@gmod/jbrowse/src/JBrowse/Store/Hash.js

JBrowse - client-side genome browser

define( [
            'dojo/_base/declare',
            'dojo/_base/array',
            'dojo/store/JsonRest',
            'dojo/store/util/QueryResults',
            'JBrowse/Digest/Crc32',
            'JBrowse/Util'
        ],
        function(
            declare,
            array,
            dojoJSONRest,
            QueryResults,
            digest,
            Util
        ) {

return declare( null, {

    constructor: function( args ) {
        // make sure url has a trailing slash
        var url = /\/$/.test( args.url ) ? args.url : args.url + '/';
        this.bucketStore = new dojoJSONRest({
            target: url
        });

        this.meta = {};

        this.browser = args.browser;

        // this.ready is a Deferred that will be resolved when we have
        // read the meta.json file with the params of this hashstore
        this.ready = this._readMeta();
    },

    _readMeta: function() {
        var thisB = this;
        return this.bucketStore.get( 'meta.json' )
            .then( function( meta ) {
                dojo.mixin( thisB.meta, meta || {} );
                thisB.meta.hash_hex_characters = Math.ceil( thisB.meta.hash_bits / 4 );
            });
    },

    query: function( query, options ) {
        return this.get( (query.name || '').toString() )
                   .then( function( value ) {
                              return QueryResults( (value||{}).exact || [] );
                          });
    },

    get: function( key ) {
        return this._getBucket(key)
                   .then( function( bucket ) {
                        return bucket[key];
                    });
    },

    _getBucket: function( key ) {
        var thisB = this;
        return this.ready
            .then( function() {
                       var bucketIdent = thisB._hash( key );
                       return thisB.bucketStore
                           .get( thisB._hexToDirPath( bucketIdent ) ).then( function(value) {
                                return value;
                            }, function(err) {
                                if (Util.isElectron() || err.status == 404) {
                                    // 404 is expected if the name is not in the store
                                    return {};
                                }
                            });
                   });
    },

    _hexToDirPath: function( hex ) {
        // zero-pad the hex string to be 8 chars if necessary
        while( hex.length < 8 )
            hex = '0'+hex;
        hex = hex.substr( 8-this.meta.hash_hex_characters );
        var dirpath = [];
        for( var i = 0; i < hex.length; i += 3 ) {
            dirpath.push( hex.substring( i, i+3 ) );
        }
        return dirpath.join('/') + '.json' + ( this.meta.compress ? 'z' : '' );
    },

    _hash: function( data ) {
        return digest.objectFingerprint( data )
                     .toString(16)
                     .toLowerCase()
                     .replace('-','n');
    },

    getIdentity: function( object ) {
        return object.id;
    }
});
});