@gmod/jbrowse/src/JBrowse/Store/SeqFeature/SPARQL.js

JBrowse - client-side genome browser

define([ 'dojo/_base/declare',
         'dojo/_base/lang',
         'dojo/_base/array',
         'dojo/request/xhr',
         'JBrowse/Store/SeqFeature',
         'JBrowse/Store/DeferredStatsMixin',
         'JBrowse/Store/SeqFeature/GlobalStatsEstimationMixin',
         'JBrowse/Util',
         'JBrowse/Model/SimpleFeature',
         'dojo/io-query'
       ],
       function(
           declare,
           lang,
           array,
           xhr,
           SeqFeatureStore,
           DeferredStatsMixin,
           GlobalStatsEstimationMixin,
           Util,
           SimpleFeature,
           ioQuery
       ) {

return declare( [ SeqFeatureStore, DeferredStatsMixin, GlobalStatsEstimationMixin ],

/**
 * @lends JBrowse.Store.SeqFeature.SPARQL
 */
{

    /**
     * JBrowse feature backend to retrieve features from a SPARQL endpoint.
     * @constructs
     */
    constructor: function(args) {
        this.url = this.urlTemplate;
        this.refSeq = args.refSeq;
        this.baseUrl = args.baseUrl;
        this.density = 0;
        this.url = Util.resolveUrl(
            this.baseUrl,
            Util.fillTemplate( args.urlTemplate,
                               { 'refseq': this.refSeq.name }
                             )
        );
        this.queryTemplate = args.queryTemplate;
        if( ! this.queryTemplate ) {
            console.error("No queryTemplate set for SPARQL backend, no data will be displayed");
        }

        var thisB = this;
        this._estimateGlobalStats()
            .then(
                function( stats ) {
                    thisB.globalStats = stats;
                    thisB._deferred.stats.resolve( stats );
                },
                lang.hitch( this, '_failAllDeferred' )
            );
    },

    // load: function() {
    //     // ping the endpoint to see if it's there
    //     dojo.xhrGet({ url: this.url+'?'+ioQuery.objectToQuery({ query: 'SELECT ?s WHERE { ?s ?p ?o } LIMIT 1' }),
    //                   handleAs: "text",
    //                   failOk: false,
    //                   load:  Util.debugHandler( this, function(o) { this.loadSuccess(o); }),
    //                   error: dojo.hitch( this, function(error) { this.loadFail(error, this.url); } )
    //     });
    // },

    _makeQuery: function( query ) {
        if( this.config.variables )
            query = dojo.mixin( dojo.mixin( {}, this.config.variables ),
                                query
                              );

        return Util.fillTemplate( this.queryTemplate, query );
    },

    _getFeatures: function() {
        this.getFeatures.apply( this, arguments );
    },

    getFeatures: function( query, featCallback, finishCallback, errorCallback ) {
        if( this.queryTemplate ) {
            var thisB = this;
            var headers = { "Accept": "application/json" };
            if(this.config.disablePreflight) {
                // https://www.sitepen.com/blog/2014/01/15/faq-cors-with-dojo/
                headers["X-Requested-With"] = null;
            }

            xhr.get( this.url+'?'+ioQuery.objectToQuery({
                                                            query: this._makeQuery( query )
                                                        }),
                     {
                          headers: headers,
                          handleAs: "json",
                          failOk: true
                     })
                .then( function(o) {
                           thisB._resultsToFeatures( o, featCallback );
                           finishCallback();
                       },
                       lang.hitch( this, '_failAllDeferred' )
                     );
        } else {
            finishCallback();
        }
    },

    _resultsToFeatures: function( results, featCallback ) {
        var rows = ((results||{}).results||{}).bindings || [];
        if( ! rows.length )
            return;
        var fields = results.head.vars;
        var requiredFields = ['start','end','strand','uniqueID'];
        for( var i = 0; i<requiredFields.length; i++ ) {
            if( fields.indexOf( requiredFields[i] ) == -1 ) {
                console.error("Required field "+requiredFields[i]+" missing from feature data");
                return;
            }
        };
        var seenFeatures = {};
        array.forEach( rows, function( row ) {

            var f = { data: { subfeatures: [] } };

            var data = f.data;
            array.forEach( fields, function(field) {
                if( field in row )
                    data[field] = row[field].value;
            });
            data.start = parseInt( data.start );
            data.end = parseInt( data.end );
            data.strand = parseInt( data.strand );

            var id = data.uniqueID;
            delete data.uniqueID;
            f.id = id;
            seenFeatures[ id ] = f;
        },this);

        // resolve subfeatures, keeping only top-level features in seenFeatures
        for( var id in seenFeatures ) {
            var f = seenFeatures[id];
            var pid = f.data.parentUniqueID;
            delete f.data.parentUniqueID;
            if( pid ) {
                var p = seenFeatures[ pid ];
                if( p ) {
                    p.data.subfeatures.push( f.data );
                    delete seenFeatures[id];
                }
            }
        }

        for( var id in seenFeatures ) {
            featCallback( new SimpleFeature( seenFeatures[id] ) );
        }
    }
});

});