My Data Provider (Epiviz 3)

my-data-provider-settings-overrides.js

epiviz.Config.SETTINGS.dataProviders.push('epiviz.plugins.data.MyDataProvider');

my-data-provider.js

/**
 * Created by Florin Chelaru ( florinc [at] umd [dot] edu )
 * Date: 4/17/14
 * Time: 10:09 PM
 */

goog.provide('epiviz.plugins.data.MyDataProvider');

/**
 * @constructor
 * @extends {epiviz.data.DataProvider}
 */
epiviz.plugins.data.MyDataProvider = function () {
  epiviz.data.DataProvider.call(this);

  this._mockMeasurement = new epiviz.measurements.Measurement(
    'my_feature_column', // The column in the data source table that contains the values for this feature measurement
    'My Feature Measurement', // A name not containing any special characters (only alphanumeric and underscores)
    epiviz.measurements.Measurement.Type.FEATURE,
    'my_datasource', // Data source: the table/data frame containing the data
    'my_datasourcegroup', // 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
    'Line Track', // Default chart type filter
    null, // Annotation
    -5, // Min Value
    25, // Max Value
    ['my_metadata'] // Metadata
  );
};

/**
 * Copy methods from upper class
 */
epiviz.plugins.data.MyDataProvider.prototype = epiviz.utils.mapCopy(epiviz.data.DataProvider.prototype);
epiviz.plugins.data.MyDataProvider.constructor = epiviz.plugins.data.MyDataProvider;

epiviz.plugins.data.MyDataProvider.DEFAULT_ID = 'myprovider';

/**
 * @param {epiviz.data.Request} request
 * @param {function(epiviz.data.Response)} callback
 * @override
 */
epiviz.plugins.data.MyDataProvider.prototype.getData = function (request, callback) {
  var requestId = request.id();
  var action = request.get('action');
  var seqName = request.get('chr');
  var start = request.get('start');
  var end = request.get('end');
  var datasource = request.get('datasource');

  // Return a genomic range of 100 base pairs every 1000 base pairs
  var step = 1000, width = 100;
  var globalStartIndex, firstStart, firstEnd;
  if (action == epiviz.data.Request.Action.GET_ROWS || action == epiviz.data.Request.Action.GET_VALUES) {
    globalStartIndex = Math.floor((start - 1) / step) + 1;
    firstStart = globalStartIndex * step + 1;
    firstEnd = firstStart + width;

    if (firstEnd < start) {
      firstStart += step;
      firstEnd += step;
    }
  }

  var globalIndex, s;
  switch (action) {
    case epiviz.data.Request.Action.GET_ROWS:
      if (firstStart >= end) {
        // Nothing to return
        callback(epiviz.data.Response.fromRawObject({
          data: {
            values: { id: null, start: [], end:[], strand: [], metadata:{my_metadata:[]} },
            globalStartIndex: null,
            useOffset: false
          },
          requestId: requestId
        }));
        return;
      }

      var ids = [], starts = [], ends = [], strands = '*', myMetadata = [];
      for (globalIndex = globalStartIndex, s = firstStart; s < end; ++globalIndex, s += step) {
        ids.push(globalIndex);
        starts.push(s);
        ends.push(s + width);
        myMetadata.push(epiviz.utils.generatePseudoGUID(5)); // Random string
      }

      callback(epiviz.data.Response.fromRawObject({
        data: {
          values: { id: ids, start: starts, end: ends, strand: strands, metadata:{ my_metadata: myMetadata } },
          globalStartIndex: globalStartIndex,
          useOffset: false
        },
        requestId: requestId
      }));
      return;

    case epiviz.data.Request.Action.GET_VALUES:
      if (firstStart >= end) {
        // Nothing to return
        callback(epiviz.data.Response.fromRawObject({
          data: { values: [], globalStartIndex: null },
          requestId: requestId
        }));
        return;
      }

      var values = [];
      for (globalIndex = globalStartIndex, s = firstStart; s < end; ++globalIndex, s += step) {
        var v = Math.random()
          * (this._mockMeasurement.maxValue() - this._mockMeasurement.minValue())
          +  this._mockMeasurement.minValue();
        values.push(v);
      }

      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._mockMeasurement.id()],
          name: [this._mockMeasurement.name()],
          type: [this._mockMeasurement.type()],
          datasourceId: [this._mockMeasurement.datasourceId()],
          datasourceGroup: [this._mockMeasurement.datasourceGroup()],
          defaultChartType: [this._mockMeasurement.defaultChartType()],
          annotation: [this._mockMeasurement.annotation()],
          minValue: [this._mockMeasurement.minValue()],
          maxValue: [this._mockMeasurement.maxValue()],
          metadata: [this._mockMeasurement.metadata()]
        }
      }));
      return;

    case epiviz.data.Request.Action.GET_SEQINFOS:
      callback(epiviz.data.Response.fromRawObject({
        requestId: request.id(),
        data: [['chr1', 1, 248956422], ['myChr', 1, 1000000000]]
      }));
      return;

    default:
      epiviz.data.DataProvider.prototype.getData.call(this, request, callback);
      break;
  }
};