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epiviz-data-source.html
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epiviz-data-source.html
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<!-- Polymer dependency -->
<link rel="import" href="../polymer/polymer-element.html">
<!-- Epiviz imports dependency -->
<link rel="import" href="../epiviz-imports/epiviz-common-js.html">
<!--
`<epiviz-data-source>` handles and manager server requests from other `<epiviz-elements>` on the page.
To use, add `<epiviz-data-source>` at the top of your body:
<epiviz-data-source></epiviz-data-source>
@demo demo/index.html Demo
-->
<dom-module id="epiviz-data-source">
<template>
<style>
/* local DOM styles go here */
</style>
</template>
<script>
// Extend Polymer.Element base class
class EpivizDataSource extends Polymer.Element {
static get is() { return 'epiviz-data-source'; }
static get properties() {
return {
/**
* Epiviz Proivder Type.
*
* Can be one of the possible values -
* `epiviz.data.WebServerDataProvider` | `epiviz.data.WebSocketDataProvider`
*
* @type {string}
*/
providerType: {
type: String,
notify: true
},
/**
* Unique ID assigned to this datasource
*
* @type {string}
*/
providerId: {
type: String,
notify: true
},
/**
* APi endpoint/URL location
*
* @type {string}
*/
providerUrl: {
type: String,
notify: true
// readOnly: true
},
measurements: {
type: Object,
notify: true
},
measurementSet: {
type: Object,
notify: true
},
seqInfos: {
type: Object,
notify: true
},
// not necessary just for testing
config: {
type: Object,
notify: true
},
dataManager: {
type: Object,
notify: true
}
}
}
// static get observers() {
// return [
// /* observer array just like 1.x */
// ]
// }
constructor() {
super();
}
connectedCallback() {
super.connectedCallback();
}
disconnectedCallback() {
super.connectedCallback();
}
ready() {
super.ready();
var settingsMap = {
configType: 'default',
// Navigation settings
zoominRatio: 0.8,
zoomoutRatio: 1.2,
navigationStepRatio: 0.2,
navigationDelay: 0,
// Data retrieval
dataServerLocation: '', //TODO: Fill in (in site-settings.js)
chartSaverLocation: 'src/chart_saving/save_svg.php',
dataProviders: [], //TODO: Fill in (in site-settings.js)
// This is the data provider that handles workspaces; it can be different from the one getting all the other data:
workspacesDataProvider: sprintf('epiviz.data.EmptyResponseDataProvider', 'empty', ''), //TODO: Fill in (in site-settings.js)
// For datasources with hierarchies, the cache must be disabled (Epiviz will crash otherwise)
useCache: true,
// Every n milliseconds, the cache will free up any data associated with parts of the genome not recently visited
cacheUpdateIntervalMilliseconds: 30000,
// For genes search box:
maxSearchResults: 12,
colorPalettes: [
new epiviz.ui.charts.ColorPalette(
['#025167', '#e7003e', '#ffcd00', '#057d9f', '#970026', '#ffe373', '#ff8100'],
'Epiviz v1.0 Colors', 'epiviz-v1'),
new epiviz.ui.charts.ColorPalette(
['#1859a9', '#ed2d2e', '#008c47', '#010101', '#f37d22', '#662c91', '#a11d20', '#b33893'],
'Epiviz v2.0 Bright', 'epiviz-v2-bright'),
new epiviz.ui.charts.ColorPalette(
['#b8d2eb', '#f2aeac', '#d8e4aa', '#cccccc', '#f2d1b0', '#d4b2d3', '#ddb8a9', '#ebbfd9'],
'Epiviz v2.0 Light', 'epiviz-v2-light'),
new epiviz.ui.charts.ColorPalette(
['#599ad3', '#f1595f', '#79c36a', '#727272', '#f9a65a', '#9e66ab', '#cd7058', '#d77fb3'],
'Epiviz v2.0 Medium', 'epiviz-v2-medium'),
new epiviz.ui.charts.ColorPalette(
["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"],
'D3 Category 10', 'd3-category10'),
new epiviz.ui.charts.ColorPalette(
["#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", "#2ca02c", "#98df8a", "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", "#c49c94", "#e377c2", "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", "#17becf", "#9edae5"],
'D3 Category 20', 'd3-category20'),
new epiviz.ui.charts.ColorPalette(
["#393b79", "#5254a3", "#6b6ecf", "#9c9ede", "#637939", "#8ca252", "#b5cf6b", "#cedb9c", "#8c6d31", "#bd9e39", "#e7ba52", "#e7cb94", "#843c39", "#ad494a", "#d6616b", "#e7969c", "#7b4173", "#a55194", "#ce6dbd", "#de9ed6"],
'D3 Category 20b', 'd3-category20b'),
new epiviz.ui.charts.ColorPalette(
["#3182bd", "#6baed6", "#9ecae1", "#c6dbef", "#e6550d", "#fd8d3c", "#fdae6b", "#fdd0a2", "#31a354", "#74c476", "#a1d99b", "#c7e9c0", "#756bb1", "#9e9ac8", "#bcbddc", "#dadaeb", "#636363", "#969696", "#bdbdbd", "#d9d9d9"],
'D3 Category 20c', 'd3-category20c'),
new epiviz.ui.charts.ColorPalette(
['#f9a65a', '#599ad3', '#79c36a', '#f1595f', '#727272', '#cd7058', '#d77fb3'],
'Genes Default', 'genes-default'),
new epiviz.ui.charts.ColorPalette(
['#1859a9', '#ed2d2e', '#008c47', '#010101', '#f37d22', '#662c91', '#a11d20', '#b33893'],
'Heatmap Default', 'heatmap-default')
],
chartSettings: {
default: {
colors: 'd3-category10',
decorations: [
'epiviz.ui.charts.decoration.RemoveChartButton',
'epiviz.ui.charts.decoration.SaveChartButton',
'epiviz.ui.charts.decoration.CustomSettingsButton',
'epiviz.ui.charts.decoration.EditCodeButton',
'epiviz.ui.charts.decoration.ChartColorsButton',
'epiviz.ui.charts.decoration.ChartLoaderAnimation',
'epiviz.ui.charts.decoration.ChartResize'
]
},
plot: {
width: 400,
height: 400,
margins: new epiviz.ui.charts.Margins(15, 30, 30, 15),
decorations: [
'epiviz.ui.charts.decoration.ToggleTooltipButton',
'epiviz.ui.charts.decoration.ChartTooltip',
'epiviz.ui.charts.decoration.ChartFilterCodeButton'
]
},
track: {
width: '100%',
height: 90,
margins: new epiviz.ui.charts.Margins(25, 20, 23, 10),
decorations: [
'epiviz.ui.charts.decoration.ToggleTooltipButton',
'epiviz.ui.charts.decoration.ChartTooltip',
'epiviz.ui.charts.decoration.ChartFilterCodeButton'
]
},
'data-structure': {
width: 800,
height: 300,
margins: new epiviz.ui.charts.Margins(20, 10, 10, 10),
colors: 'd3-category20',
decorations: [
'epiviz.ui.charts.tree.decoration.TogglePropagateSelectionButton',
'epiviz.ui.charts.decoration.HierarchyFilterCodeButton'
]
},
'epiviz.plugins.charts.GenesTrack': {
height: 120,
colors: 'genes-default'
},
'epiviz.plugins.charts.LineTrack': {
colors: 'epiviz-v2-bright',
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByMeasurementsCodeButton'
]
},
'epiviz.plugins.charts.StackedLineTrack': {
height: 300
},
'epiviz.plugins.charts.ScatterPlot': {
margins: new epiviz.ui.charts.Margins(15, 50, 50, 15),
decorations: [
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton'
]
},
'epiviz.plugins.charts.HeatmapPlot': {
width: 800,
height: 400,
margins: new epiviz.ui.charts.Margins(80, 120, 40, 40),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton'
],
colors: 'heatmap-default'
},
'epiviz.plugins.charts.LinePlot': {
width: 800,
height: 400,
margins: new epiviz.ui.charts.Margins(30, 30, 50, 15),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton'
],
colors: 'd3-category20b'
},
'epiviz.plugins.charts.StackedLinePlot': {
width: 800,
height: 400,
margins: new epiviz.ui.charts.Margins(30, 30, 50, 15),
decorations: [
'epiviz.ui.charts.decoration.ChartGroupByMeasurementsCodeButton',
'epiviz.ui.charts.decoration.ChartColorByRowCodeButton',
'epiviz.ui.charts.decoration.ChartOrderByMeasurementsCodeButton'
],
colors: 'd3-category20b'
}
},
chartCustomSettings: {
'epiviz.plugins.charts.BlocksTrack': {
minBlockDistance: 3,
useColorBy: false,
blockColorBy: 'label'
},
'epiviz.plugins.charts.GenesTrack': {
},
'epiviz.plugins.charts.LineTrack': {
step: 1,
showPoints: false,
showLines: true,
pointRadius: 1,
lineThickness: 2
},
'epiviz.plugins.charts.ScatterPlot': {
circleRadiusRatio: 0.01
},
'epiviz.plugins.charts.HeatmapPlot': {
colLabel: 'label',
maxColumns: 120,
clusteringAlg: 'agglomerative'
},
'epiviz.plugins.charts.StackedLinePlot': {
colLabel: 'label'
}
},
};
epiviz.Config.SETTINGS.dataProviders = [[this.providerType, this.providerId, this.providerUrl]];
var config = new epiviz.Config(settingsMap);
config.dataProviders = [];
config.dataProviders.push([this.providerType, this.providerId, this.providerUrl]);
/** @type {epiviz.data.DataProviderFactory} */
var dataProviderFactory = new epiviz.data.DataProviderFactory(config);
/** @type {epiviz.data.DataManager} */
var dataManager = new epiviz.data.DataManager(config, dataProviderFactory);
this.config = config;
this.dataProviderFactory = dataProviderFactory;
this.dataManager = dataManager;
var self = this;
this.dataManager.getMeasurements(function (result) {
self.measurements = result.raw();
self.measurementSet = result;
});
this.dataManager.getSeqInfos(function (result) {
self.seqInfos = result;
});
}
}
customElements.define(EpivizDataSource.is, EpivizDataSource);
</script>
</dom-module>