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UCSC Demo (Epiviz 3)
/**
* Created by Florin Chelaru ( florinc [at] umd [dot] edu )
* Date: 5/6/14
* Time: 2:41 PM
*/
goog.provide('epiviz.plugins.data.UCSCDataProvider');
/**
* @constructor
* @param {string} id
* @param {string} endpoint
* @extends {epiviz.data.DataProvider}
*/
epiviz.plugins.data.UCSCDataProvider = function (id, endpoint) {
epiviz.data.DataProvider.call(this, id || epiviz.plugins.data.UCSCDataProvider.DEFAULT_ID);
/**
* @type {string}
* @private
*/
this._endpoint = endpoint;
this._refGene = new epiviz.measurements.Measurement(
'refGene', // The column in the data source table that contains the values for this feature measurement
'refGene', // A name not containing any special characters (only alphanumeric and underscores)
epiviz.measurements.Measurement.Type.RANGE,
'refGene', // Data source: the table/data frame containing the data
'ucsc_refGene', // An identifier for use to group with other measurements from different data providers
// that have the same seqName, start and end values
this.id(), // Data provider
null, // Formula: always null for measurements coming directly from the data provider
'any', // Default chart type filter
null, // Annotation
null, // Min Value
null, // Max Value
['bin', 'exonCount', 'exonFrames', 'exon_starts', 'exon_ends', 'gene'] // Metadata
);
};
/**
* Copy methods from upper class
*/
epiviz.plugins.data.UCSCDataProvider.prototype = epiviz.utils.mapCopy(epiviz.data.DataProvider.prototype);
epiviz.plugins.data.UCSCDataProvider.constructor = epiviz.plugins.data.UCSCDataProvider;
epiviz.plugins.data.UCSCDataProvider.DEFAULT_ID = 'ucsc';
/**
* @param {epiviz.data.Request} request
* @param {function(epiviz.data.Response)} callback
* @override
*/
epiviz.plugins.data.UCSCDataProvider.prototype.getData = function (request, callback) {
var requestId = request.id();
var action = request.get('action');
var seqName = request.get('seqName');
var start = request.get('start');
var end = request.get('end');
var datasource = request.get('datasource');
var query =
'select * from ' +
'(select *, @rownum:=@rownum+1 AS globalIndex ' +
'from refGene JOIN (SELECT @rownum:=0) r ' +
'order by chrom, txStart, txEnd) t ' +
//'where chrom=\'' + seqName + '\' and txEnd > \'' + start + '\' and txStart < \'' + end + '\';';
'where chrom=\'' + seqName + '\' and txStart < \'' + end + '\' and txEnd > ' +
'(select min(txStart) ' +
'from refGene where ' +
'chrom=\'' + seqName + '\' and txEnd > \'' + start + '\' and txStart < \'' + end + '\');';
var getQuery =
this._endpoint + '?server=genome-mysql.cse.ucsc.edu&db=hg19&u=genome&q=' +
encodeURIComponent(query);
switch (action) {
case epiviz.data.Request.Action.GET_ROWS:
if (datasource != this._refGene.datasourceId()) {
// Nothing to return
callback(epiviz.data.Response.fromRawObject({
data: {
values: { id: null, start: [], end:[], strand: [], metadata:{
'bin': [],
'exonCount': [],
'exon_starts': [],
'exon_ends': [],
'gene': [],
'exonFrames': []
}},
globalStartIndex: null,
useOffset: false
},
requestId: requestId
}));
return;
}
epiviz.data.WebServerDataProvider.makeGetRequest(getQuery, function(jsondata) {
if (!jsondata['results'] || jsondata['results'].length == 0) {
// Nothing to return
callback(epiviz.data.Response.fromRawObject({
data: {
values: { id: null, start: [], end:[], strand: [], metadata:{
'bin': [],
'exonCount': [],
'exon_starts': [],
'exon_ends': [],
'gene': [],
'exonFrames': []
}},
globalStartIndex: null,
useOffset: false
},
requestId: requestId
}));
return;
}
var ids = [], starts = [], ends = [], strands = [], metadata = {
'bin': [],
'exonCount': [],
'exon_starts': [],
'exon_ends': [],
'gene': [],
'exonFrames': []
};
var columns = epiviz.utils.arrayFlip(jsondata['columns']);
var results = jsondata['results'];
for (var i = 0; i < results.length; ++i) {
ids.push(parseInt(results[i][columns['globalIndex']]));
starts.push(parseInt(results[i][columns['txStart']]));
ends.push(parseInt(results[i][columns['txEnd']]));
strands.push(results[i][columns['strand']]);
for (var col in metadata) {
if (!metadata.hasOwnProperty(col)) { continue; }
switch (col) {
case 'exon_starts':
var exonStarts = results[i][columns['exonStarts']];
if (exonStarts && epiviz.utils.stringEndsWith(exonStarts, ',')) {
exonStarts = exonStarts.substr(0, exonStarts.length - 1);
}
metadata[col].push(exonStarts);
break;
case 'exon_ends':
var exonEnds = results[i][columns['exonEnds']];
if (exonEnds && epiviz.utils.stringEndsWith(exonEnds, ',')) {
exonEnds = exonEnds.substr(0, exonEnds.length - 1);
}
metadata[col].push(exonEnds);
break;
case 'gene':
metadata[col].push(results[i][columns['name2']]);
break;
default:
metadata[col].push(results[i][columns[col]]);
break;
}
}
}
var globalStartIndex = ids[0];
callback(epiviz.data.Response.fromRawObject({
data: {
values: { id: ids, start: starts, end: ends, strand: strands, metadata: metadata },
globalStartIndex: globalStartIndex,
useOffset: false
},
requestId: requestId
}));
});
return;
case epiviz.data.Request.Action.GET_VALUES:
// Nothing to return
callback(epiviz.data.Response.fromRawObject({
data: { values: [], globalStartIndex: null },
requestId: requestId
}));
return;
case epiviz.data.Request.Action.GET_MEASUREMENTS:
callback(epiviz.data.Response.fromRawObject({
requestId: request.id(),
data: {
id: [this._refGene.id()],
name: [this._refGene.name()],
type: [this._refGene.type()],
datasourceId: [this._refGene.datasourceId()],
datasourceGroup: [this._refGene.datasourceGroup()],
defaultChartType: [this._refGene.defaultChartType()],
annotation: [this._refGene.annotation()],
minValue: [this._refGene.minValue()],
maxValue: [this._refGene.maxValue()],
metadata: [this._refGene.metadata()]
}
}));
return;
case epiviz.data.Request.Action.GET_SEQINFOS:
var seqInfoQuery =
this._endpoint + '?server=genome-mysql.cse.ucsc.edu&db=hg19&u=genome&q=' +
encodeURIComponent('select chrom, min(txStart), max(txEnd) from refGene group by chrom order by chrom;');
epiviz.data.WebServerDataProvider.makeGetRequest(seqInfoQuery, function(jsondata) {
if (!jsondata['results'] || jsondata['results'].length == 0) {
// Nothing to return
callback(epiviz.data.Response.fromRawObject({
requestId: request.id(),
data: []
}));
} else {
callback(epiviz.data.Response.fromRawObject({
requestId: request.id(),
data: jsondata['results']
}));
}
});
return;
default:
epiviz.data.DataProvider.prototype.getData.call(this, request, callback);
break;
}
};
epiviz.Config.SETTINGS.dataProviders.push(
sprintf('epiviz.plugins.data.UCSCDataProvider,%s,%s',
'', 'http://epiviz.cbcb.umd.edu/data/mysql.php'));
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