UCSC Demo 2

ucsc-data-provider2.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
  );

  this._heartMet = new epiviz.measurements.Measurement(
    'percentMeth', // The column in the data source table that contains the values for this feature measurement
    'BioChain_heart:Ventricle_L__A705026_rep2', // A name not containing any special characters (only alphanumeric and underscores)
    epiviz.measurements.Measurement.Type.FEATURE,
    'wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2', // Data source: the table/data frame containing the data
    'ucsc_wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2', // 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
    0, // Min Value
    100, // Max Value
    ['score', 'reserved', 'readCount'] // Metadata
  );

  this._colMap = {
    refGene: {
      seqName: 'chrom',
      start: 'txStart',
      end: 'txEnd',
      strand: 'strand'
    },
    wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2: {
      seqName: 'chrom',
      start: 'chromStart',
      end: 'chromEnd',
      strand: 'strand'
    }
  };
};

/**
 * 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');

  if (datasource) {
    var colMap = this._colMap[datasource];
    var query =
      'select * from ' +
        '(select *, @rownum:=@rownum+1 AS globalIndex ' +
        'from ' + datasource + ' JOIN (SELECT @rownum:=0) r ' +
        'order by ' + colMap.seqName + ',' + colMap.start + ',' + colMap.end +') t ' +
        'where ' + colMap.seqName +'=\'' + seqName + '\' and ' + colMap.start + '< \'' + end + '\' and ' + colMap.end + '> ' +
        '(select min(' + colMap.start + ') ' +
        'from ' + datasource + ' where ' +
        colMap.seqName + '=\'' + seqName + '\' and ' + colMap.end + ' > \'' + start + '\' and ' + colMap.start + '< \'' + 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:
      var metadata = {};
      var metadataCols = (datasource == this._refGene.datasourceId()) ? this._refGene.metadata() : this._heartMet.metadata();
      for (var i = 0; i < metadataCols.length; ++i) {
        metadata[metadataCols[i]] = [];
      }
      var data = {data:{ values: {id:[], start:[], end:[], strand:[], metadata:metadata}, globalStartIndex:null, useOffset:false}, requestId:requestId};

      epiviz.data.WebServerDataProvider.makeGetRequest(getQuery, function(jsondata) {
        if (!jsondata['results'] || jsondata['results'].length == 0) {
          // Nothing to return
          callback(epiviz.data.Response.fromRawObject(data));
          return;
        }

        var ids = data.data.values.id, starts = data.data.values.start, ends = data.data.values.end,
          strands = data.data.values.strand, metadata = data.data.values.metadata;
        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[colMap.start]]));
          ends.push(parseInt(results[i][columns[colMap.end]]));
          strands.push(results[i][columns[colMap.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;
            }
          }
        }
        data.data.globalStartIndex = ids[0];

        callback(epiviz.data.Response.fromRawObject(data));
      });

      return;

    case epiviz.data.Request.Action.GET_VALUES:
      if (datasource != this._heartMet.datasourceId()) {
        // Nothing to return
        callback(epiviz.data.Response.fromRawObject({
          data: { values: [], globalStartIndex: null },
          requestId: requestId
        }));
        return;
      }

      var self = this;
      epiviz.data.WebServerDataProvider.makeGetRequest(getQuery, function(jsondata) {
        if (!jsondata['results'] || jsondata['results'].length == 0) {
          // Nothing to return
          callback(epiviz.data.Response.fromRawObject({
            data: { values: [], globalStartIndex: null },
            requestId: requestId
          }));
          return;
        }

        var columns = epiviz.utils.arrayFlip(jsondata['columns']);
        var results = jsondata['results'];
        var globalStartIndex = parseInt(results[0][columns['globalIndex']]);
        var values = [];
        for (var i = 0; i < results.length; ++i) {
          values.push(results[i][columns[self._heartMet.id()]]);
        }
        callback(epiviz.data.Response.fromRawObject({
          data: { values: values, globalStartIndex: globalStartIndex },
          requestId: requestId
        }));
      });
      return;

    case epiviz.data.Request.Action.GET_MEASUREMENTS:
      callback(epiviz.data.Response.fromRawObject({
        requestId: request.id(),
        data: {
          id: [this._refGene.id(), this._heartMet.id()],
          name: [this._refGene.name(), this._heartMet.name()],
          type: [this._refGene.type(), this._heartMet.type()],
          datasourceId: [this._refGene.datasourceId(), this._heartMet.datasourceId()],
          datasourceGroup: [this._refGene.datasourceGroup(), this._heartMet.datasourceGroup()],
          defaultChartType: [this._refGene.defaultChartType(), this._heartMet.defaultChartType()],
          annotation: [this._refGene.annotation(), this._heartMet.annotation()],
          minValue: [this._refGene.minValue(), this._heartMet.minValue()],
          maxValue: [this._refGene.maxValue(), this._heartMet.maxValue()],
          metadata: [this._refGene.metadata(), this._heartMet.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 seqName, min(start), max(end) from (' +
              'select chrom as seqName, min(txStart) as start, max(txEnd) as end from refGene group by chrom union all ' +
              'select chrom as seqName, min(chromStart) as start, max(chromEnd) as end from wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2 group by chrom) t ' +
            'group by seqName order by seqName;');

      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-override2.js

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