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intoroduce webpack fix alignment fix css issues, sync dependecies versions
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config/plugins/visualizations/chiraviz/config/chiraviz.xml
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<?xml version="1.0" encoding="UTF-8"?> | ||
<!DOCTYPE visualization SYSTEM "../../visualization.dtd"> | ||
<visualization name="ChiRAViz"> | ||
<description>ChiRAViz</description> | ||
<data_sources> | ||
<data_source> | ||
<model_class>HistoryDatasetAssociation</model_class> | ||
<test type="isinstance" test_attr="datatype" result_type="datatype">binary.ChiraSQLite</test> | ||
<to_param param_attr="id">dataset_id</to_param> | ||
</data_source> | ||
</data_sources> | ||
<params> | ||
<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> | ||
</params> | ||
<template>chiraviz.mako</template> | ||
</visualization> |
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{ | ||
"devDependencies": { | ||
"copy-webpack-plugin": "^5.1.1", | ||
"css-loader": "^3.4.2", | ||
"file": "^0.2.2", | ||
"file-loader": "^5.0.2", | ||
"mini-css-extract-plugin": "^0.9.0", | ||
"script-loader": "^0.7.2", | ||
"system": "^2.0.1", | ||
"url-loader": "^4.0.0", | ||
"webpack": "^4.42.1", | ||
"webpack-cli": "^3.3.11" | ||
}, | ||
"dependencies": { | ||
"bootstrap": "3.3.7", | ||
"font-awesome": "^4.7.0", | ||
"jquery": "3.2.1", | ||
"plotly.js": "^1.52.3", | ||
"underscore": "1.8.3" | ||
}, | ||
"name": "galaxy-chiraviz", | ||
"version": "1.1.0", | ||
"main": "index.js", | ||
"license": "MIT", | ||
"scripts": { | ||
"build": "webpack --mode production" | ||
} | ||
} |
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config/plugins/visualizations/chiraviz/src/css/rna.viz.css
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html, body { | ||
height: 100%; | ||
width: 100%; | ||
} | ||
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.body-rna-viz { | ||
font-family: -apple-system,BlinkMacSystemFont,Segoe UI,Roboto,Helvetica Neue,Arial,sans-serif,Apple Color Emoji,Segoe UI Emoji,Segoe UI Symbol; | ||
font-size: 9pt; | ||
background-color: #f8f8f8; | ||
overflow: hidden; | ||
} | ||
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.samples-overlay { | ||
display: none; | ||
position: absolute; | ||
background-color: rgba(0, 0, 0, 0.2); | ||
left: 0; | ||
top: 0; | ||
width: 100%; | ||
height: 100%; | ||
z-index: 1; | ||
} | ||
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.samples-overlay > span { | ||
margin-left: 45%; | ||
} | ||
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.main-container { | ||
height: 100%; | ||
width: 100%; | ||
} | ||
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.row { | ||
margin: 0; | ||
} | ||
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.col-sm-1, .col-sm-2, .col-sm-3, .col-sm-4, | ||
.col-sm-5, .col-sm-6, .col-sm-7, .col-sm-8, | ||
.col-sm-9, .col-sm-10, .col-sm-11, .col-sm-12 { | ||
padding-left: 0px; | ||
} | ||
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.rna-header { | ||
background-color: #2c3143; | ||
color: white; | ||
padding-left: 2.5%; | ||
cursor: pointer; | ||
} | ||
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.rna-header-row { | ||
margin: 0 -7.9%; | ||
} | ||
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.one-sample { | ||
display: none; | ||
height: 100%; | ||
width: 100%; | ||
margin: 0 1% 0 1%; | ||
} | ||
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.top-row { | ||
height: 6%; | ||
width: 100%; | ||
margin-top: 0.5%; | ||
} | ||
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.filter-row { | ||
display: none; | ||
height: 4%; | ||
width: 100%; | ||
margin-top: 0.1%; | ||
} | ||
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.heading { | ||
margin-left: 5.5%; | ||
} | ||
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.elem-rna { | ||
font-size: 9pt; | ||
} | ||
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.rna-transcriptions-container { | ||
padding-left: 0; | ||
width: 16%; | ||
height: 100%; | ||
border-right: 1px solid black; | ||
overflow: auto; | ||
} | ||
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.landing-page { | ||
margin-top: 1%; | ||
border-top: 1px solid black; | ||
border-bottom: 1px solid black; | ||
background-color: white; | ||
height: 84%; | ||
width: 100%; | ||
overflow: auto; | ||
} | ||
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.rna-results { | ||
margin-top: 1%; | ||
border-top: 1px solid black; | ||
border-bottom: 1px solid black; | ||
background-color: white; | ||
height: 83%; | ||
width: 100%; | ||
display: none; | ||
} | ||
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.footer-row { | ||
height: 8%; | ||
width: 100%; | ||
display: none; | ||
} | ||
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.transcriptions-ids { | ||
overflow-y: auto; | ||
padding-top: 0.5%; | ||
height: 100%; | ||
font-size: 8pt; | ||
} | ||
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.sample-name { | ||
margin-top: 1%; | ||
font-weight: bold; | ||
} | ||
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.sample-current-size { | ||
font-size: 8pt; | ||
} | ||
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.common-genes { | ||
display: none; | ||
height: 50%; | ||
width: 84%; | ||
overflow: auto; | ||
border-bottom: 1px solid black; | ||
} | ||
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.first-gene { | ||
height: 50%; | ||
width: 42%; | ||
border-right: 1px solid black; | ||
overflow: auto; | ||
display: none; | ||
} | ||
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.second-gene { | ||
height: 50%; | ||
width: 42%; | ||
overflow: auto; | ||
display: none; | ||
} | ||
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.both-genes { | ||
display: none; | ||
height: 100%; | ||
width: 84%; | ||
} | ||
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.selected-item { | ||
background-color: #5cb85c; | ||
font-weight: bold; | ||
} | ||
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.btn-rna { | ||
margin: 0.5% 0 0 0.3%; | ||
} | ||
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.interaction-header { | ||
margin: 0.5% 0 0 1%; | ||
background-color: #f8f8f8; | ||
font-weight: bold; | ||
height: 3%; | ||
} | ||
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.interaction-header a { | ||
margin-left: 1%; | ||
font-weight: normal; | ||
color: black; | ||
} | ||
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.single-interactions-info { | ||
padding-top: 0.5%; | ||
display: inline-block; | ||
width: 49%; | ||
height: 50%; | ||
overflow: auto; | ||
} | ||
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#info-gene1 { | ||
margin: 0 1% 0 1%; | ||
overflow: hidden; | ||
} | ||
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#info-gene2 { | ||
border-left: 1px solid black; | ||
padding-left: 1%; | ||
overflow: hidden; | ||
} | ||
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.alignment-canvas { | ||
margin-left: 5%; | ||
} | ||
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#rna-alignment-graphics1 p, #rna-alignment-graphics2 p { | ||
margin-left: 10%; | ||
font-size: 13pt; | ||
} | ||
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#rna-alignment-graphics1 svg, #rna-alignment-graphics2 svg { | ||
margin-top: 3%; | ||
} | ||
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.rna-footer { | ||
margin-left: 45%; | ||
} | ||
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.rna-footer a { | ||
color: black; | ||
} | ||
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.symbol-link { | ||
cursor: pointer; | ||
} | ||
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.search-input { | ||
position: relative; | ||
} | ||
.search-input input { | ||
border: none; | ||
background: #fff; | ||
display: block; | ||
width: 100%; | ||
box-sizing: border-box; | ||
} | ||
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.search-input img { | ||
position: absolute; | ||
width: 10%; | ||
top: 7px; | ||
right: 20px; | ||
cursor: pointer; | ||
} | ||
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.chkbx-interaction { | ||
margin: 1%; | ||
} | ||
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.plus-icon { | ||
vertical-align: text-bottom; | ||
margin: 1%; | ||
width: 8%; | ||
cursor: pointer; | ||
} | ||
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.rna-pair-interaction { | ||
vertical-align: text-bottom; | ||
margin: 1%; | ||
} | ||
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.symbols-records { | ||
padding-left: 10%; | ||
} | ||
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.sym-record { | ||
border-bottom: 1px black solid; | ||
width: max-content; | ||
cursor: pointer; | ||
} | ||
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.check-all-interactions span { | ||
vertical-align: text-bottom; | ||
padding: 0.5%; | ||
} | ||
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.mfe-info { | ||
margin-left: 1%; | ||
} |
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import 'script-loader!jquery' | ||
import 'script-loader!./js/rna-viz' | ||
import 'script-loader!underscore/underscore-min' | ||
import 'script-loader!plotly.js/dist/plotly.min' | ||
import 'script-loader!./js/visualize-alignment' | ||
import 'script-loader!bootstrap/dist/js/bootstrap.min'; | ||
import 'bootstrap/dist/css/bootstrap.min.css'; | ||
import 'font-awesome/css/font-awesome.min.css'; | ||
import './css/rna.viz.css' |
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