
||||
nodes: nodesView,
|
||||
edges: edges
|
||||
};
|
||||
|
||||
var network = new vis.Network(container, data, options);
|
||||
|
||||
loops_filter.addEventListener('change', (e) => {
|
||||
if (loops_filter.checked){
|
||||
for (index = 0; index < self_loops.length; index++) {
|
||||
edges.add(self_loops[index]);
|
||||
}
|
||||
} else {
|
||||
for (index = 0; index < self_loops.length; index++) {
|
||||
edges.remove({id: self_loops[index].id});
|
||||
}
|
||||
}
|
||||
});
|
||||
|
||||
border_filter.addEventListener('change', (e) => {
|
||||
if (border_filter.checked){
|
||||
for (index = 0; index < border_nodes.length; index++) {
|
||||
nodes.update({id: border_nodes[index].id, shape: "box"});
|
||||
}
|
||||
} else {
|
||||
for (index = 0; index < border_nodes.length; index++) {
|
||||
nodes.update({id: border_nodes[index].id, shape: "ellipse"});
|
||||
}
|
||||
}
|
||||
});
|
||||
|
||||
var stabil = true;
|
||||
'''
|
||||
|
||||
secondpart_2_1 = '''
|
||||
network.on("click", function (params) {
|
||||
params.event = "[original event]";
|
||||
var tmp = " ";
|
||||
|
||||
|
||||
for (var i = 1; i <= nodes.length; i++) {
|
||||
if (nodes.get(i).id == params.nodes) {
|
||||
tmp = nodes.get(i).text;
|
||||
};
|
||||
};
|
||||
|
||||
if(params.nodes.length === 0 && params.edges.length > 0) {
|
||||
for (var i = 1; i <= edges.length; i++) {
|
||||
if (edges.get(i).id == params.edges) {
|
||||
tmp = edges.get(i).text;
|
||||
};
|
||||
};
|
||||
};
|
||||
|
||||
document.getElementById('rectangle').innerHTML = '<div style="width:100%;height:100%;text-align:center;border:0px solid #000;">' + tmp + '</div>';
|
||||
});
|
||||
|
||||
network.on("stabilized", function (params) {
|
||||
if(stabil) {
|
||||
network.fit();
|
||||
stabil = false;
|
||||
};
|
||||
});
|
||||
|
||||
network.on("stabilizationProgress", function(params) {
|
||||
'''
|
||||
|
||||
secondpart_2_2 = '''
|
||||
var width = 5*(params.iterations/updateInterval);
|
||||
var widthFactor = params.iterations/iterations;
|
||||
|
||||
document.getElementById('bar').style.width = width + 'px';
|
||||
document.getElementById('text').innerHTML = Math.round(widthFactor*100) + '%';
|
||||
});
|
||||
|
||||
network.once("stabilizationIterationsDone", function() {
|
||||
document.getElementById('text').innerHTML = '100%';
|
||||
document.getElementById('bar').style.width = '496px';
|
||||
document.getElementById('loadingBar').style.opacity = 0;
|
||||
// really clean the dom element
|
||||
setTimeout(function () {document.getElementById('loadingBar').style.display = 'none';}, 0);
|
||||
});
|
||||
|
||||
clickedNode = nodes.get(fromNode);
|
||||
clickedNode.color = {
|
||||
border: 'orange',
|
||||
background: 'orange',
|
||||
highlight: {
|
||||
border: 'orange',
|
||||
background: 'orange'
|
||||
}
|
||||
}
|
||||
nodes.update(clickedNode);
|
||||
|
||||
network.on("doubleClick", function (params) {
|
||||
params.event = "[original event]";
|
||||
network.focus(params.nodes);
|
||||
});
|
||||
}, 5);
|
||||
</script>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
'''
|
||||
|
||||
stabil_physics = \
|
||||
''' iterations: {},
|
||||
updateInterval: {}
|
||||
'''
|
||||
|
||||
stabil_bar = \
|
||||
''' var iterations = {};
|
||||
var updateInterval = {};
|
||||
'''
|
||||
|
||||
# for testing
|
||||
# filename = open('bigger_pMC.json', "r")
|
||||
# graph = create_HTML_graph(filename)
|
||||
|
||||
graph = create_HTML_graph()
|
||||
%>
|
||||
|
||||
${graph}
|
||||
Reference in New Issue
Block a user