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chart-data-behavior.html
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chart-data-behavior.html
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<script>
/**
* `ChartDataBehavior` object manages data requests.
* `<epiviz-environment>` & `<epiviz-navigation>` inherit this behavior to get/update chart data.
*
* @polymerBehavior
**/
EpivizChartDataBehavior = function (superClass) {
return class extends superClass {
constructor() {
super();
var self = this;
var settingsMap = {
configType: 'default',
dataProviders: [],
workspacesDataProvider: sprintf(
"epiviz.data.EmptyResponseDataProvider",
"empty",
""
),
useCache: true,
colorPalettes: [],
maxSearchResults: 12
}
// var dataManagerElem = document.querySelector("epiviz-app").shadowRoot.querySelectorAll('epiviz-data-source');
var dataManagerElem = document.querySelectorAll('epiviz-data-source');
if (dataManagerElem && dataManagerElem.length > 0) {
dataManagerElem.forEach(function (ds) {
settingsMap.dataProviders.push([ds.providerType, ds.providerId, ds.providerUrl]);
});
var config = new epiviz.Config(settingsMap);
var dataProviderFactory = new epiviz.data.DataProviderFactory(config);
this.dataManager = new epiviz.data.DataManager(config, dataProviderFactory);
this.dataManager.getMeasurements(function (result) {
var measurements = result.raw();
self.measurementsSet = result;
if (measurements) {
var mArray = measurements;
var measurementsObj = {}
mArray.forEach(function (m) {
measurementsObj[m.id] = m
});
self.measurementSet = measurementsObj;
self.measurementAll = result;
}
}, function (jqXHR, textStatus, errorThrown) {
// var toast = document.createElement("paper-toast");
// toast.setAttribute("text", textStatus + " - " + errorThrown);
// toast.setAttribute("openned", true);
// self.shadowRoot.appendChild(toast);
// toast.show();
});
}
}
static get properties() {
return {
/**
* Whether to apply a data transformation function
*
* @type {boolean}
*/
transformData: {
type: Boolean,
notify: true,
value: false
},
/**
* Data Transformation function
*
* @type {string}
*/
transformDataFunc: {
type: String,
notify: true
}
};
}
static get observers() {
return ['_barChanged(bar.*)'];
}
/**
* Formats an epiviz data object into json.
* output data format
* {
* columns: Collection <Object> {measurement-id: <Epiviz measurement>}
* values : Array [measurement-id: Val <Integer>, row: rowInfo]
* }
*
* @param {Object} data data object `epiviz.datatypes.*`
*
* @return {Object} transformed data object
*/
epivizToJSON(data) {
if (!this.transformData) {
return data;
}
var fromDataMeasurements = [];
var range = this.range;
var firstGlobalIndex = data.firstSeries().globalStartIndex();
var lastGlobalIndex = data.firstSeries().globalEndIndex();
data.foreach(function (measurement, series) {
fromDataMeasurements.push(measurement);
var firstIndex = series.globalStartIndex();
var lastIndex = series.globalEndIndex();
if (firstIndex > firstGlobalIndex) { firstGlobalIndex = firstIndex; }
if (lastIndex < lastGlobalIndex) { lastGlobalIndex = lastIndex; }
});
var nItems = lastGlobalIndex - firstGlobalIndex;
var i, index;
var grid = {};
grid.measurements = fromDataMeasurements;
grid.columns = {};
grid.measurements.forEach(function (m) {
grid.columns[m.datasourceId() + "-" + m.id()] = m;
});
grid.values = [];
var nSeries = fromDataMeasurements.length;
for (i = 0; i < nItems; ++i) {
index = i + firstGlobalIndex;
var valArray = {};
var row = {};
var rowData = data.getSeries(fromDataMeasurements[0]).getRowByGlobalIndex(index);
row.start = rowData.start();
row.end = rowData.end();
row.metadata = rowData.rowMetadata();
row.strand = rowData.strand();
row.index = rowData.index();
row.globalIndex = rowData.globalIndex();
row.id = rowData.id();
row.seqName = rowData.seqName();
valArray.row = row;
grid.measurements.forEach(function (m) {
var cellX = data.getSeries(m).getByGlobalIndex(index);
valArray[m.datasourceId() + "-" + m.id()] = cellX.value;
});
grid.values.push(valArray);
}
return grid;
}
/**
* Handles search requests for gene names /probeid
*
* @param {string} gene keyword to search for genes
* @param {HTMLElement} currentChild child HTML element where request was created
* @param {HTMLElement} pDom parent HTML element of the child
* @callback cb
* @param {cb} cb Callback that handles the response
*/
_getElementSearch(gene, currentChild, pDom, cb) {
if (this.dataManager) {
this.dataManager.search(function (data) {
if (pDom) {
data.forEach(function (item) {
item.value = item.gene + " - " + item.chr + " : " + item.start + " - " + item.end;
});
pDom.shadowRoot.querySelector("#geneSearch").items = data;
}
else {
cb(data);
}
}, gene, currentChild.range);
}
}
/**
* Handles gene in range requests.
* Given a genomic region, get the gene close to the center.
*
* @param {HTMLElement} currentChild child HTML element where request was created
* @param {HTMLElement} pDom parent HTML element of the child
*/
_getGenesInRange(currentChild, pDom) {
var self = this;
var mSet = new epiviz.measurements.MeasurementSet();
var m = new epiviz.measurements.Measurement(
"genes",
"Genes",
"range",
"genes",
"genes",
"umd",
null,
"Genes Track",
null,
null,
null,
["gene", "exon_starts", "exon_ends"]
)
mSet.add(m);
var chartMeasMap = {};
chartMeasMap[currentChild.plotId] = mSet;
if (this.dataManager) {
this.dataManager.getData(currentChild.range, chartMeasMap, function (id, data) {
// Get gene (based on size)
// var index = data.globalStartIndex(m) + Math.round((data.size(m) - 1) / 2);
var nItems = data.firstSeries().globalEndIndex() - data.firstSeries().globalStartIndex();
if (nItems == 0) {
var toast = document.createElement("paper-toast");
toast.setAttribute("text", currentChild.nodeName.toLowerCase() + ": query return empty - choose a different genomic region");
// toast.setAttribute("openned", true);
// self.shadowRoot.appendChild(toast);
// toast.show();
}
// Get gene (based on position)
var searchIndex = data.binarySearchStarts(m, new epiviz.datatypes.GenomicRange(pDom.range.seqName(), (pDom.range.start() + pDom.range.end()) / 2, 1000000));
var index = data.globalStartIndex(m) + searchIndex.index;
if (data.getRowByGlobalIndex(m, index)) {
var gene = data.getRowByGlobalIndex(m, index).rowMetadata().gene;
pDom.geneInRange = gene;
}
},
function (jqXHR, textStatus, errorThrown) {
// var toast = document.createElement("paper-toast");
// toast.setAttribute("text", textStatus + " - " + errorThrown);
// toast.setAttribute("openned", true);
// self.shadowRoot.appendChild(toast);
// toast.show();
});
}
}
/**
* Handles SeqInfo requests
*
* @param {HTMLElement} currentChild child HTML element where request was created
* @param {HTMLElement} pDom parent HTML element of the child
*/
_getElementSeqInfo(currentChild, pDom) {
var self = this;
if (this.dataManager) {
this.dataManager.getSeqInfos(function (data) {
// data = [{seqName: "chrI" , min: 1, max: 230218}, {seqName: "chrII" , min: 1, max: 813184}, {seqName: "chrIII" , min: 1, max: 316620}, {seqName: "chrIV" , min: 1, max: 1531933}, {seqName: "chrIX" , min: 1, max: 439888}, {seqName: "chrM" , min: 1, max: 85779}, {seqName: "chrV" , min: 1, max: 576874}, {seqName: "chrVI" , min: 1, max: 270161}, {seqName: "chrVII" , min: 1, max: 1090940}, {seqName: "chrX" , min: 1, max: 745751}, {seqName: "chrXI" , min: 1, max: 666816}, {seqName: "chrXII" , min: 1, max: 1078177}, {seqName: "chrXIII" , min: 1, max: 924431}, {seqName: "chrXIV" , min: 1, max: 784333}, {seqName: "chrXV" , min: 1, max: 1091291}, {seqName: "chrXVI" , min: 1, max: 948066}]
var seqinfo = {};
var genomes = {};
data.forEach(function (s) {
seqinfo[s.seqName] = s;
genomes[s.genome] = s;
});
currentChild.seqInfo = seqinfo;
currentChild.genomes = genomes;
currentChild.set("genomes", genomes)
if (!(currentChild.start && currentChild.end)) {
if (currentChild.chr && currentChild.seqInfo) {
currentChild.start = 0;
currentChild.end = currentChild.seqInfo[currentChild.chr].max;
}
}
},
function (jqXHR, textStatus, errorThrown) {
// var toast = document.createElement("paper-toast");
// toast.setAttribute("text", textStatus + " - " + errorThrown);
// toast.setAttribute("openned", true);
// self.shadowRoot.appendChild(toast);
// toast.show();
});
}
}
/**
* Handles data requests
*
* @param {HTMLElement} currentChild child HTML element where request was created
* @param {HTMLElement} pDom parent HTML element of the child
* @param {Array<string>} measurements measurements to request data
*/
_getElementData(currentChild, pDom, measurements) {
var self = this;
if (self.dataManager != null) {
var dims = currentChild.dimS || currentChild.getAttribute("dim-s");
if (typeof (dims) == "string") {
dims = JSON.parse(dims);
}
// if (!measurements) {
// var mArray = document.querySelector("epiviz-data-source").measurements;
// measurements = {}
// mArray.forEach(function(m) {
// measurements[m.id] = m
// });
// self.measurements = measurements;
// }
// var id = self._generateChartId();
var mSet = new epiviz.measurements.MeasurementSet();
var tMeasurements = [];
if (dims != null && dims.length > 0) {
for (var idim = 0; idim < dims.length; idim++) {
var mtdx = measurements[dims[idim]];
mSet.add(new epiviz.measurements.Measurement(
mtdx.id,
mtdx.name,
mtdx.type,
mtdx.datasourceId,
mtdx.datasourceGroup,
mtdx.dataprovider,
mtdx.formula,
mtdx.defaultChartType,
mtdx.annotation,
mtdx.minValue,
mtdx.maxValue,
mtdx.metadata
));
tMeasurements.push(mtdx);
}
}
else if (currentChild.measurements != null && currentChild.measurements.length > 0) {
for (var idim = 0; idim < currentChild.measurements.length; idim++) {
var mtdx = currentChild.measurements[idim];
mSet.add(new epiviz.measurements.Measurement(
mtdx.id,
mtdx.name,
mtdx.type,
mtdx.datasourceId,
mtdx.datasourceGroup,
mtdx.dataprovider,
mtdx.formula,
mtdx.defaultChartType,
mtdx.annotation,
mtdx.minValue,
mtdx.maxValue,
mtdx.metadata
));
tMeasurements.push(mtdx);
}
}
var id = currentChild.plotId;
if (tMeasurements.length != 0) {
currentChild.range = currentChild.range || self.range || pDom.range;
if (!currentChild.measurements) {
// currentChild.measurements = tMeasurements;
currentChild.set("measurements", tMeasurements);
}
var chartMeasMap = {};
chartMeasMap[id] = mSet;
self.dataManager.getData(currentChild.range, chartMeasMap, function (id, data) {
if (data.measurements().length > 0) {
var nItems = data.firstSeries().globalEndIndex() - data.firstSeries().globalStartIndex();
// if (nItems == 0) {
// // var toast = document.createElement("paper-toast");
// // toast.setAttribute("text", currentChild.nodeName.toLowerCase() + ": query return empty - choose a different genomic region");
// // toast.setAttribute("openned", true);
// // self.shadowRoot.appendChild(toast);
// // toast.show();
// }
var dataChartElem = pDom.querySelector('[plot-id$="' + id + '"]') || Polymer.dom(pDom).querySelector('[plot-id$="' + id + '"]');
if (dataChartElem) {
var tdata = pDom.transformFunc(data);
if (["interaction", "gwas_pip", "gwas", "blocks", "stacked-blocks"].includes(dataChartElem.chartType.chartHtmlAttributeName())) {
var msFlag = false;
data.foreach(function (m, series, i) {
if (series.getRow(0)) {
var metadataFromData = Object.keys(series.getRow(0).rowMetadata());
var ms = dataChartElem.chart._properties.visConfigSelection.measurements.get(i)
ms._metadata = metadataFromData;
msFlag = true;
}
});
if (msFlag) {
dataChartElem.chart._properties.customSettingsDefs = dataChartElem.chartType.customSettingsDefs();
// dataChartElem.chart._customSettingsValues = {};
for (var i = 0; i < dataChartElem.chart._properties.customSettingsDefs.length; ++i) {
var setting = dataChartElem.chart._properties.customSettingsDefs[i];
var val = dataChartElem.chart._customSettingsValues[setting.id];
switch (setting.type) {
case epiviz.ui.charts.CustomSetting.Type.MEASUREMENTS_METADATA:
var possibleValues = {};
dataChartElem.chart._properties.visConfigSelection.measurements.foreach(function (m) {
m.metadata().forEach(function (metadataCol) {
possibleValues[metadataCol] = metadataCol;
});
});
setting.possibleValues = Object.keys(possibleValues);
setting.possibleValues.sort();
val = val || setting.defaultValue;
dataChartElem.chart._customSettingsValues[setting.id] =
val in possibleValues
? val
: setting.possibleValues.length
? setting.possibleValues[0]
: "";
break;
case epiviz.ui.charts.CustomSetting.Type.MEASUREMENTS_ANNOTATION:
var possibleValues = { name: "name" };
dataChartElem.chart._properties.visConfigSelection.measurements.foreach(function (m) {
var anno = m.annotation();
if (!anno) {
return;
}
Object.keys(anno).forEach(function (key) {
possibleValues[key] = key;
});
});
setting.possibleValues = Object.keys(possibleValues);
setting.possibleValues.sort();
val = val || setting.defaultValue;
dataChartElem.chart._customSettingsValues[setting.id] =
val in possibleValues
? val
: setting.possibleValues.length
? setting.possibleValues[0]
: "";
break;
default:
dataChartElem.chart._customSettingsValues[setting.id] = val != null || val != undefined ? val : setting.defaultValue;
break;
}
}
}
}
// dataChartElem.data = pDom.transformFunc(data);
dataChartElem.set("data", tdata);
}
dataChartElem._onResize();
}
}, function (jqXHR, textStatus, errorThrown) {
// var toast = document.createElement("paper-toast");
// toast.setAttribute("text", textStatus + " - " + errorThrown);
// self.shadowRoot.appendChild(toast);
// toast.show();
});
// if (self._zoomIn != 0 && self._zoomIn % 2 == 0) {
// self._reupdateDataSet(mSet);
// // delete self.dataManager._cache._data[mtdx.datasourceGroup];
// }
}
}
}
// _reupdateDataSet(mlist) {
// var self = this;
// console.log("updating data in the background")
// var mset = new epiviz.measurements.MeasurementSet();
// mlist.foreach(function(m) {
// // if(m.datasourceId == "computed") {
// mset.add(m);
// delete self.dataManager._cache._data[m.datasourceGroup()];
// // }
// });
// var chartMeasMap = {};
// chartMeasMap["update"] = mset;
// self.dataManager.getData(self.range, chartMeasMap, function (id, data) {
// console.log("got data, do not have to assign to chart")
// console.log(data);
// }, function (jqXHR, textStatus, errorThrown) {
// console.log("error")
// });
// }
_reupdateAllData() {
var self = this;
console.log("updating data in the background")
var mlist = new epiviz.measurements.MeasurementSet();
for (var key in self.dataManager._cache._data) {
var tdata = self.dataManager._cache._data[key];
if (tdata._values._size > 0) {
mlist.add(tdata._values._order[0].key);
delete self.dataManager._cache._data[tdata._values._order[0].key._datasourceGroup];
}
// if(tdata._rowData._measurement._id == "computed") {
// tdata._rowData._measurement._type = "feature";
// mlist.add(tdata._rowData._measurement);
// delete self.dataManager._cache._data[tdata._rowData._measurement._datasourceGroup];
// }
}
var chartMeasMap = {};
chartMeasMap[self.plotId] = mlist;
self.dataManager.getData(self.range, chartMeasMap, function (id, data) {
console.log("got data, do not have to assign to chart")
console.log(data);
}, function (jqXHR, textStatus, errorThrown) {
console.log("error")
});
}
/**
* Handles data requests when dimensions are changed/updated.
*
* @param {string} cId plot-id of the chart to update.
*/
_updateChart(cId) {
if (cId == undefined) { return; }
var self = this;
var currentChild = Polymer.dom(self).querySelector('[plot-id$="' + cId + '"]');
var dims = currentChild.dimS || currentChild.getAttribute("dim-s");
$('#' + cId).empty();
if (typeof (dims) == "string") {
dims = JSON.parse(dims);
}
var mSet = new epiviz.measurements.MeasurementSet();
var tMeasurements = [];
if (dims != null && dims.length > 0) {
for (var idim = 0; idim < dims.length; idim++) {
var mtdx = self.measurements[dims[idim]];
mSet.add(new epiviz.measurements.Measurement(
mtdx.id,
mtdx.name,
mtdx.type,
mtdx.datasourceId,
mtdx.datasourceGroup,
mtdx.dataprovider,
mtdx.formula,
mtdx.defaultChartType,
mtdx.annotation,
mtdx.minValue,
mtdx.maxValue,
mtdx.metadata
));
tMeasurements.push(mtdx);
}
}
else if (currentChild.measurements != null && currentChild.measurements.length > 0) {
for (var idim = 0; idim < currentChild.measurements.length; idim++) {
var mtdx = currentChild.measurements[idim];
mSet.add(new epiviz.measurements.Measurement(
mtdx.id,
mtdx.name,
mtdx.type,
mtdx.datasourceId,
mtdx.datasourceGroup,
mtdx.dataprovider,
mtdx.formula,
mtdx.defaultChartType,
mtdx.annotation,
mtdx.minValue,
mtdx.maxValue,
mtdx.metadata
));
tMeasurements.push(mtdx);
}
}
if (tMeasurements.length != 0) {
currentChild.range = currentChild.range || self.range;
currentChild.measurements = tMeasurements;
var chartMeasMap = {};
chartMeasMap[cId] = mSet;
if (self.dataManager) {
self.dataManager.getData(currentChild.range, chartMeasMap, function (id, data) {
var nItems = data.firstSeries().globalEndIndex() - data.firstSeries().globalStartIndex();
// if (nItems == 0) {
// // var toast = document.createElement("paper-toast");
// // toast.setAttribute("text", currentChild.nodeName.toLowerCase() + ": Query return empty - choose a different genomic region");
// // self.shadowRoot.appendChild(toast);
// // toast.show();
// }
var dataChartElem = Polymer.dom(self).querySelector('[plot-id$="' + id + '"]');
if (dataChartElem) {
dataChartElem.data = self.transformFunc(data);
}
}, function (jqXHR, textStatus, errorThrown) {
// var toast = document.createElement("paper-toast");
// toast.setAttribute("text", textStatus + " - " + errorThrown);
// self.shadowRoot.appendChild(toast);
// toast.show();
});
}
}
}
}
}
</script>