UCSC Demo

ucsc-data-provider.js

/**
 * 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;
  }
};

ucsc-settings-override.js

epiviz.EpiViz.SETTINGS.dataProviders.push(
  sprintf('epiviz.plugins.data.UCSCDataProvider,%s,%s',
  '', 'http://epiviz.cbcb.umd.edu/data/mysql.php'));